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WO2011046635A1 - Differentially methylated regions of reprogrammed induced pluripotent stem cells, method and compositions thereof - Google Patents

Differentially methylated regions of reprogrammed induced pluripotent stem cells, method and compositions thereof Download PDF

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Publication number
WO2011046635A1
WO2011046635A1 PCT/US2010/033281 US2010033281W WO2011046635A1 WO 2011046635 A1 WO2011046635 A1 WO 2011046635A1 US 2010033281 W US2010033281 W US 2010033281W WO 2011046635 A1 WO2011046635 A1 WO 2011046635A1
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disjoint
gene
nucleic acid
chrl
acid sequences
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French (fr)
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Andrew Paul Feinberg
George Q. Daley
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The Johns Hopkins University
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Priority to US13/184,426 priority Critical patent/US20120164110A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present invention relates generally to differentially methylated regions (DMRs) in the genome outside CpG islands in induced pluripotent stem (iPS) cells, and more specifically to methods for detecting and analyzing alterations in the methylation status of DMRs in iPS cells, somatic cells and embryonic stem (ES) cells as well as methods for reprogramming somatic cells to generate an iPS cell.
  • DMRs differentially methylated regions
  • iPS induced pluripotent stem
  • Epigenetics is the study of non-sequence information of chromosome DNA during cell division and differentiation.
  • the molecular basis of epigenetics is complex and involves modifications of the activation or inactivation of certain genes. Additionally, the chromatin proteins associated with DNA may be activated or silenced.
  • Epigenetic changes are preserved when cells divide. Most epigenetic changes only occur within the course of one individual organism's lifetime, but some epigenetic changes are inherited from one generation to the next.
  • DNA methylation a covalent modification of the nucleotide cytosine.
  • DNAm DNA methylation
  • DNA methylation involves the addition of methyl groups to cytosine nucleotides in the DNA, to convert cytosine to 5-methylcytosine.
  • DNA methylation plays an important role in determining whether some genes are expressed or not.
  • Abnormal DNA methylation is one of the mechanisms known to underlie the changes observed with aging and development of many cancers.
  • DNAm DNA methylation
  • iPS cells are derived by epigenetic reprogramming.
  • iPS cells can be derived from somatic cells by introduction of a small number of genes: for example,
  • iPS cells offer considerable therapeutic promise, avoiding both immunologic and ethical barriers to their use. iPS cells differ from their somatic parental cells epigenetically, and thus a comprehensive comparison of the epigenome in iPS and somatic cells would provide insight into the mechanism of tissue reprogramming. Although two previous targeted studies examined a subset of the genome, 7,000 (Ball et al. (Nat. Biotechnol. (27)485 (2009)) and 66,000 (Deng et al. (Nat. Biotechnol. (27)353-360 (2009))) CpG sites in a small cohort of three iPS- fibroblast pairs, a global assessment of genome-wide methylation has not yet been performed.
  • the present invention is based on the discovery that alterations in DNA
  • methylation in iPS cells as compared to both ES cells and parental fibroblasts, occur not only in promoters or CpG islands, but in sequences up to 2 kb distant from such CpG islands (such sequences are termed "CpG island shores").
  • DMR of reprogrammed iPS cells R-DMRs
  • a method of generating an iPS cell includes contacting a somatic cell with an agent that alters the methylation status of one or more nucleic acid sequences of the somatic cell, the one or more nucleic acid sequences being outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in reprogrammed somatic cells as compared with parent somatic cells, thereby generating an iPS cell.
  • the one or more nucleic acid sequences are any combination of DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, the IGFIR gene, and any combination thereof.
  • the method further comprises detecting the methylation status profile of the one or more nucleic acid sequences of the induced iPS.
  • the method further comprises comparing the methylation status profile to a methylation status profile of the one or more nucleic acid sequences of a parental somatic cell from which the iPS is induced.
  • the agent is a nuclear reprogramming factor.
  • the nuclear reprogramming factor is a nucleic acid encoding a SOX family gene, a KLF family gene, a MYC family gene, POU5F1, SALL4, OCT4, NANOG, LIN28, or the expression product thereof.
  • the nuclear reprogramming factor is one or more of POU5F1, OCT4, SOX2, KLF4, or C-MYC.
  • an iPS cell produced using the methods of the invention.
  • nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequence is up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in the reprogramming of a somatic cell to generate an iPS cell.
  • the nucleic acid sequence are any DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, and the IGFIR gene.
  • the plurality of nucleic acid sequences is a microarray.
  • nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the methylation status of the nucleic acid sequences is altered in an iPS cell as compared to an ES cell.
  • the nucleic acid sequence are any DMR sequences as set forth in Table 7, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene.
  • the plurality of nucleic acid sequences is a microarray.
  • a method of identifying an iPS cell includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of an iPS cell, wherein a similarity in methylation status is indicative of the putative cell being an iPS cell.
  • the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4C-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • a method of identifying an iPS cell includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of a corresponding somatic cell from which the iPS cell is induced or ES cell, wherein an alteration in methylation status is indicative of the putative cell being an iPS cell.
  • the method further includes comparing the methylation status of the one or more nucleic acid sequences of the putative iPS cell to a known methylation status of the one or more nucleic acid sequences of a corresponding somatic cell from which the iPS cell is induced.
  • the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 9, Figures 1B- 1C, Figures 4A-4G, the the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • the method further includes comparing the methylation status of the one or more nucleic acid sequences of the putative iPS cell to the methylation status of the one or more nucleic acid sequences of a known ES cell.
  • the one or more nucleic acid sequences are DMR sequences as set forth in Table 6, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • the one or more nucleic acid sequences are within a gene.
  • the one or more nucleic acid sequences are upstream or downstream of a gene.
  • determination of methylation status is performed by one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequencing, single-strand conformation polymorphism (SSCP) analysis, restriction analysis, microarray technology, and proteomics.
  • PCR polymerase chain reaction
  • SSCP single-strand conformation polymorphism
  • a method for providing a methylation map of a region of genomic DNA isolated from an iPS cell includes performing comprehensive high-through array-based relative methylation
  • the method further includes performing one or more techniques, such as a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequencing, single-strand conformation polymorphism (SSCP) analysis, and restriction analysis.
  • PCR polymerase chain reaction
  • SSCP single-strand conformation polymorphism
  • a method of characterizing the methylation status of the nucleic acid of an iPS cell includes a) hybridizing labeled and digested nucleic acid of an iPS cell to a DNA microarray comprising at least 2000 nucleic acid sequences, with the proviso that the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island; and b) determining a pattern of methylation from the hybridizing of (a), thereby characterizing the methylation status for the iPS cell.
  • the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene and any combination thereof.
  • the method further includes comparing the methylation status profile to a methylation profile from hybridization of the microarray with labeled and digested nucleic acid from a parental somatic cell from which the iPS is induced or from an ES cell.
  • a method of treating a subject includes a) obtaining a somatic cell from a subject; b) reprogramming the somatic cell into an iPS cell using the methods of the invention; c) culturing the pluripotent stem (iPS) cell to differentiate the cell into a desired cell type suitable for treating a condition; and d) introducing into the subject the differentiated cell, thereby treating the condition.
  • iPS pluripotent stem
  • Figure 1A shows plots depicting the distribution of distance of R-DMRs from CpG islands.
  • Figures IB and 1C, upper panels, show plots of M value versus genomic location for fibroblast and iPS cells and plots of CpG density versus genomic location, where the curve represents averaged smoothed M values; the location of CpG dinucleotides (black tick marks), CpG density, location of CpG islands (filled boxes along the x-axis (zero)), along with the gene annotation.
  • Figures IB and 1C lower panels show validation by bisulfite pyrosequencing of methylation percentage mapping to the unfilled box along the x-axis of the plots of CpG density versus genomic location in the upper panels of Figures IB and 1C for various iPS cells, fibroblasts, ES cells (BGOl, BG03 and H9) as well as the highly methylated HCT116 colon cancer cell line and a generally hypomethylated double DNA methyltransferase 1/3B double knockout line (DKO) derived from it.
  • DKO double DNA methyltransferase 1/3B double knockout line
  • Figure 2 shows plots depicting the distribution of distance of R-DMRs from CpG islands.
  • Figure 3A shows a clustering of M values of all tissues from the 4,401 regions (FDR ⁇ 0.05) corresponding to R-DMRs (iPS cells compared to parental fibroblasts) comparing normal brain, spleen and liver tissues (denoted as Br, Sp and Lv, respectively).
  • Figure 3B shows a clustering of M values of all tissues from the 4,401 regions (FDR ⁇ 0.05) corresponding to R-DMRs (iPS cells compared to parental fibroblasts) comparing colorectal cancer and matched normal colonic mucosa (denoted as T and N, respectively).
  • Figure 4 shows plots depicting differential DNA methylation (upper panels) and confirmation by bisulfite pyrosequencing (lower panels) for DMRs found by comparison between iPS cells and fibroblasts (A and B) as well as various genes (C-G).
  • Figures 4A-G, upper panels, show plots of M value versus genomic location, where the curve represents averaged smoothed M values.
  • CpG dinucleotide black tick marks on x-axis
  • CpG density smoothed black line
  • location of CpG islands filled boxes along the x-axis (zero)
  • gene annotation indicating the transcript thin outer gray line
  • coding region thin inner gray line
  • exons filled gray box
  • gene transcription directionality on the y-axis sense marked as +, antisense as -.
  • Figures 4A-G, lower panels depict plots showing the degree of DNA methylation as measured by bisulfite
  • the unfilled box indicated on the x-axis of the CpG density plot in the upper panel indicates the CpG sites that were measured. Reactions were performed in triplicate; bars represent the mean methylation ⁇ SD of iPS cells, fibroblasts, and ES cells (BGOl, BG03 and H9) as well as DKO (DNMT1 and DNMT3B Double KO cell line) and HCT116 (parental colon cancer cell line) for each individual CpG site measured.
  • DKO DNMT1 and DNMT3B Double KO cell line
  • HCT116 parental colon cancer cell line
  • Figure 5 shows plots of differential gene expression versus differential methylation for R-DMRs at CpG island shores.
  • the present invention is based on the discovery that alterations in DNA
  • CpG island shores cytosine-phosphate-guanine island shores
  • the DMRs in the reprogrammed cells were significantly enriched in tissue-specific (T-DMRs) and cancer-specific DMRs (C-DMRs).
  • T-DMRs tissue-specific
  • C-DMRs cancer-specific DMRs
  • iPS cells are derived from fibroblasts
  • their R-DMRs can distinguish between cells of normal tissue and between cancer and normal cells, e.g., colon cancer and normal colon cells.
  • DM s are broadly involved in tissue differentiation, epigenetic reprogramming and cancer.
  • hypomethylated C-DMRs and the absence of bivalent marks were observed, suggesting two mechanisms for epigenetic reprogramming in iPS cells and cancer.
  • a method of generating an iPS cell includes contacting a somatic cell with an agent that alters the methylation status of one or more nucleic acid sequences of the somatic cell, the one or more nucleic acid sequences being outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in reprogrammed somatic cells as compared with parent somatic cells, thereby generating an iPS cell.
  • reprogramming is intended to refer to a process that alters or reverses the differentiation status of a somatic cell that is either partially or terminally differentiated.
  • Reprogramming of a somatic cell may be a partial or complete reversion of the differentiation status of the somatic cell.
  • reprogramming is complete wherein a somatic cell is reprogrammed into an iPS cell.
  • reprogramming may be partial, such as reversion into any less differentiated state. For example, reverting a terminally differentiated cell into a cell of a less differentiated state, such as a multipotent cell.
  • pluripotent cells include cells that have the potential to divide in vitro for an extended period of time (greater than one year) and have the unique ability to differentiate into cells derived from all three embryonic germ layers, namely endoderm, mesoderm and ectoderm.
  • Somatic cells for use with the present invention may be primary cells or immortalized cells.
  • Such cells may be primary cells (non-immortalized cells), such as those freshly isolated from an animal, or may be derived from a cell line (immortalized cells).
  • the somatic cells are mammalian cells, such as, for example, human cells or mouse cells. They may be obtained by well-known methods, from different organs, such as, but not limited to skin, brain, lung, pancreas, liver, spleen, stomach, intestine, heart, reproductive organs, bladder, kidney, urethra and other urinary organs, or generally from any organ or tissue containing living somatic cells, or from blood cells.
  • Mammalian somatic cells useful in the present invention include, by way of example, adult stem cells, Sertoli cells, endothelial cells, granulosa epithelial cells, neurons, pancreatic islet cells, epidermal cells, epithelial cells, hepatocytes, hair follicle cells, keratinocytes, hematopoietic cells,
  • somatic cell is also intended to include adult stem cells.
  • An adult stem cell is a cell that is capable of giving rise to all cell types of a particular tissue.
  • Exemplary adult stem cells include hematopoietic stem cells, neural stem cells, and mesenchymal stem cells.
  • alterations in methylation patterns occur during differentiation or dedifferention of a cell which work to regulate gene expression of critical factors that are 'turned on' or 'turned off at various stages of differentiation.
  • agents are capable of altering the methylation status of one or more nucleic acid sequences of a somatic cell to induce pluripotency that may be suitable for use with the present invention.
  • an agent is intended to include any agent capable of altering the methylation status of one or more nucleic acid sequences of a somatic cell.
  • an agent useful in any of the method of the invention may be any type of molecule, for example, a polynucleotide, a peptide, a peptidomimetic, peptoids such as vinylogous peptoids, chemical compounds, such as organic molecules or small organic molecules, or the like.
  • the agent may be a polynucleotide, such as DNA molecule, an antisense oligonucleotide or RNA molecule, such as microRNA, dsRNA, siRNA, stRNA, and shRNA.
  • MicroRNA are single-stranded RNA molecules whose expression is known to be regulated by methylation to play a key role in regulation of gene expression during differentiation and dedifferentiation of cells.
  • an agent may be one that inhibits or induces expression of miRNA or may be a mimic miRNA.
  • miRNAs which are intended to mean a microRNA exogenously introduced into a cell that have the same or substantially the same function as their endogenous counterpart.
  • an agent that alters the methylation status of one or more nucleic acid sequences is a nuclear reprogramming factor.
  • Nuclear reprogramming factors may be genes that induce pluripotency and utilized to reprogram differentiated or semi-differentiated cells to a phenotype that is more primitive than that of the initial cell, such as the phenotype of a pluripotent stem cell.
  • genes and agents are capable of generating a pluripotent stem cell from a somatic cell upon expression of one or more such genes having been integrated into the genome of the somatic cell or upon contact of the somatic cell with the agent or expression product of the gene.
  • a gene that induces pluripotency is intended to refer to a gene that is associated with pluripotency and capable of generating a less differentiated cell, such as a pluripotent stem cell from a somatic cell upon integration and expression of the gene.
  • the expression of a pluripotency gene is typically restricted to pluripotent stem cells, and is crucial for the functional identity of pluripotent stem cells.
  • genes have been found to be associated with pluripotency and suitable for use with the present invention as reprogramming factors.
  • Such genes include, by way of example, SOX family genes (SOXl, SOX2, SOX3, SOX15, SOX18), KLF family genes (KLF1, KLF2, KLF4, KLF5), MYC family genes (C-MYC, L-MYC, N- MYC), SALL4, OCT4, NANOG, LIN28, STELLA, NOBOX, POU5F1 or a STAT family gene.
  • STAT family members may include for example STAT1 , STAT2, STAT3, STAT4, STAT5 (STAT5 A and STAT5B), and STAT6 .
  • pluripotency While in some instances, use of only one gene to induce pluripotency may be possible, in general, expression of more than one gene is required to induce pluripotency.
  • two, three, four or more genes may be simultaneously integrated into the somatic cell genome as a polycistronic construct to allow simultaneous expression of such genes.
  • four genes are utilized to induce pluripotency including OCT4, POU5F1, SOX2, KLF4 and C-MYC. Additional genes known as reprogramming factors suitable for use with the present invention are disclosed in U.S. Patent Application No. 10/997,146 and U.S. Patent Application No. 12/289,873, incorporated herein by reference.
  • genes commonly exist in mammals, including human, and thus homologues from any mammals may be used in the present invention, such as genes derived from mammals including, but not limited to mouse, rat, bovine, ovine, horse, and ape.
  • mutant gene products including substitution, insertion, and/or deletion of several (e.g., 1 to 10, 1 to 6, 1 to 4, 1 to 3, and 1 or 2) amino acids and having similar function to that of the wild-type gene products can also be used.
  • the combinations of factors are not limited to the use of wild-type genes or gene products.
  • Myc chimeras or other Myc variants can be used instead of wild-type Myc.
  • the present invention is not limited to any particular combination of nuclear reprogramming factors.
  • a nuclear reprogramming factor may comprise one or more gene products.
  • the nuclear reprogramming factor may also comprise a combination of gene products as discussed herein.
  • Each nuclear reprogramming factor may be used alone or in combination with other nuclear reprogramming factors as disclosed herein.
  • nuclear reprogramming factors of the present invention can be identified by screening methods, for example, as discussed in U.S. Patent Application No. 10/997,146, incorporated herein by reference.
  • the nuclear reprogramming factor of the present invention may contain one or more factors relating to differentiation, development, proliferation or the like and factors having other physiological activities, as well as other gene products which can function as a nuclear reprogramming factor.
  • the nuclear reprogramming factor may include a protein or peptide.
  • the protein may be produced from a gene as discussed herein, or alternatively, in the form of a fusion gene product of the protein with another protein, peptide or the like.
  • the protein or peptide may be a fluorescent protein and/or a fusion protein.
  • a fusion protein with green fluorescence protein (GFP) or a fusion gene product with a peptide such as a histidine tag can also be used.
  • fusion protein with the TAT peptide derived from the virus HIV, intracellular uptake of the nuclear reprogramming factor through cell membranes can be promoted, thereby enabling induction of reprogramming only by adding the fusion protein to a medium thus avoiding complicated operations such as gene transduction. Since preparation methods of such fusion gene products are well known to those skilled in the art, skilled artisans can easily design and prepare an appropriate fusion gene product depending on the purpose.
  • the agent alters the methylation status of one or more nucleic acid sequences, such as DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G
  • the BMP7 gene the GSC gene
  • the TBX3 gene the HOXD3 gene
  • the PTPRT gene the POU3F4 gene
  • the AZBP1 gene the ZNF184 gene
  • IGF1R gene any combination thereof.
  • Detecting the methylation status profile of the one or more nucleic acid sequences of the induced iPS and/or comparing the methylation status profile to a methylation status profile of the one or more nucleic acid sequences of a parental somatic cell from which the iPS is induced may also be performed to assess pluripotency characteristics.
  • expression profiling of reprogrammed somatic cells to assess their pluripotency characteristics may also be conducted. Expression of individual genes associated with pluripotency may also be examined. Additionally, expression of embryonic stem cell surface markers may be analyzed.
  • expression refers to the production of a material or substance as well as the level or amount of production of a material or substance. Thus, determining the expression of a specific marker refers to detecting either the relative or absolute amount of the marker that is expressed or simply detecting the presence or absence of the marker.
  • marker refers to any molecule that can be observed or detected.
  • a marker can include, but is not limited to, a nucleic acid, such as a transcript of a specific gene, a polypeptide product of a gene, a non-gene product polypeptide, a glycoprotein, a carbohydrate, a glycolipd, a lipid, a lipoprotein or a small molecule.
  • a nucleic acid such as a transcript of a specific gene, a polypeptide product of a gene, a non-gene product polypeptide, a glycoprotein, a carbohydrate, a glycolipd, a lipid, a lipoprotein or a small molecule.
  • Detection and analysis of a variety of genes known in the art to be associated with pluripotent stem cells may include analysis of genes such as, but not limited to OCT4, NANOG, SALL4, SSEA-1, SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, or a combination thereof.
  • iPS cells may express any number of pluripotent cell markers, including: alkaline phosphatase (AP); ABCG2; stage specific embryonic antigen- 1 (SSEA-1); SSEA-3; SSEA-4; TRA-1-60; TRA-1-81; Tra-2-49/6E; ERas/ECAT5, E-cadherin; ⁇ - ⁇ -tubulin; ⁇ -smooth muscle actin ( ⁇ -SMA); fibroblast growth factor 4 (Fgf4), Cripto, Daxl; zinc finger protein 296 (Zfp296); N-acetyltransferase-1 (Natl); ES cell associated transcript 1 (ECAT1);
  • AP alkaline phosphatase
  • SSEA-1 stage specific embryonic antigen- 1
  • SSEA-3 stage specific embryonic antigen- 1
  • SSEA-4 SSEA-1-60
  • TRA-1-81 Tra-2-49/6E
  • ERas/ECAT5 E-cadherin
  • differentiation refers to a change that occurs in cells to cause those cells to assume certain specialized functions and to lose the ability to change into certain other specialized functional units.
  • Cells capable of differentiation may be any of totipotent, pluripotent or multipotent cells. Differentiation may be partial or complete with respect to mature adult cells.
  • Differentiated cell refers to a non-embryonic, non-parthenogenetic or non- pluripotent cell that possesses a particular differentiated, i.e., non-embryonic, state.
  • the three earliest differentiated cell types are endoderm, mesoderm, and ectoderm.
  • Pluripotency can also be confirmed by injecting the cells into a suitable animal, e.g., a SCID mouse, and observing the production of differentiated cells and tissues. Still another method of confirming pluripotency is using the subject pluripotent cells to generate chimeric animals and observing the contribution of the introduced cells to different cell types. Methods for producing chimeric animals are well known in the art and are described in U.S. Pat. No. 6,642,433, incorporated by reference herein.
  • Yet another method of confirming pluripotency is to observe cell differentiation into embryoid bodies and other differentiated cell types when cultured under conditions that favor differentiation (e.g., removal of fibroblast feeder layers).
  • the invention further provides iPS cells produced using the methods described herein, as well as populations of such cells.
  • the reprogrammed cells of the present invention capable of differentiation into a variety of cell types, have a variety of applications and therapeutic uses.
  • the present invention further provides a method of treatment or prevention of a disorder and/or condition in a subject using induced pluripotent stem cells generated using the methods described herein.
  • the method includes obtaining a somatic cell from a subject and reprogramming the somatic cell into an iPS cell using the methods described herein.
  • the cell is then cultured under suitable conditions to differentiate the cell into a desired cell type suitable for treating the condition.
  • the differentiated cell may then be introducing into the subject to treat or prevent the condition.
  • One advantage of the present invention is that it provides an essentially limitless supply of isogenic or synegenic human cells suitable for transplantation.
  • the iPS cells are tailored specifically to the patient, avoiding immune rejection. Therefore, it will obviate the significant problem associated with current transplantation methods, such as, rejection of the transplanted tissue which may occur because of host versus graft or graft versus host rejection.
  • iPS cells or fully differentiated somatic cells prepared from iPS cells from somatic cells derived from healthy humans can be stored in an iPS cell bank as a library of cells, and one kind or more kinds of the iPS cells in the library can be used for preparation of somatic cells, tissues, or organs that are free of rejection by a patient to be subjected to stem cell therapy.
  • the iPS cells of the present invention may be differentiated into a number of different cell types to treat a variety of disorders by methods known in the art.
  • iPS cells may be induced to differentiate into hematopoetic stem cells, muscle cells, cardiac muscle cells, liver cells, cartilage cells, epithelial cells, urinary tract cells, neuronal cells, and the like.
  • the differentiated cells may then be transplanted back into the patient's body to prevent or treat a condition.
  • the methods of the present invention may be used to treat a subject having a myocardial infarction, congestive heart failure, stroke, ischemia, peripheral vascular disease, alcoholic liver disease, cirrhosis, Parkinson's disease, Alzheimer's disease, diabetes, cancer, arthritis, wound healing, immunodeficiency, aplastic anemia, anemia, Huntington's disease, amyotrophic lateral sclerosis (ALS), lysosomal storage diseases, multiple sclerosis, spinal cord injuries, genetic disorders, and similar diseases, where an increase or replacement of a particular cell type/ tissue or cellular de-differentiation is desirable.
  • ALS amyotrophic lateral sclerosis
  • the method increases the number of cells of the tissue or organ by at least about 5%, 10%, 25%, 50%, 75% or more compared to a corresponding untreated control tissue or organ.
  • the method increases the biological activity of the tissue or organ by at least about 5%, 10%, 25%, 50%, 75% or more compared to a corresponding untreated control tissue or organ.
  • the method increases blood vessel formation in the tissue or organ by at least about 5%, 10%, 25%, 50%, 75% or more compared to a corresponding untreated control tissue or organ.
  • the cell is administered directly to a subject at a site where an increase in cell number is desired either before or after differentiation of the cell to a desired cell type.
  • the present invention provides a method of identifying an iPS cell.
  • the method includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of an iPS cell, wherein a similarity in methylation status is indicative of the putative cell being an iPS cell.
  • the known methylation status of the one or more nucleic acid sequences of an iPS cell may include the R-DMRs set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4C-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • the method of identifying an iPS cell includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of a corresponding somatic cell from which the iPS cell is induced and/or an ES cell, wherein an alteration in methylation status is indicative of the putative cell being an iPS cell.
  • the one or more nucleic acid sequences may be DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • the invention further provides a plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequence is up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in the reprogramming of a somatic cell to generate an iPS cell.
  • the nucleic acid sequences are the DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A- 4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene.
  • the invention further provides a plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the methylation status of the nucleic acid sequences is altered in an iPS cell as compared to an ES cell.
  • the nucleic acid sequences are the DMR sequences as set forth in Table 7, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene.
  • the plurality of nucleic acid sequences may be utilized to provide a microarray for performing the methods described herein.
  • One skilled in the art would appreciate the many techniques that are well known for attaching nucleic acids on a substrate that may be utilized along with the various types of substrates and configurations.
  • the invention further provides a method of characterizing the methylation status of the nucleic acid of an iPS cell.
  • the method includes a) hybridizing labeled and digested nucleic acid of an iPS cell to a DNA microarray comprising at least 2000 nucleic acid sequences, with the proviso that the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island; and b) determining a pattern of methylation from the hybridizing of (a), thereby characterizing the methylation status for the iPS cell.
  • the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • Characterizing the methylation status of the nucleic acid of an iPS cell may further include comparing the methylation status profile to a methylation profile from hybridization of the microarray with labeled and digested nucleic acid from a parental somatic cell from which the iPS is induced or from an ES cell.
  • the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • methylation status is converted to an M value.
  • an M value can be a log ratio of intensities from total (Cy3) and McrBC- fractionated DNA (Cy5): positive and negative M values are quantitatively associated with methylated and unmethylated sites, respectively.
  • DMR may be hypermethylated or
  • hypomethylated Hypomethylation of a DMR is present when there is a measurable decrease in methylation of the DMR. In some embodiments, a DMR can be determined to be hypomethylated when less than 50% of the methylation sites analyzed are not methylated. Hypermethylation of a DMR is present when there is a measurable increase in methylation of the DMR. In some embodiments, a DMR can be determined to be hypermethylated when more than 50% of the methylation sites analyzed are methylated. Methods for determining methylation states are provided herein and are known in the art. In some embodiments methylation status is converted to an M value.
  • an M value can be a log ratio of intensities from total (Cy3) and McrBC-fractionated DNA (Cy5): positive and negative M values are quantitatively associated with methylated and unmethylated sites, respectively. M values are calculated as described in the Examples. In some embodiments, M values which range from -0.5 to 0.5 represent unmethylated sites as defined by the control probes, and values from 0.5 to 1.5 represent baseline levels of methylation.
  • determining of methylation status in the methods of the invention is performed by one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequenceing, single-strand conformation polymorphism (SSCP) analysis, restriction analysis, microarray technology, and proteomics.
  • analysis of methylation can be performed by bisulfite genomic sequencing.
  • Bisulfite treatment modifies DNA converting unmethylated, but not methylated, cytosines to uracil.
  • Bisulfite treatment can be carried out using the
  • bisulfite pyrosequencing which is a sequencing-based analysis of DNA methylation that quantitatively measures multiple, consecutive CpG sites individually with high accuracy and reproducibility
  • Exemplary primers for such analysis are set forth in Table 11.
  • Table 11 It will be recognized that depending on the site bound by the primer and the direction of extension from a primer, that the primers listed above can be used in different pairs.
  • additional primers can be identified within the DMRs, especially primers that allow analysis of the same methylation sites as those analyzed with primers that correspond to the primers disclosed herein.
  • Altered methylation can be identified by identifying a detectable difference in methylation. For example, hypomethylation can be determined by identifying whether after bisulfite treatment a uracil or a cytosine is present a particular location. If uracil is present after bisulfite treatment, then the residue is unmethylated. Hypomethylation is present when there is a measurable decrease in methylation.
  • the method for analyzing methylation of the DMR can include amplification using a primer pair specific for methylated residues within a DMR.
  • selective hybridization or binding of at least one of the primers is dependent on the methylation state of the target DNA sequence (Herman et al., Proc. Natl. Acad. Sci. USA, 93:9821 (1996)).
  • the amplification reaction can be preceded by bisulfite treatment, and the primers can selectively hybridize to target sequences in a manner that is dependent on bisulfite treatment.
  • one primer can selectively bind to a target sequence only when one or more base of the target sequence is altered by bisulfite treatment, thereby being specific for a methylated target sequence.
  • Methods using an amplification reaction can utilize a real-time detection amplification procedure.
  • the method can utilize molecular beacon technology (Tyagi et al., Nature Biotechnology, 14: 303 (1996)) or TaqmanTM technology (Holland et al., Proc. Natl. Acad. Sci. USA, 88:7276 (1991)).
  • methyl light Trinh et al., Methods 25(4):456-62 (2001), incorporated herein in its entirety by reference
  • Methyl Heavy Methyl Heavy
  • SNuPE single nucleotide primer extension
  • selective hybridization or “selectively hybridize” refers to hybridization under moderately stringent or highly stringent physiological conditions, which can distinguish related nucleotide sequences from unrelated nucleotide sequences.
  • the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (for example, relative GC:AT content), and nucleic acid type, for example, whether the oligonucleotide or the target nucleic acid sequence is DNA or RNA, can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter. Methods for selecting appropriate stringency conditions can be determined empirically or estimated using various formulas, and are well known in the art ⁇ see, e.g., Sambrook et al., supra, 1989).
  • An example of progressively higher stringency conditions is as follows: 2X SSC/0.1% SDS at about room temperature (hybridization conditions); 0.2X SSC/0.1% SDS at about room temperature (low stringency conditions); 0.2X SSC/0.1% SDS at about 42°C (moderate stringency conditions); and 0.1X SSC at about 68°C (high stringency conditions). Washing can be carried out using only one of these conditions, for example, high stringency conditions, or each of the conditions can be used, for example, for 10 to 15 minutes each, in the order listed above, repeating any or all of the steps listed.
  • the degree of methylation in the DNA associated with the DMRs being assessed may be measured by fluorescent in situ hybridization (FISH) by means of probes which identify and differentiate between genomic DNAs, associated with the DMRs being assessed, which exhibit different degrees of DNA methylation.
  • FISH fluorescent in situ hybridization
  • the biological sample will typically be any which contains sufficient whole cells or nuclei to perform short term culture.
  • the sample will be a sample that contains 10 to 10,000, or, for example, 100 to 10,000, whole cells.
  • methyl light, methyl heavy, and array-based methylation analysis can be performed, by using bisulfite treated DNA that is then PCR- amplified, against microarrays of oligonucleotide target sequences with the various forms corresponding to unmethylated and methylated DNA.
  • nucleic acid molecule is used broadly herein to mean a sequence of deoxyribonucleotides or ribonucleotides that are linked together by a phosphodiester bond.
  • nucleic acid molecule is meant to include DNA and RNA, which can be single stranded or double stranded, as well as DNA/RNA hybrids.
  • nucleic acid molecule includes naturally occurring nucleic acid molecules, which can be isolated from a cell, as well as synthetic molecules, which can be prepared, for example, by methods of chemical synthesis or by enzymatic methods such as by the polymerase chain reaction (PCR), and, in various embodiments, can contain nucleotide analogs or a backbone bond other than a phosphodiester bond.
  • PCR polymerase chain reaction
  • polynucleotide and oligonucleotide also are used herein to refer to nucleic acid molecules. Although no specific distinction from each other or from “nucleic acid molecule” is intended by the use of these terms, the term “polynucleotide” is used generally in reference to a nucleic acid molecule that encodes a polypeptide, or a peptide portion thereof, whereas the term “oligonucleotide” is used generally in reference to a nucleotide sequence useful as a probe, a PCR primer, an antisense molecule, or the like. Of course, it will be recognized that an "oligonucleotide” also can encode a peptide. As such, the different terms are used primarily for convenience of discussion.
  • a polynucleotide or oligonucleotide comprising naturally occurring nucleotides and phosphodiester bonds can be chemically synthesized or can be produced using recombinant DNA methods, using an appropriate polynucleotide as a template.
  • a polynucleotide comprising nucleotide analogs or covalent bonds other than phosphodiester bonds generally will be chemically synthesized, although an enzyme such as T7 polymerase can incorporate certain types of nucleotide analogs into a polynucleotide and, therefore, can be used to produce such a polynucleotide recombinantly from an appropriate template.
  • kits that are useful for carrying out the methods of the present invention.
  • the components contained in the kit depend on a number of factors, including: the particular analytical technique used to detect methylation or measure the degree of methylation or a change in methylation, and the one or more DMRs is being assayed for methylation status.
  • the present invention provides a kit for determining a methylation status of one or more DMRs of the invention.
  • the one or more DMRs are selected from one or more of the sequences as set forth in Tables 2, 6, 7, 9, Figures 1B- 1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
  • the kit includes an oligonucleotide probe, primer, or primer pair, or combination thereof for carrying out a method for detecting hypomethylation, as discussed above.
  • the probe, primer, or primer pair can be capable of selectively hybridizing to the DMR either with or without prior bisulfite treatment of the DMR.
  • the kit can further include one or more detectable labels.
  • the kit can also include a plurality of oligonucleotide probes, primers, or primer pairs, or combinations thereof, capable of selectively hybridizing to the DMR with or without prior bisulfite treatment of the DMR.
  • the kit can include an oligonucleotide primer pair that hybridizes under stringent conditions to all or a portion of the DMR only after bisulfite treatment.
  • the kit can provide reagents for bisulfite pyrosequencing including one or more primer pairs set forth in Table 11.
  • the kit can include instructions on using kit components to identify, for example, the presence of cancer or an increased risk of developing cancer.
  • CHARM is 100% specific at 90% sensitivity for known methylation marks identified by other methods (for example, in promoters) and includes the approximately half of the genome not identified by conventional region preselection .
  • the CHARM results were also extensively corroborated by quantitative bisulfite pyrosequencing analysis.
  • IPS cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not peviously been analyzed on a genome-wide scale. Substantial
  • cytosine-phosphate-guanine (CpG) island shores in nine human iPS cell lines as compared to their parental fibroblasts was determined.
  • the R- DMRs in the reprogrammed cells were significantly enriched in tissue-specific (T-DMRs; 2.6-fold, P ⁇ I Q- 4 ) and cancer-specific DMRs (C-DMRs; 3.6-fold, P ⁇ 10 "4 ).
  • T-DMRs tissue-specific
  • C-DMRs cancer-specific DMRs
  • P ⁇ 10 "4 cancer-specific DMRs
  • many DMRs are broadly involved in tissue differentiation, epigenetic reprogramming and cancer. Colocalization of hypomethylated R-DMRs with hypermethylated C-DMRs and bivalent chromatin marks, and colocalization of hypermethylated R-DMRs with
  • hypomethylated C-DMRs and the absence of bivalent marks were observed, suggesting two mechanisms for epigenetic reprogramming in iPS cells and cancer.
  • methylation density is determined for a region of nucleic acid. Density may be used as an indication of production of an iPS cell, for example. A density of about 0.2 to 0.7, about 0.3 to 0.7 , 0.3 to 0.6 or 0.3 to 0.4, or 0.3, may be indicative of generation of an iPS cell (the calculated DNA methylation density is the number of methylated CpGs divided by the total number of CpGs sequenced for each sample).
  • Methods for determining methylation density are well known in the art. For example, a method for determining methylation density of target CpG islands has been established by Luo et al. Analytical Biochemistry, Vol. 387:2 2009, pp. 143-149. In the method, DNA microarray was prepared by spotting a set of PCR products amplified from bisulfite- converted sample DNAs. This method not only allows the quantitative analysis of regional methylation density of a set of given genes but also could provide information of methylation density for a large amount of clinical samples as well as use in the methods of the invention regarding iPS cell generation and detection. Other methods are well known in the art (e.g., Holemon et al., BioTechniques, 43:5, 2007, pp. 683-693).
  • RNA and genomic DNA from fibroblast, hES cells and iPS cells.
  • iPS cell lines and their parental fibroblasts used were described in Park et al. (Nature (451)141-146 (2008)) and Park et al. Cell (134)877-886 (2008)).
  • MRC5 14-week-old fetal lung fibroblast from the ATCC cell biology collection
  • Detroit 551 551, fetal skin fibroblast from ATCC
  • hFib2 adult dermal fibroblast
  • SBDS SBDS
  • DMD GM04981 from Coriell
  • GD GM00852A from Coriell
  • PD AG20446 from Coriell
  • JDM GM02416 from Coriell
  • ADA GM01390 from Coriell.
  • Human ES cells BGOl, BG03 and H9 were used. Fibroblasts were grown in a-MEM containing 10% W 201
  • RNA and genomic DNA were isolated using RNeasyTM kit (Qiagen) with in-column DNase treatment and DNeasyTM kit (Qiagen), respectively, according to manufacturer's protocol.
  • CHARM DNA methylation analysis For each sample, 5 ⁇ g of genomic DNA was digested, fractionated, labeled and hybridized to a CHARM microarray as described in Irizarry et al. (Nat. Genet. (41)178-186 (2009)) and Irizarry et al. ⁇ Genome Res. (18)780-790 (2008)).
  • FDR false discovery rates
  • the parental fibroblast lines for this experiment were MRC5, SBDS, DMD, GD, Detroit551 and PD, and they were compared to the iPS cell lines derived from them.
  • ⁇ n 3 for each cell type
  • an absolute FDR could not be calculated, so we used an absolute area cutoff of 10.0, which corresponded in magnitude to the 5% FDR cutoff of the first set of experiments.
  • the parental fibroblast lines for the second experiment were JMD, ADA and hFib2 and were compared to the iPS cell lines derived from them, as well as to three ES cell lines, BGOl, BG03 and H9.
  • Unsupervised cluster analysis Using the R-DMRs, we performed unsupervised cluster analysis to determine to what degree the methylation at these locations distinguished normal brain, liver and spleen as well as colon cancer from its matched counterpart. As a test of significance, we randomly generated 1,000 CHARM array regions of length and number equal to those of the R-DMRs and then assessed the median euclidean distance among samples of a given tissue type and the median euclidean distance among samples of different tissue types. This test was also applied to the cancer and normal samples.
  • Table 1 1 provides the primer sequences used for the bisulfite pyrosequencing reactions, as well as the chromosomal coordinates in the University of California at Santa Cruz March 2006 human genome assembly for each CpG site interrogated.
  • the annealing temperature used for all PCR reactions was 50 °C.
  • Affymetrix microarray expression analysis Genome-wide gene expression analysis was done using Affymetrix U133 Plus 2.0TM microarrays. For each sample, 1 ⁇ g of high-quality total RNA was amplified, labeled and hybridized onto the microarray according to Affymetrix's specifications, and data were normalized as previously described in Irizarry et al. (Biostatistics (4)249-264 (2003)).
  • NCBI GEO Gene expression microarray data and CHARM microarray data have been submitted under accession number GSE18111.
  • IPS cells can be derived from somatic cells by introduction of a small number of genes: for example, POU5F1, MYC, KLF4 and SOX2.
  • iPS cells offer considerable therapeutic promise, avoiding both immunologic and ethical barriers to their use.
  • iPS cells differ from their somatic parental cells epigenetically, and thus a comprehensive comparison of the epigenome in iPS and somatic cells would provide insight into the mechanism of tissue reprogramming.
  • two previous targeted studies examined a subset of the genome, 7,000 (Ball et al. (Nat. Biotechnol. (27)485 (2009)) and 66,000 (Deng et al. (Nat. Biotechnol. (27)353-360 (2009))) CpG sites in a small cohort of three iPS-fibroblast pairs, a global assessment of genome- wide methylation has not yet been performed.
  • T-DMRs normal tissue types
  • C-DMRs colorectal cancer tissue from matched normal tissues
  • Genomic DNA from iPS cells, their parental fibroblasts and human embryonic stem (hES) cells was digested with the enzyme McrBC, fractionated, labeled and hybridized to a
  • Figure 1 details reprogramming differentially methylated regions (R-DMRs).
  • Figure 1 A depicts enrichment of R-DMRs at CpG island shores.
  • the CHARM array (left, labeled CpG regions) is enriched in CpG islands, and the R-DMRs (right, labeled R-DMR) show marked enrichment at CpG island shores.
  • Islands are denoted as regions that include >50% of a CpG island or are wholly contained in an island, and overlap regions are denoted as regions that include 0.1-50% of a CpG island. Specific base intervals of regions not overlapping islands are indicated; (0-500) means from 1 to 500 bases.
  • Percentage of the distribution is given for the CpG regions (CHARM array, null hypothesis) and reprogramming differentially methylated regions (R-DMRs).
  • Figures IB and C show examples of DMRs.
  • the gene encoding bone morphogenetic protein 7 (BMP7) is indicated in B, and the gene encoding goosecoid (GSC) is indicated in C.
  • BMP7 bone morphogenetic protein 7
  • GSC gene encoding goosecoid
  • the upper panels show a plot of methylation ( value; see Methods) versus genomic location, where the curve represents averaged smoothed M values; the location of CpG dinucleotides (black tick marks), CpG density, location of CpG islands (filled boxes along the x-axis (zero)), as well as the gene annotation are shown.
  • the bottom panels show validation by bisulfite
  • Figure 2 depicts the distribution of distance of reprogramming differentially methylated regions (R-DMRs) from CpG islands.
  • Islands are regions that are inside, cover, or overlap more than 50% of a CpG island. Overlap are regions that overlap 0.1-50% of a CpG island.
  • Regions denoted by (0, 500] are regions located ⁇ 500 bp but do not overlap an island.
  • Regions denoted by (500, 1000] are regions located >500 bp and ⁇ 1000 bp from an island.
  • Regions denoted by (1000, 2000] are regions located >1000 bp and ⁇ 2000 bp from an island.
  • Regions denoted by (2000, 3000] are regions located >2000 bp and ⁇ 3000 bp from an island. Regions denoted by >3000 are >3000 bp from an island. Percentage are given for the CpG regions (CHARM array, null hypothesis) and reprogramming differentially methylated regions (R-DMRs) as well as the R-DMRs subdivided into hypermethylation and
  • the methylation in iPS cells was intermediate between differentiated fibroblasts and ES cells; this was true, for example, of TBX5, which encodes a transcription factor that is involved in cardiac and limb development.
  • methylation in iPS cells differed from both fibroblasts and ES cells, suggesting that the iPS cells occupy a distinct and possibly aberrant epigenetic state.
  • An example was PTPRT, encoding a protein tyrosine phosphatase involved in many cellular processes including differentiation.
  • methylation levels changed in the same direction as for ES cells compared to fibroblasts, but to a greater degree; for example, methylation of the homeobox gene HOXA9 was greater in iPS compared to ES, whose methylation at this gene was greater than in fibroblasts.
  • Figure 4 includes examples of differential DNA methylation (upper panels) and confirmation by bisulfite pyrosequencing (lower panels).
  • Upper panels are a plot of M value versus genomic location, where the curve represents averaged smoothed M values. Also shown in the upper panels are the locations of CpG dinucleotide (black tick marks on x axis), CpG density (smoothed black line) calculated across the region using a standard density estimator, location of CpG islands (filled boxes along the x-axis (zero)), as well as gene annotation indicating the transcript (thin outer gray line), coding region (thin inner gray line), exons (filled gray box) and gene transcription directionality on the y axis (sense marked as +, antisense as -).
  • the lower panels represent the degree of DNA methylation as measured by bisulfite pyrosequencing.
  • the unfilled box indicated on the x axis of the CpG density plot in the upper panel indicates the CpG sites that were measured. Reactions were done in triplicate; bars represent the mean methylation ⁇ SD of iPS cells, fibroblasts, and ES cells (BGOl, BG03 and H9) as well as DKO (DNMT1 and DNMT3B Double KO cell line) and HCT116 (parental colon cancer cell line) for each individual CpG site measured.
  • A TBX3 (T-box 3 protein),
  • B HOXD3 (Homeobox D3),
  • C POU3F4 (POU domain, class 3, transcription factor 4),
  • D A2BP1 (ataxin 2-binding protein 1),
  • E ZNF184 (zinc finger protein 184),
  • W W
  • IGF1R insulin-like growth factor 1 receptor
  • G PTPRT (protein tyrosine phosphatase, receptor type, T).
  • HGU133 PlusTM 2.0 microarray There was a strong inverse correlation between differential gene expression and differential DNA methylation at R-DMRs that are within 500 bp of the transcriptional start site (TSS) of a gene: P ⁇ 10-3 for both hypermethylation and
  • FIG. 5 illustrates that gene expression strongly correlates with reprogramming differentially methylated regions (R-DMRs) at CpG island shores.
  • Red circles represent R- DMRs that are within 2kb from a CpG island
  • blue circles represent those that are more than 2kb away from a CpG island
  • black circles represent log ratios for all genes not within (A) 500bp or (B) lkb from the transcriptional start site (TSS) of an annotated gene.
  • TSS transcriptional start site
  • the log2 ratios of fibroblast to iPS expression were plotted against ⁇ values (fibroblast minus iPS) for R-DMRs in which one of the two points had approximately no methylation.
  • A DMRs that are within 500bp from a TSS of a gene.
  • B DMRs that are within lkb from a TSS of a gene.
  • FIG. 3 shows that DNA methylation at R-DMRs distinguishes normal tissues from each other and colon cancer from normal colon.
  • a and B The M values of all tissues from the 4,401 regions (FDR ⁇ 0.05) corresponding to R-DMRs (iPS cells compared to parental fibroblasts) were used for unsupervised hierarchical clustering comparing (A) normal brain, spleen and liver (denoted as Br, Sp and Lv, respectively) and (B) colorectal cancer and matched normal colonic mucosa (denoted as T and N, respectively).
  • R-DMRs colorectal cancer and matched normal colonic mucosa
  • the R-DMRs were compared to those obtained in a genome-scale comparison of DNA methylation in colorectal cancer and matched normal colonic mucosa from the same individuals (C-DMRs) as discussed in Irizarry et al. (Nat. Genet. (41)178-186 (2009)).
  • a secondary finding is that certain loci in iPS cells remain incompletely reprogrammed, whereas others are aberrantly reprogrammed, thus establishing that the methylation pattern of iPS cells differs both from those of the parent somatic cells and from those of human ES cells.
  • R-DMRs are regions that differ in DNA methylation between 6 iPS lines and the fibroblasts from which they were derived.
  • FDR false discovery rate.
  • R-DMRs were defined by using a FDR cutoff of 5%.
  • chrl5 94686085 94687818 1.33256 -0.0655 66.1928 NR2F2 11136 downstream -548 disjoint 0.00966 chrl4 64239302 64240573 1.82985 -0.0939 65.9892 PLE HG3 372 promoter 56 disjoint 0.00966 chrl6 71654610 71657245 1.01951 -0.0039 65.925 ATBF1 14836 upstream 0 overlap 0.00966 chrl2 128900598 128903997 0.11442 1.39687 65.8968 TMEM132D 50168 inside intron 1639 disjoint 0.00966 chrl2 6531060 6534095 0.50762 1.47267 65.1372 HOM-TES- 1394 inside intron 591 disjoint 0.00967
  • chr4 174664434 174666750 1.5136 0.35561 52.1861 HAND2 21202 downstream 0 cover 0.00994 chrl 112853554 112854782 1.61085 0.09865 51.8868 NT2B 166 overlaps exon 0 overlap 0.00995 downstream chr9 102276338 102277667 1.71233 0.25285 51.8343 TMEFF1 801 inside intron 0 overlap 0.00995 chr22 36S28744 36530199 1.21846 -0.0042 51.8264 H1F0 860 promoter 419 disjoint 0.00995 chrl9 16049883 16051512 -0.1787 1.11299 51.5279 TPM4 1559 inside intron -608 disjoint 0.00996 chrl 154961985 154963849 0.75971 1.95945 51.4944 ISG20L2 479 overlaps exon 886 disjoint 0.00997 downstream
  • chrl8 52963741 52965315 -0.0673 2.05326 45.079 WDR7 494128 downstream -23549 disjoint 0.01031 chr2 63132869 63134574 1.39985 0.39203 44.9938 OTX1 1401 covers exon(s) 0 overlap 0.01032 chr6 101020166 101021773 1.17303 0.13573 44.8811 SMI 1895 promoter 0 overlap 0.01033 chrlO 102485639 102487566 0.86061 0.0674 44.8699 PAX2 7755 upstream 0 overlap 0.01033 chr8 68139975 68141466 0.2847 1.56861 44.8163 CSPP1 819 inside intron 0 overlap 0.01033 chr2 100088245 100089913 1.14828 0.28393 44.6781 AFF3 35555 covers exon(s) -1072 disjoint 0.01034 chrl2 121
  • BHLHB2 1171 covers exon(s) -155 disjoint 0.01117 chr4 174667570 174669252 1.48981 0.49152 37.1108 HAND2 18700 downstream -134 disjoint 0.01118 chr6 31777467 31778888 -0.1092 0.71282 37.0848
  • BAT5 178 covers exon(s) 0 overlap 0.01 118 chrl4 103935048 103937957 0.18051 1.60718 37.048 LOC400258 179143 upstream 28992 disjoint 0.01119 chrl7 7491 5 087 74916508 0.47516 1.48744 37.0215 LOC146713 15057 inside intron 55332 disjoint 0.01119 chrl3 9267 5 166 92676682 1.04767 0.1 36.941
  • CLK1 713 covers exon(s) 184 disjoint 0.01232 chrlO 104669314 104670494 0.9997 0.01097 31.8062
  • C NM2 1211 overlaps exon -12 disjoint 0.01232 downstream
  • chrlO 26264471 26266406 0.27575 0.97024 23.8259 MY03A 1270 covers exon(s) -443 disjoint 0.01595 chrl4 92460706 92462209 0.28844 1.34755 23.8137 CHGA 1462 inside intron -1054 disjoint 0.01595 chr3 171240759 171241541 0.75819 1.81464 23.7874 GPR160 1363 inside intron -1221 disjoint 0.01597 chr6 150501895 150502887 0.30216 1.19675 23.7868 PPP1R14C 3038 upstream 2577 disjoint 0.01597 chrl 5 65601462 65602211 -0.1765 0.92526 23.7578 MAP2K5 19863 upstream -227 disjoint 0.01599 chr21 37000964 37001823 0.96679 -0.096 23.7463 SIM2 7104 inside intron 0
  • chrX 9939268 9940550 1.35799 0.2174 22.6607 WWC3 3061 upstream 1963 disjoint 0.01677 chrl8 54683040 54684032 0.40773 1.24646 22.6458 ZNF532 2000 covers exon(s) -772 disjoint 0.01678 chr9 126044511 126045440 0.785 1.84458 22.638 NEK6 14629 upstream 14630 disjoint 0.01679 chr2 115135470 115136151 0.29254 1.65873 22.6326 DPP10 219102 inside intron 47 disjoint 0.01679 chr7 43763958 43764428 1.78764 0.10568 22.6326 BLVRA 368 promoter 0 overlap 0.01679 chrl3 45322884 45324348 0.14484 0.75737 22.6322 LOC283514 0 overlaps 5' -136669 disjoint 0.01679 ch
  • GSTA4 846 covers exon(s) 272 disjoint 0.0177
  • chr6 31739482 31740684 0.34771 1.01018 21.6425
  • BAT4 457 covers exon(s) 110 disjoint 0.01771 chrl l 2659433 2660734 0.32085 0.93189 21.6423
  • MGC39900 375 inside in
  • chr2 238863009 238863692 1.89525 0.84663 19.2023
  • PER2 1179 promoter -370 disjoint 0.02031 chr7 130890067 130891273 0.75923 0.19851 19.2 PODXL 634 inside intron 0 overlap 0.02031 chr 5 180168460 180169309 0.96098 1.8665 19.1971 MGAT1 5807 upstream 289 disjoint 0.02032 chrl 8 66850594 66851589 0.51106 1.34133 19.1943 SOCS6 743352 downstream -601518 disjoint 0.02032 chr 5 72562287 7256303030 1.64336 0.50733 19.1905 TMEM174 62458 downstream -34 disjoint 0.02032 chr6 27837986 27838651 1.4716 0.4615 19.1862 HIST1H2BL 45036 downstream 44657 disjoint 0.02033 chr5
  • EIF4A1 1394 covers exon(s) -120 disjoint 0.02134 chrl6 67779903 67780862 0.17074 0.94074 18.4204 SNTB2 1353 inside intron -295 disjoint 0.02135 chr9 95755626 95756444 1.01266 0.26401 18.4154 BARX1 978 inside intron 0 inside 0.02136 chrl 149212099 149212953 0.17984 0.93111 18.4124 LASS2 1110 inside intron 167 disjoint 0.02136 chrl8 491107 491721 1.51967 0.34696 18.4021 COLEC12 423 promoter -385 disjoint 0.02138 chr9 136676317 136677114 0.39819 1.1694 18.4019 COL5A1 2845 inside intron -2099 disjoint 0.02138 chr 5 150059
  • chrl2 56294113 56294691 2.79263 1.74026 16.353 GEFT 2151 covers exon(s) -2495 disjoint 0.02472 chrl 6 19993114 19994020 0.04981 0.92352 16.3503 GPR139 514 promoter -308 disjoint 0.02473 chrl 33667959 33668537 1.082 -0.0701 16.3492 ZNF31 42308 upstream 52 disjoint 0.02473 chrl 8 42169270 42170295 0.52437 -0.0768 16.3444 RNF165 1086 inside intron -795 disjoint 0.02474 chr22 44850960 44851727 0.4 5 29 1.23622 16.3394 FLJ27365 8819 upstream -3768 disjoint 0.02474 chrlO 22655295 22655951 1.13875 0.15556 16.3371 BMI1 5150 covers exon(s) -355 disjoint 0.0
  • chrl 9 60838061 60839128 0.07448 0.56366 16.1214 ZNF580 5075 upstream 4200 disjoint 0.02517 chr20 21320460 21321039 0.97801 -0.0483 16.1132 XRN2 88519 downstream 0 overlap 0.02518 chr 5 50295795 50296517 1.27811 0.29459 16.1102 PARP8 297226 downstream 4325 disjoint 0.02518 chr2 71358949 71359598 1.18824 0.2614 16.1043 ZNF638 52798 upstream -1208 disjoint 0.0252 chr4 81104306 81104941 1.51951 0.50483 16.1038 ANTXR2 108335 inside intron 0 overlap 0.0252 chr6 41483828 41484646 1.07438 0.34236 16.0982 NCR2 72324 downstream 0 overlap 0.02521 chrl 212219253 212219828 1.51148
  • chr2 176723900 176724580 1.17517 0.3365 15.585 HOXD4 0 overlaps 5' 82 disjoint 0.02624 chr9 138810115 138812923 0.52237 1.23234 15.5828 KIAA1984 0 overlaps 5' 881 disjoint 0.02625 chr3 197107717 197108427 0.28981 1.13194 15.582 TN 2 11849 inside intron -290 disjoint 0.02625 chrX 136479176 136479820 0.64895 -0.2463 15.58 ZIC3 3165 overlaps exon 0 overlap 0.02625 upstream
  • chrl7 25468769 25469534 -0.1972 0.73541 15.5395 CCDC55 810 covers exon(s) -632 disjoint 0.02633 chrl l 2233400 2234180 0.8216 1.63515 15.5367 ASCL2 14577 downstream 12500 disjoint 0.02634 chr9 132701631 132702763 0.14232 0.83722 15.5352 ABL1 980 inside intron -525 disjoint 0.02635 chr4 171205682 171206224 0.15767 1.21789 15.5327 AADAT 41533 downstream -20199 disjoint 0.02635 chrI9 47121534 47122274 0.08171 0.84473 15.5182 ARHGEF1 41249 downstream 1482 disjoint 0.02639 chrl4 52326302 52327205 1.20365 0.30153 15.5168 GNPNAT1 927 inside intron 209 disjoint 0.02639 chrl
  • chrl 7 43403472 43404023 0.19458 1.02332 11.5793 CDK5RAP3 45 covers exon(s) 0 overlap 0.03783 chr5 140190451 140191134 -0.0502 0.59791 11.5783 PCDHA6 2618 inside intron -310 disjoint 0.03784 chr9 131409275 131409911 0.661 1.45848 11.5771 C9orf50 12964 downstream 2253 disjoint 0.03784 chrl l 69597308 69598097 0.77316 1.29387 11.5754 TMEM16A 4196 upstream 3889 disjoint 0.03785 chr7 29814368 29815312 1.04575 1.69584 11.5744 SC N1 180589 downstream -1092 disjoint 0.03785 chr7 2639523 2640101 0.467 1.19223 11.5735 TTYH3 1395 inside intron -1060 disjoint 0.03785
  • chrl 9 49023637 49023969 0.84112 1.92747 9.99264 LYPD5 7012 upstream -6788 disjoint 0.04525 chrl l 59138466 59139005 0.21259 0.88183 9.99106 OSBP 1187 inside intron 258 disjoint 0.04525 chr7 100398484 100398984 0.31237 1.02067 9.99061 MUC17 51099 upstream -1971 disjoint 0.04526 chr2 176698813 176699280 1.04925 0.17915 9.98569 HOXD9 3480 downstream -980 disjoint 0.04528 chrl 7 4404264 4404980 0.33318 0.79S26 9.98192 MYBBP1A 412 overlaps two exons 0 overlap 0.0453 chrl 148126311 148127372 -0.0647 0.27136 9.98162 HIST2H2AB 222 promoter -217 dis
  • chr4 40954889 40955503 1.32665 0.78182 9.39132 UCHL1 1204 inside intron -265 disjoint 0.04856 chrlO 42571857 42572513 0.89274 1.46374 9.38879 BMS1L 25751 upstream -939 disjoint 0.04858 chrl 7 33920924 33921412 1.20868 0.42304 9.38675 SNIP 94296 downstream -164 disjoint 0.04859 chrl 7 69708441 69708917 1.07719 1.78064 9.38381 RPL38 2472 promoter 2610 disjoint 0.04861 chrl4 70179420 70179959 0.82681 0.2202 9.38342 MED6 42284 upstream -335 disjoint 0.04861 chrl 8 32018645 32019115 1.29571 0.54563 9.38226 MOCOS 2364 promoter 1274 disjoint 0.0
  • chrX 118708883 118709458 0.72868 1.34083 9.19249 1902 inside intron 1022 disjoint 0.04972 chr4 90446622 90447152 2.55265 1.8928 9.1883 GPRJN3 1031 inside intron 585 disjoint 0.04975 chr5 88021299 88021841 0.61157 -0.001 9.18808 MEF2C 192938 downstream 0 overlap 0.04975 chr20 61477279 61477695 0.82053 1.66728 9.188 CHRNA4 14088 upstream -3802 disjoint 0.04975 chrl 65387779 65388180 0.80959 -0.0079 9.18249 AK3L2 1101 inside intron -293 disjoint 0.04979 chrl 7 45560093 45560766 0.93987 0.41026 9.18193 SAMD14 1399 inside intron 896 disjoint 0.04979 chr8 143400176 14
  • chr6 34966181 34966594 0.56238 1.52146 9.15576 AN S1A 1163 inside intron -539 disjoint 0.04995 chrl 7 34116469 34117469 0.8161 0.44096 9.15554 MLLT6 1069 covers exon(s) -1246 disjoint 0.04996 chr2 16708633 16709362 0.89128 1.57406 9.15118 FAM49A 1214 inside intron -155330 disjoint 0.04998
  • R-DMRs differentially methylated regions
  • chrl l 31784606 31787983 1.41933931 -0.31644601 159.697521
  • PAX6 1450 covers exon(s) -109 disjoint chr4 111780296 111782892 1.63173739 -0.17319743 132.277796
  • PITX2 2340 promoter -39 disjoint chr 6 101009118 101012166 1.56292862 0.07999288 121.511837
  • PAX6 9303 covers exon(s) -260 disjoint chr 5 174086712 174088442 1.75529701 0.00109963 85.6376081 MSX2 2532 inside intron -1742 disjoint chr2 66523155 66525137 1.53956949 -0.09867546 85.0156191
  • MEIS1 7120 covers exon(s) 798 disjoint chr 5 122456101 122458523 1.38936079 -0.02772582 82.6647917 PPIC 55778 upstream 52 disjoint chrl4 69416842 69419462 -0.19824968 1.20834882 82.6223597 SMOCl 947 inside intron -562 disjoint chrlO 22661208 22663161 1.4779070707 -0.07457995
  • chrl 2 113615569 113617118 1.45655962 -0.0416652 63.996903 TBX3 9218 upstream -944 disjoint chr2 144408857 144410536 -0.10667617 1.22862162 63.4659312 GTDC1 395962 downstream 600 disjoint chr20 49847751 49849925 1.04888608 -0.18236327 62.6992872 SALL4 2495 inside intron 794 disjoint chrl3 49600378 49601736 1.55239767 -0.106977 62.687492 KCNRG 112988 downstream 0 overlap chrlO 21827602 21828807 1.40520939 -0.48129466 62.5304957 C10orfl l4 1406 promoter 0 overlap chrl2 79626961 79628584 1.3730142 0.04232383 62.2483215 MYF6 1385 overlaps 3'
  • chr2 176736313 176737800 1.63327343 0.19509096 58.7718208 H0XD3 0 overlaps 5' 0 overlap chr7 27106893 27108134 1.61198644 0.01775409 58.6008133 H0XA2 784 overlaps exon 1572 disjoint upstream
  • chr3 148620314 148621273 1.90219036 -0.15922394 53.257094 ZICl 10444 downstream -299 disjoint chr4 151722401 151723404 1.86044619 -0.29765235 53.0965912 AB21L2 0 overlaps 5' 57 disjoint chr3 148614542 148615993 1.33962917 -0.03015777 52.9759123 ZICl 4672 inside exon -522 disjoint chrl l 31780431 31782210 1.31971017 -0.02747236 52.8408389 PAX6 7223 covers exon(s) 109 disjoint chr3 148587638 148589395 1.2363237 0.19347292 52.7520873 ZIC4 17701 overlaps exon 1803 disjoint upstream
  • chrlO 22652675 22653622 1.54940518 -0.48360594 52.6684368 BMI1 2530 inside intron 659 disjoint chr4 81403269 81404477 1.71294929 0.14782841 52.6540894 FGF5 2288 promoter 2041 disjoint chr 6 10513143 10514243 1.64823552 -0.16251431 52.4938953 TFAP2A 6349 inside intron 0 overlap chrl 212223887 212225199 1.41267876 -0.1036052 52.2142965 PROX1 3283 upstream 150 disjoint chr 5 72631433 72632752 1.55907375 0.03752966 51.5934543 TME 174 131604 downstream 0 overlap chr4 54663407 54664534 1.52539942 -0.1795399 51.3548036 GSH2 2453 close to 3' -587 disjoint chrl 7
  • chr 5 154219106 154220032 -0.13990552 1.31206448 35.9618646 CNOT8 716 inside intron -551 disjoint chrl9 36538829 36539809 1.08996256 -0.3296489 35.9512967 TSHZ3 76815 upstream 0 overlap chrl 162811165 162812119 1.58327994 0.21300667 35.9431306 PBX1 15605 inside intron 45 disjoint chr8 976495 978327 3.5304042 2.196131 35.9429244 ERICH1 305270 upstream 0 cover chr 6 134540510 134541574 -0.02928008 1.30769243 35.9333102 SG 2816 upstream -1061 disjoint chrl 219128497 219129717 1.40212372 0.15148187 35.792526 HLX1 9116 downstream -803 disjoint chr5
  • chrlO 124218089 124218979 0.06066256 1.27337721 29.5720366 HTRA1 7043 inside intron -5859 disjoint chr8 22355564 22356594 -0.1443314 0.83979129 29.5297431 PPP3CC 1024 inside intron -477 disjoint chr4 174659289 174660227 1.43921915 0.30342524 29.5293354 HAND2 27725 downstream -271 disjoint chrl4 51849417 51850354 -0.22788891 1.02669463 29.4617456 PTGER2 508 promoter 83 disjoint chr 5 11955022 11955804 0.24408633 1.6879937 29.3342179 CTNND2 1305 inside intron 746 disjoint chr8 75396686 75397561 -0.35371547 0.94986888 29.331202 JPH1 570 promoter -30
  • chr 5 87476895 87477930 1.2118908 0.33832881 25.812755 TMEM161B 122490 downstream -3634 disjoint chr3 198959742 198960636 -0.00700548 1.14414767 25.8028177 FYTTDl 443 promoter 20 disjoint chr5 87990657 87991382 1.40850902 0.17300754 25.7994468 MEF2C 223397 downstream 12 disjoint chrl 6 78193900 78194718 -0.25593462 0.86733562 25.7980389 MAF 1789 promoter -862 disjoint chr 5 45732504 45733256 0.11040816 1.40923399 25.7931255 HCN1 528 promoter -237 disjoint chr4 108964323 108964958 0.98319248 -0.4743061 25.7718278 MGC26963 68920 upstream
  • chrl 6 83877307 83877974 -0.09566556 1.16751429 24.6951009 FAM92B 173693 upstream 101 disjoint chr6 26152486 26153633 -0.08242374 1.23088597 24.6457558 HIST1H3C 0 overlaps 5' 0 overlap chrl7 35473832 35474651 -0.24125587 1.04278392 24.6187759 THRA 1244 inside intron -426 disjoint chrl7 56884781 56885461 1.13423668 -0.09680232 24.5924833 TBX4 3127 upstream 0 overlap chr3 24847250 24848266 -0.1072094 0.8417926 24.5730156 THRB 335934 upstream -877 disjoint chrl 119349858 119350709 1.63505916 0.44995063 24.5494468 TBX15 16157 upstream
  • chrl 7 78634924 78635571 -0.03917123 1.3151442 23.3594199 ETRNL 4069 inside intron 344 disjoint chr7 27169657 27170448 -0.00150461 0.96758684 23.3384608 HOXA9 1225 overlaps exon 0 overlap upstream
  • chrl 4 102744495 102745371 -0.08638888 0.97119929 23.3303348
  • TNFAIP2 82079 downstream -399 disjoint chrl 7 39992624 39993398 1.09543418 -0.02947563 23.3280657
  • FZD2 2174 close to 3' -247 disjoint chr2 60637613 60638356 1.04020067 -0.15752936 23.2394687 BCL11A 3477 upstream -1330 disjoint chr6 107544512 107545588 0.5903851 -0.22704599 23.2119459 PDSS2 341859 downstream -509 disjoint chrl 6 85168280 85168919 1.39358483 -0.03315958 23.1997553 FOXL1 696 promoter -314 disjoint chr2 96563766 96564515 0.02491383 1.04824304 23
  • chr6 1337367 1338080 0.90474756 -0.13948429 20.9499525 FOXF2 2300 inside intron 0 overlap chrlO 80872778 80873673 0.22766148 1.08428375 20.929173 C10orf56 1712 inside intron 785 disjoint chrl2 28015483 28016172 1.10397108 -0.15753488 20.9143598 PTHLH 10 overlaps exon -443 disjoint downstream
  • chr5 43080648 43081358 1.32666084 0.21708381 20.8618919 LOC389289 4551 upstream -1414 disjoint chr 6 34468801 34469546 -0.0602856 1.25743283 20.838668 NUDT3 383 promoter -21 disjoint chrl 168896553 168897161 1.41376343 0.18887288 20.8231393 PRRX1 2775 upstream 0 overlap chr7 25866943 25867761 1.58011652 0.37347007 20.8204436 NFE2L3 290623 upstream 885 disjoint chr4 141437002 141437853 0.42826366 1.36598175 20.8158184 SCOC 39113 inside intron -42985 disjoint chr2 28471161 28471700 -0.12084794 1.29905966 20.7885446 FOSL2 1879 inside intron -909 disjoint chrl
  • chrl 6 23756839 23758051 0.24801637 1.11289981 19.9848659 PRKCB1 2017 inside intron -1236 disjoint chr2 139252241 139253103 0.81921501 -0.0704156 19.9665534 NXPH2 1177 inside intron 1059 disjoint chr9 20614264 20614909 0.86475669 -0.16525658 19.9608637 MLLT3 1815 promoter -2402 disjoint chr3 170867640 170868332 0.83735758 -0.12887168 19.9211925 MDS1 3473 upstream 627 disjoint chr22 29696207 29696866 1.81017429 0.45033463 19.9047729 M0RC2 2021 promoter -632 disjoint chr8 1494643 1495250 0.41947829 1.58733939 19.8995937 DLGAP2 57668 inside intron 2007 disjoint ch
  • chr2 120019890 120020363 -0.23899867 1.25658172 19.442545 MGC33657 1374 covers exon(s) -965 disjoint chrl3 44782546 44783223 0.11652972 1.07695178 19.4397457 TPT1 30073 downstream 531 disjoint chr6 44147359 44147862 -0.11434842 1.28576208 19.4385456 MRPL14 55306 downstream 1130 disjoint chr5 92930972 92931733 1.16465651 0.25631026 19.4249583 NR2F1 13065 upstream 262 disjoint chrl6 52882066 52882578 1.1163736 -0.38002026 19.4201993 IRX3 4188 upstream 0 overlap chr6 1560799 1561626 1.27314557 0.3309289 19.4179463 FOXC1 5120 downstream 0 overlap chr7 27171652
  • chrl 2 45510421 45511068 1.29054192 0.22500936 19.2418273
  • NPEPL1 1650 promoter 1316 disjoint chrl 6221722 6222315 1.25712975 0.0500916 19.2328187
  • PCDHB6 442 promoter 1761 disjoint chr6 101024531 101025091 1.63725372 0.35335814 19.209085
  • chrl 6 48746440 48747336 -0.1732433 0.5566583 19.0881656
  • PAPD5 872 inside intron -88405 disjoint chr3 62330365 62331099 0.91118533 -0.10977465 19.080657
  • FEZF2 2961 overlaps 3' 0 overlap chrlO 69318244 69318888 -0.19935737 0.97219612 19.0792984
  • SIRT1 3812 covers exon(s) -3060 disjoint chr7 153213687 153214225 -0.08637869 1.31414203 19.0737415 DPP6 1126 promoter 25 disjoint chrl4 60191248 60192143 0.95850211 0.19798588 19.0612964 SKI 5316 upstream 1223 disjoint chr7 115639913 115640451 -0.31251243 1.01967809 19.0491695 TES 2097 inside intron
  • chrl 47466118 47466876 0.95632283 0.01352992 15.6017797 TALI 1153 inside intron -1804 disjoint chrl 7 5614070 5614799 -0.47487606 0.9144511 15.5936072 NALP1 185518 upstream -268744 disjoint chrl 7 70660138 70660729 1.07432545 0.07260763 15.5919191 HN1 1639 inside intron 696 disjoint chr3 165201691 165202224 0.24859832 1.4654294 15.5877523 SI 1076751 downstream 2517 disjoint chr2 205119425 205120105 -0.02652207 0.93653152 15.5801167 PARD3B 665 inside intron -270 disjoint chr2 218423333 218423914 0.09888264 1.28928094 15.5751583 TNS1 93091 inside intron -93590 disjoint ch
  • chrl 3 49598457 49599030 1.15950904 0.09131337 15.2857251 KCNRG 111067 downstream 0 inside chr7 27173819 27174511 0.10011545 0.88385961 15.2832056 HOXA9 2146 promoter -832 disjoint chr22 24129361 24130027 -0.15022157 0.94820338 15.2813576 LRP5L 40838 upstream 527 disjoint chr 6 7488826 7489329 1.16963066 0.10705188 15.259984 DSP 1958 inside intron -355 disjoint chrl 4 89917469 89918260 0.02019087 0.78768982 15.2481162 CALM1 14865 upstream 487 disjoint chrlO 127573396 127574007 -0.2562742 0.59364582 15.2413475 FANK1 1093 promoter 232 disjoint chrl 8 27991860 2799
  • chrl4 55115260 55115838 0.06026981 1.09635989 15.0477114 KTN1 954 promoter 549 disjoint chr3 188943023 188943515 1.6105657 0.50409136 15.0425538 BCL6 2653 inside intron 1150 disjoint chrl 184914668 184915177 0.17700789 1.23620617 15.0401466
  • PTGS2 1001 covers exon(s) 756 disjoint chrl2 52061585 52062272 -0.21970938 0.74744373 15.030235
  • SP1 1340 covers exon(s) -715 disjoint chrl 6 51136372 51136986 0.58749123 -0.30327507 15.0205933
  • chrl 7 6859295 6859972 0.06620085 0.8593832 14.5886562 C17orf49 448 covers exon(s) -32 disjoint chrll 125733920 125734803 0.12385162 1.24439347 14.5763201 ST3GAL4 2615 inside intron -2637 disjoint chrl 3 23050160 23050851 0.61891944 1.58584558 14.5760977 TNFRSF19 7438 inside intron 48 disjoint chr4 75936247 75936936 0.45554409 1.24062466 14.5747766 BTC 1916 inside intron 1189 disjoint chrlO 9488815 9489495 2.93836283 1.96294354 14.5698227 LOC389936 0 overlaps 5' 0 overlap chrlO 6663566 6664277 1.80616017 0.96291777 14.5633303 PRKCQ 1323 promoter -9
  • chrl l 31782580 31782945 1.10190013 -0.23662348 13.8188127 PAX6 6488 inside intron 0 inside chr6 27755547 27756240 1.13397798 0.16548022 13.8140645 HIST1H2BL 127447 downstream 0 cover chrl2 56523029 56523635 0.1909465 1.0978757 13.8108104 CTDSP2 3378 inside intron 1472 disjoint chrlO 118881250 118881870 0.92836145 0.04348301 13.8095704 VAX1 5931 overlaps exon 281 disjoint upstream
  • chr20 5 0156049 50156749 1.22096739 0.293302 13.1724017 ZFP64 85181 inside intron -730 disjoint chr5 66336576 66337220 0.81359734 0.08392192 13.1722767 LOC375449 408613 downstream -737 disjoint chrl 36625214 36626043 0.11955891 1.10377077 13.1690871 STK40 1143 promoter -754 disjoint chr2 120233007 120233357 0.9856377 -0.4603832 13.1562836 PTPN4 319 promoter 179 disjoint chr5 50296152 50296517 1.2761158 0.02949335 13.1485789 PARP8 297583 downstream 4325 disjoint chr2 211048605 211049051 -0.1551726 1.04103474 13.1461749 LANCL1 624 inside intron 375 disjoint chrl2 52655707
  • chr7 31341062 31341670 0.30081097 1.140024 13.0989209 NEUROD6 5392 downstream 700 disjoint chr2 176748865 176749335 0.81165516 -0.20298357 13.0976195 HOXD3 11815 downstream -668 disjoint chrlO 116382204 116382707 -0.21133972 0.71330692 13.0927624
  • ABLIM1 25340 inside intron -387 disjoint chrl 3 21140853 21141359 0.97782451 -0.005568 13.0810497 FGF9 2515 upstream 0 overlap chr3 158358839 158359426 -0.07770354 0.72699375 13.0517254 CCNL1 1749 overlaps exon 440 disjoint downstream
  • chrl 6 30596705 30597566 1.06026734 0.08908104 13.0511148 FBS1 12578 downstream -18049 disjoint chr8 102574006 102574620 1.11597252 0.04037331 13.0463219 GRHL2 0 overlaps 5' 0 overlap chrl 182621283 182621981 1.09931176 0.12661556 13.0417553 Clorf21 791 promoter 57 disjoint chrl 5 46722744 46723391 -0.53647504 0.19198763 13.0403565 FBN1 1818 inside intron 711 disjoint chr7 157064591 157064986 0.08689137 1.2722443 13.0388822 PTPRN2 1008192 inside intron -2436 disjoint chr2 200033986 200034541 0.8934441 -0.12674405 13.0319511 SATB2 541 promoter 0 inside ch
  • GDAP1 737 covers exon(s) -345 disjoint chr6 1557371 1557966 0.88765319 0.06395249 12.871152 FOXC1 1692 close to 3' 0 inside chr6 3693931 3694510 0.24966374 1.05134019 12.8677269 C6orfl45 2424 inside intron 1277 disjoint chr20 31748839 31749277 0.50588464 1.57785806 12.8636811 PXMP4 22519 downstream -10673 dis
  • chrll 7230822 7231223 1.01295717 -0.07891836 11.7446629 SYT9 1066 inside intron -11 disjoint chrl 6 71654712 71655274 0.9935094 0.21870991 11.744265 ATBF1 14938 upstream -96 disjoint chr6 24512676 24513041 1.52213034 0.26582346 11.7414747 MRS2L 1545 inside intron -1011 disjoint chr 5 122449676 122450107 1.18345786 0.14911913 11.7159406 PPIC 49353 upstream 2129 disjoint chr5 77181413 77181882 1.4502124 0.38568228 11.7098314 TBCA 73473 upstream 872 disjoint chrl 7 44062558 44063061 0.4059112 1.2010684 11.7085174 H0XB9 3725 upstream 2750 disjoint chr3
  • chr9 76305586 76306126 0.72579163 -0.10460337 11.0305174 RO B 3515 inside intron -1839 disjoint chrl 7 67623025 67623616 1.02502585 0.20738829 11.0251212 SOX9 5139 upstream 0 overlap chrX 136474847 136475400 1.17127285 0.07339791 11.0198597 ZIC3 611 promoter 0 overlap chrX 102489173 102489608 0.97582405 -0.01364143 11.0152644 WBP5 8427 upstream 28369 disjoint chr2 171385173 171385930 1.03045756 0.35936051 11.0138522 GADl 3728 inside intron 0 overlap chr3 185805542 185806029 1.43642482 0.50212969 11.0095501 EPHB3 43262 downstream -574 disjoint chr2 175058791 1750
  • chr20 55271171 55271722 1.03787897 0.37135108 10.9080068 BMP7 2985 inside intron 972 disjoint chr7 56141094 56141420 -0.34870077 0.92816033 10.906647 CHCHD2 260 inside intron 0 overlap chrl 7 41214998 41215399 0.09873197 1.0752817 10.8924431 CRHR1 2049 promoter 1048 disjoint chrl2 26157097 26157579 0.98283759 -0.20596333 10.8905497 BHLHB3 11533 downstream 746 disjoint chrX 119014627 119015199 -0.47682618 0.24357145 10.8805575 NKAP 52865 upstream 2680 disjoint chr4 36924025 36924570 0.27188648 1.08052563 10.8630867 C4orfl9 337679 upstream -651 disjoint chrl
  • chrl 2 70121556 70122098 0.10724426 0.79213639 10.2135731 LGR5 1477 inside intron -900 disjoint chr2 144807731 144808096 1.47855782 0.46355056 10.2126472 GTDC1 1233 promoter -864 disjoint chrlO 134388042 134388491 2.67713318 1.67824327 10.2016004 INPP5A 186700 inside intron 1316 disjoint chr 5 151765213 151765608 0.52900023 1.41472367 10.1997065 NMUR2 197 promoter -480196 disjoint chrl3 32060799 32061194 -0.11708394 0.80996368 10.1975238 APRIN 2176 inside intron -964 disjoint chr2 174904668 174905162 0.85683204 0.09466623 10.1974261 FLJ46347 5377 downstream 2547 disjo
  • chrl 6 2902926 2903396 0.52022455 1.35335458 10.1461996 FLYWCH1 946 inside intron -393 disjoint chr5 170765553 170766023 0.16191373 1.01722263 10.1418714 PM1 18151 overlaps exon 12342 disjoint upstream
  • Table 7 Regions of differential methylation between iPS cells and ES cells.
  • DMRs were defined by using a absolute area cutoff of 10.0 which corresponds in magnitude to the 5% FDR cutoff of the R-DMRs.
  • chrl 5 97225652 97227801 0.227471611 1.080152523 51.5937901 IGF1R 215365 inside intron -12153 disjoint chr6 27633621 27634805 0.108399472 1.289575618 38.81697032 ZNF184 84764 upstream -38573 disjoint chr5 43072850 43074823 1.466157509 0.5817001 37.26230862 LOC389289 1274 close to 3' 0 cover chr20 9437038 9438216 0.051275945 0.987698218 31.22453135 C20orfl03 5054 upstream -1149 disjoint chrl 4 28316507 28317651 0.760956759 -0.17642005 28.07
  • Table 8 Gene ontology functional categories enriched in differentially methylated regions between iPS cells and ES cells.

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Abstract

Provided herein are differentially methylated regions (DMRs) of reprogrammed iPS cells (R-DMRs) and methods of use thereof. The invention provides methods for detecting and analyzing alterations in the methylation status of DMRs in iPS cells, somatic cells and embryonic stem (ES) cells as well as methods for reprogramming somatic cells to generate an iPS cell.

Description

DIFFERENTIALLY METHYLATED REGIONS OF REPROGRAMMED INDUCED PLURIPOTENT STEM CELLS, METHOD AND COMPOSITIONS THEREOF
BACKGROUND OF THE INVENTION
FIELD OF THE INVENTION
[0001] The present invention relates generally to differentially methylated regions (DMRs) in the genome outside CpG islands in induced pluripotent stem (iPS) cells, and more specifically to methods for detecting and analyzing alterations in the methylation status of DMRs in iPS cells, somatic cells and embryonic stem (ES) cells as well as methods for reprogramming somatic cells to generate an iPS cell.
BACKGROUND INFORMATION
[0002] Epigenetics is the study of non-sequence information of chromosome DNA during cell division and differentiation. The molecular basis of epigenetics is complex and involves modifications of the activation or inactivation of certain genes. Additionally, the chromatin proteins associated with DNA may be activated or silenced. Epigenetic changes are preserved when cells divide. Most epigenetic changes only occur within the course of one individual organism's lifetime, but some epigenetic changes are inherited from one generation to the next.
[0003] One example of an epigenetic mechanism is DNA methylation (DNAm), a covalent modification of the nucleotide cytosine. In particular, it involves the addition of methyl groups to cytosine nucleotides in the DNA, to convert cytosine to 5-methylcytosine. DNA methylation plays an important role in determining whether some genes are expressed or not. Abnormal DNA methylation is one of the mechanisms known to underlie the changes observed with aging and development of many cancers.
[0004] It has been shown that alterations in DNA methylation (DNAm) occur in cancer, including hypomethylation of oncogenes and hypermethylation of tumor suppressor genes. However, most studies of cancer methylation assumed that functionally important DNAm will occur in promoters, and that most DNAm changes in cancer occur in CpG islands.
However, it was determined that most methylation alterations in certain cancers occur not in promoters, and also not in CpG islands, but in sequences up to 2 kb distant, which are termed 'CpG island shores'. Differential methylation patterns that distinguish among normal tissue types (T-DMRs) and patterns that can segregate colorectal cancer tissue from matched normal tissues (C-DMRs) have been described. Unexpectedly, these two DMRs occur 13- fold more frequently at CpG island 'shores', regions of comparatively low CpG density that are located near traditional CpG islands, than at the CpG islands themselves. Cancers showed approximately equal numbers of hypomethylated and hypermethylated regions, and 45% of C-DMRs overlapped T-DMRs, suggesting that epigenetic changes in cancer involve reprogramming of the normal pattern of tissue-specific differentiation.
[0005] iPS cells are derived by epigenetic reprogramming. For example, iPS cells can be derived from somatic cells by introduction of a small number of genes: for example,
POU5F1, MYC, KLF4 and SOX2. As direct derivatives of an individual's own tissue, iPS cells offer considerable therapeutic promise, avoiding both immunologic and ethical barriers to their use. iPS cells differ from their somatic parental cells epigenetically, and thus a comprehensive comparison of the epigenome in iPS and somatic cells would provide insight into the mechanism of tissue reprogramming. Although two previous targeted studies examined a subset of the genome, 7,000 (Ball et al. (Nat. Biotechnol. (27)485 (2009)) and 66,000 (Deng et al. (Nat. Biotechnol. (27)353-360 (2009))) CpG sites in a small cohort of three iPS- fibroblast pairs, a global assessment of genome-wide methylation has not yet been performed.
SUMMARY OF THE INVENTION
[0006] The present invention is based on the discovery that alterations in DNA
methylation in iPS cells, as compared to both ES cells and parental fibroblasts, occur not only in promoters or CpG islands, but in sequences up to 2 kb distant from such CpG islands (such sequences are termed "CpG island shores"). In accordance with this discovery, there are provided herein DMR of reprogrammed iPS cells (R-DMRs) and methods of use thereof.
[0007] In one aspect of the invention, there is provided a method of generating an iPS cell. The method includes contacting a somatic cell with an agent that alters the methylation status of one or more nucleic acid sequences of the somatic cell, the one or more nucleic acid sequences being outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in reprogrammed somatic cells as compared with parent somatic cells, thereby generating an iPS cell. In certain embodiments, the one or more nucleic acid sequences are any combination of DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, the IGFIR gene, and any combination thereof. In certain embodiments, the method further comprises detecting the methylation status profile of the one or more nucleic acid sequences of the induced iPS. In yet another aspect, the method further comprises comparing the methylation status profile to a methylation status profile of the one or more nucleic acid sequences of a parental somatic cell from which the iPS is induced.
[0008] In particular embodiments, the agent is a nuclear reprogramming factor. In various embodiments, the nuclear reprogramming factor is a nucleic acid encoding a SOX family gene, a KLF family gene, a MYC family gene, POU5F1, SALL4, OCT4, NANOG, LIN28, or the expression product thereof. For example, in exemplary embodiments, the nuclear reprogramming factor is one or more of POU5F1, OCT4, SOX2, KLF4, or C-MYC.
[0009] In another aspect, there is provided an iPS cell produced using the methods of the invention.
[0010] In another aspect, there is provided a population of iPS cells produced using the methods the invention.
[0011] In yet another aspect of the invention, there is provided a plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequence is up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in the reprogramming of a somatic cell to generate an iPS cell. In some embodiments, the nucleic acid sequence are any DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, and the IGFIR gene. In one embodiment, the plurality of nucleic acid sequences is a microarray.
[0012] In another aspect of the invention, there is provided a plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the methylation status of the nucleic acid sequences is altered in an iPS cell as compared to an ES cell. In some embodiments, the nucleic acid sequence are any DMR sequences as set forth in Table 7, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene. In one embodiment, the plurality of nucleic acid sequences is a microarray.
[0013] In yet another aspect of the invention, there is provided a method of identifying an iPS cell. The method includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of an iPS cell, wherein a similarity in methylation status is indicative of the putative cell being an iPS cell. In certain embodiments, the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4C-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
[0014] In yet another aspect of the invention, there is provided a method of identifying an iPS cell. The method includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of a corresponding somatic cell from which the iPS cell is induced or ES cell, wherein an alteration in methylation status is indicative of the putative cell being an iPS cell. In certain embodiments the method further includes comparing the methylation status of the one or more nucleic acid sequences of the putative iPS cell to a known methylation status of the one or more nucleic acid sequences of a corresponding somatic cell from which the iPS cell is induced. In such embodiments, the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 9, Figures 1B- 1C, Figures 4A-4G, the the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof. In certain embodiments the method further includes comparing the methylation status of the one or more nucleic acid sequences of the putative iPS cell to the methylation status of the one or more nucleic acid sequences of a known ES cell. In such embodiments, the one or more nucleic acid sequences are DMR sequences as set forth in Table 6, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
[0015] In various aspect of the invention, the one or more nucleic acid sequences are within a gene. Alternatively, the one or more nucleic acid sequences are upstream or downstream of a gene. In various embodiments, determination of methylation status is performed by one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequencing, single-strand conformation polymorphism (SSCP) analysis, restriction analysis, microarray technology, and proteomics.
[0016] In yet another aspect of the invention, there is provided a method for providing a methylation map of a region of genomic DNA isolated from an iPS cell. The method includes performing comprehensive high-through array-based relative methylation
(CHARM) analysis on a sample of labeled, digested genomic DNA isolated from the iPS cell, thereby providing a methylation map for the iPS cell. In certain embodiments, the method further includes performing one or more techniques, such as a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequencing, single-strand conformation polymorphism (SSCP) analysis, and restriction analysis.
[0017] In yet another aspect of the invention, there is provided a method of characterizing the methylation status of the nucleic acid of an iPS cell. The method includes a) hybridizing labeled and digested nucleic acid of an iPS cell to a DNA microarray comprising at least 2000 nucleic acid sequences, with the proviso that the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island; and b) determining a pattern of methylation from the hybridizing of (a), thereby characterizing the methylation status for the iPS cell. In particular embodiments, the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene and any combination thereof. In certain embodiments, the method further includes comparing the methylation status profile to a methylation profile from hybridization of the microarray with labeled and digested nucleic acid from a parental somatic cell from which the iPS is induced or from an ES cell.
[0018] In yet another embodiment, there is provided a method of treating a subject. The method includes a) obtaining a somatic cell from a subject; b) reprogramming the somatic cell into an iPS cell using the methods of the invention; c) culturing the pluripotent stem (iPS) cell to differentiate the cell into a desired cell type suitable for treating a condition; and d) introducing into the subject the differentiated cell, thereby treating the condition.
BRIEF DESCRIPTION OF THE DRAWINGS
[0019] Figure 1A shows plots depicting the distribution of distance of R-DMRs from CpG islands. Figures IB and 1C, upper panels, show plots of M value versus genomic location for fibroblast and iPS cells and plots of CpG density versus genomic location, where the curve represents averaged smoothed M values; the location of CpG dinucleotides (black tick marks), CpG density, location of CpG islands (filled boxes along the x-axis (zero)), along with the gene annotation. Figures IB and 1C, lower panels show validation by bisulfite pyrosequencing of methylation percentage mapping to the unfilled box along the x-axis of the plots of CpG density versus genomic location in the upper panels of Figures IB and 1C for various iPS cells, fibroblasts, ES cells (BGOl, BG03 and H9) as well as the highly methylated HCT116 colon cancer cell line and a generally hypomethylated double DNA methyltransferase 1/3B double knockout line (DKO) derived from it.
[0020] Figure 2 shows plots depicting the distribution of distance of R-DMRs from CpG islands.
[0021] Figure 3A shows a clustering of M values of all tissues from the 4,401 regions (FDR < 0.05) corresponding to R-DMRs (iPS cells compared to parental fibroblasts) comparing normal brain, spleen and liver tissues (denoted as Br, Sp and Lv, respectively). Figure 3B shows a clustering of M values of all tissues from the 4,401 regions (FDR < 0.05) corresponding to R-DMRs (iPS cells compared to parental fibroblasts) comparing colorectal cancer and matched normal colonic mucosa (denoted as T and N, respectively). [0022] Figure 4 shows plots depicting differential DNA methylation (upper panels) and confirmation by bisulfite pyrosequencing (lower panels) for DMRs found by comparison between iPS cells and fibroblasts (A and B) as well as various genes (C-G). Figures 4A-G, upper panels, show plots of M value versus genomic location, where the curve represents averaged smoothed M values. Also shown in the upper panels are the location of CpG dinucleotide (black tick marks on x-axis), CpG density (smoothed black line) calculated across the region using a standard density estimator, location of CpG islands (filled boxes along the x-axis (zero)), as well as gene annotation indicating the transcript (thin outer gray line), coding region (thin inner gray line), exons (filled gray box) and gene transcription directionality on the y-axis (sense marked as +, antisense as -). Figures 4A-G, lower panels depict plots showing the degree of DNA methylation as measured by bisulfite
pyrosequencing. The unfilled box indicated on the x-axis of the CpG density plot in the upper panel indicates the CpG sites that were measured. Reactions were performed in triplicate; bars represent the mean methylation ±SD of iPS cells, fibroblasts, and ES cells (BGOl, BG03 and H9) as well as DKO (DNMT1 and DNMT3B Double KO cell line) and HCT116 (parental colon cancer cell line) for each individual CpG site measured.
[0023] Figure 5 shows plots of differential gene expression versus differential methylation for R-DMRs at CpG island shores.
DETAILED DESCRIPTION OF THE INVENTION
[0024] The present invention is based on the discovery that alterations in DNA
methylation occur not only in promoters or CpG islands of an iPS cell genome during reprogramming of the cell, but in sequences up to 2 kb distant (termed "CpG island shores"). iPS cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not peviously been analyzed on a genome-wide scale. Substantial hypermethylation and hypomethylation of cytosine-phosphate-guanine (CpG) island shores in iPS cell lines as compared to ES cells and parental fibroblasts is described herein.
[0025] The DMRs in the reprogrammed cells (denoted R-DMRs) were significantly enriched in tissue-specific (T-DMRs) and cancer-specific DMRs (C-DMRs). Notably, even though iPS cells are derived from fibroblasts, their R-DMRs can distinguish between cells of normal tissue and between cancer and normal cells, e.g., colon cancer and normal colon cells. Thus, many DM s are broadly involved in tissue differentiation, epigenetic reprogramming and cancer. Colocalization of hypomethylated R-DMRs with hypermethylated C-DMRs and bivalent chromatin marks, and colocalization of hypermethylated R-DMRs with
hypomethylated C-DMRs and the absence of bivalent marks were observed, suggesting two mechanisms for epigenetic reprogramming in iPS cells and cancer.
[0026] Before the present compositions and methods are described, it is to be understood that this invention is not limited to particular compositions, methods, and experimental conditions described, as such compositions, methods, and conditions may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only in the appended claims.
[0027] As used in this specification and the appended claims, the singular forms "a", "an", and "the" include plural references unless the context clearly dictates otherwise. Thus, for example, references to "the method" includes one or more methods, and/or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.
[0028] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, the preferred methods and materials are now described.
[0029] In accordance with this discovery, there are provided herein DMRs of
reprogrammed iPS cells (R-DMRs) and methods of use thereof. In one aspect of the invention, there is provided a method of generating an iPS cell. The method includes contacting a somatic cell with an agent that alters the methylation status of one or more nucleic acid sequences of the somatic cell, the one or more nucleic acid sequences being outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in reprogrammed somatic cells as compared with parent somatic cells, thereby generating an iPS cell. [0030] As used herein, reprogramming, is intended to refer to a process that alters or reverses the differentiation status of a somatic cell that is either partially or terminally differentiated. Reprogramming of a somatic cell may be a partial or complete reversion of the differentiation status of the somatic cell. In an exemplary aspect, reprogramming is complete wherein a somatic cell is reprogrammed into an iPS cell. However, reprogramming may be partial, such as reversion into any less differentiated state. For example, reverting a terminally differentiated cell into a cell of a less differentiated state, such as a multipotent cell.
[0031] As used herein, pluripotent cells include cells that have the potential to divide in vitro for an extended period of time (greater than one year) and have the unique ability to differentiate into cells derived from all three embryonic germ layers, namely endoderm, mesoderm and ectoderm.
[0032] Somatic cells for use with the present invention may be primary cells or immortalized cells. Such cells may be primary cells (non-immortalized cells), such as those freshly isolated from an animal, or may be derived from a cell line (immortalized cells). In an exemplary aspect, the somatic cells are mammalian cells, such as, for example, human cells or mouse cells. They may be obtained by well-known methods, from different organs, such as, but not limited to skin, brain, lung, pancreas, liver, spleen, stomach, intestine, heart, reproductive organs, bladder, kidney, urethra and other urinary organs, or generally from any organ or tissue containing living somatic cells, or from blood cells. Mammalian somatic cells useful in the present invention include, by way of example, adult stem cells, Sertoli cells, endothelial cells, granulosa epithelial cells, neurons, pancreatic islet cells, epidermal cells, epithelial cells, hepatocytes, hair follicle cells, keratinocytes, hematopoietic cells,
melanocytes, chondrocytes, lymphocytes (B and T lymphocytes), erythrocytes, macrophages, monocytes, mononuclear cells, fibroblasts, cardiac muscle cells, other known muscle cells, and generally any live somatic cells. In particular embodiments, fibroblasts are used. The term somatic cell, as used herein, is also intended to include adult stem cells. An adult stem cell is a cell that is capable of giving rise to all cell types of a particular tissue. Exemplary adult stem cells include hematopoietic stem cells, neural stem cells, and mesenchymal stem cells. [0033] As discussed herein, alterations in methylation patterns occur during differentiation or dedifferention of a cell which work to regulate gene expression of critical factors that are 'turned on' or 'turned off at various stages of differentiation. As such, one of skill in the art would appreciate that many types of agents are capable of altering the methylation status of one or more nucleic acid sequences of a somatic cell to induce pluripotency that may be suitable for use with the present invention.
[0034] An agent, as used herein, is intended to include any agent capable of altering the methylation status of one or more nucleic acid sequences of a somatic cell. For example, an agent useful in any of the method of the invention may be any type of molecule, for example, a polynucleotide, a peptide, a peptidomimetic, peptoids such as vinylogous peptoids, chemical compounds, such as organic molecules or small organic molecules, or the like. In various aspects, the agent may be a polynucleotide, such as DNA molecule, an antisense oligonucleotide or RNA molecule, such as microRNA, dsRNA, siRNA, stRNA, and shRNA.
[0035] MicroRNA (miRNA) are single-stranded RNA molecules whose expression is known to be regulated by methylation to play a key role in regulation of gene expression during differentiation and dedifferentiation of cells. Thus an agent may be one that inhibits or induces expression of miRNA or may be a mimic miRNA. As used herein, "mimic" microRNAs which are intended to mean a microRNA exogenously introduced into a cell that have the same or substantially the same function as their endogenous counterpart.
[0036] In various aspects of the present invention, an agent that alters the methylation status of one or more nucleic acid sequences is a nuclear reprogramming factor. Nuclear reprogramming factors may be genes that induce pluripotency and utilized to reprogram differentiated or semi-differentiated cells to a phenotype that is more primitive than that of the initial cell, such as the phenotype of a pluripotent stem cell. Those skilled in the art would understand that such genes and agents are capable of generating a pluripotent stem cell from a somatic cell upon expression of one or more such genes having been integrated into the genome of the somatic cell or upon contact of the somatic cell with the agent or expression product of the gene. As used herein, a gene that induces pluripotency is intended to refer to a gene that is associated with pluripotency and capable of generating a less differentiated cell, such as a pluripotent stem cell from a somatic cell upon integration and expression of the gene. The expression of a pluripotency gene is typically restricted to pluripotent stem cells, and is crucial for the functional identity of pluripotent stem cells.
[0037] Several genes have been found to be associated with pluripotency and suitable for use with the present invention as reprogramming factors. Such genes are known in the art and include, by way of example, SOX family genes (SOXl, SOX2, SOX3, SOX15, SOX18), KLF family genes (KLF1, KLF2, KLF4, KLF5), MYC family genes (C-MYC, L-MYC, N- MYC), SALL4, OCT4, NANOG, LIN28, STELLA, NOBOX, POU5F1 or a STAT family gene. STAT family members may include for example STAT1 , STAT2, STAT3, STAT4, STAT5 (STAT5 A and STAT5B), and STAT6 . While in some instances, use of only one gene to induce pluripotency may be possible, in general, expression of more than one gene is required to induce pluripotency. For example, two, three, four or more genes may be simultaneously integrated into the somatic cell genome as a polycistronic construct to allow simultaneous expression of such genes. In an exemplary aspect, four genes are utilized to induce pluripotency including OCT4, POU5F1, SOX2, KLF4 and C-MYC. Additional genes known as reprogramming factors suitable for use with the present invention are disclosed in U.S. Patent Application No. 10/997,146 and U.S. Patent Application No. 12/289,873, incorporated herein by reference.
[0038] All of these genes commonly exist in mammals, including human, and thus homologues from any mammals may be used in the present invention, such as genes derived from mammals including, but not limited to mouse, rat, bovine, ovine, horse, and ape.
Further, in addition to wild-type gene products, mutant gene products including substitution, insertion, and/or deletion of several (e.g., 1 to 10, 1 to 6, 1 to 4, 1 to 3, and 1 or 2) amino acids and having similar function to that of the wild-type gene products can also be used. Furthermore, the combinations of factors are not limited to the use of wild-type genes or gene products. For example, Myc chimeras or other Myc variants can be used instead of wild-type Myc.
[0039] The present invention is not limited to any particular combination of nuclear reprogramming factors. As discussed herein a nuclear reprogramming factor may comprise one or more gene products. The nuclear reprogramming factor may also comprise a combination of gene products as discussed herein. Each nuclear reprogramming factor may be used alone or in combination with other nuclear reprogramming factors as disclosed herein. Further, nuclear reprogramming factors of the present invention can be identified by screening methods, for example, as discussed in U.S. Patent Application No. 10/997,146, incorporated herein by reference. Additionally, the nuclear reprogramming factor of the present invention may contain one or more factors relating to differentiation, development, proliferation or the like and factors having other physiological activities, as well as other gene products which can function as a nuclear reprogramming factor.
[0040] The nuclear reprogramming factor may include a protein or peptide. The protein may be produced from a gene as discussed herein, or alternatively, in the form of a fusion gene product of the protein with another protein, peptide or the like. The protein or peptide may be a fluorescent protein and/or a fusion protein. For example, a fusion protein with green fluorescence protein (GFP) or a fusion gene product with a peptide such as a histidine tag can also be used. Further, by preparing and using a fusion protein with the TAT peptide derived from the virus HIV, intracellular uptake of the nuclear reprogramming factor through cell membranes can be promoted, thereby enabling induction of reprogramming only by adding the fusion protein to a medium thus avoiding complicated operations such as gene transduction. Since preparation methods of such fusion gene products are well known to those skilled in the art, skilled artisans can easily design and prepare an appropriate fusion gene product depending on the purpose.
[0041] In certain embodiments, the agent alters the methylation status of one or more nucleic acid sequences, such as DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
[0042] Detecting the methylation status profile of the one or more nucleic acid sequences of the induced iPS and/or comparing the methylation status profile to a methylation status profile of the one or more nucleic acid sequences of a parental somatic cell from which the iPS is induced may also be performed to assess pluripotency characteristics.
[0043] Similarly, expression profiling of reprogrammed somatic cells to assess their pluripotency characteristics may also be conducted. Expression of individual genes associated with pluripotency may also be examined. Additionally, expression of embryonic stem cell surface markers may be analyzed. As used herein, "expression" refers to the production of a material or substance as well as the level or amount of production of a material or substance. Thus, determining the expression of a specific marker refers to detecting either the relative or absolute amount of the marker that is expressed or simply detecting the presence or absence of the marker. As used herein, "marker" refers to any molecule that can be observed or detected. For example, a marker can include, but is not limited to, a nucleic acid, such as a transcript of a specific gene, a polypeptide product of a gene, a non-gene product polypeptide, a glycoprotein, a carbohydrate, a glycolipd, a lipid, a lipoprotein or a small molecule.
[0044] Detection and analysis of a variety of genes known in the art to be associated with pluripotent stem cells may include analysis of genes such as, but not limited to OCT4, NANOG, SALL4, SSEA-1, SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, or a combination thereof. iPS cells may express any number of pluripotent cell markers, including: alkaline phosphatase (AP); ABCG2; stage specific embryonic antigen- 1 (SSEA-1); SSEA-3; SSEA-4; TRA-1-60; TRA-1-81; Tra-2-49/6E; ERas/ECAT5, E-cadherin; β-ΙΙΙ-tubulin; γ -smooth muscle actin (γ-SMA); fibroblast growth factor 4 (Fgf4), Cripto, Daxl; zinc finger protein 296 (Zfp296); N-acetyltransferase-1 (Natl); ES cell associated transcript 1 (ECAT1);
ESG1/DPPA5/ECAT2; ECAT3; ECAT6; ECAT7; ECAT8; ECAT9; ECAT10; ECAT15-1; EC AT 15-2; Fthll7; Sall4; undifferentiated embryonic cell transcription factor (Utfl); Rexl; p53; G3PDH; telomerase, including TERT; silent X chromosome genes; Dnmt3a; Dnmt3b; TRIM28; F-box containing protein 15 (Fbxl5); Nanog/ECAT4; Oct3/4; Sox2; Klf4; c-Myc; Esrrb; TDGF1; GABRB3; Zfp42, FoxD3; GDF3; CYP25A1; developmental pluripotency- associated 2 (DPPA2); T-cell lymphoma breakpoint 1 (Tell); DPPA3/Stella; DPPA4; as well as other general markers for pluripotency, for example any genes used during induction to reprogram the cell. iPS cells can also be characterized by the down-regulation of markers characteristic of the differentiated cell from which the iPS cell is induced.
[0045] As used herein, "differentiation" refers to a change that occurs in cells to cause those cells to assume certain specialized functions and to lose the ability to change into certain other specialized functional units. Cells capable of differentiation may be any of totipotent, pluripotent or multipotent cells. Differentiation may be partial or complete with respect to mature adult cells. W 201
14
[0046] "Differentiated cell" refers to a non-embryonic, non-parthenogenetic or non- pluripotent cell that possesses a particular differentiated, i.e., non-embryonic, state. The three earliest differentiated cell types are endoderm, mesoderm, and ectoderm.
[0047] Pluripotency can also be confirmed by injecting the cells into a suitable animal, e.g., a SCID mouse, and observing the production of differentiated cells and tissues. Still another method of confirming pluripotency is using the subject pluripotent cells to generate chimeric animals and observing the contribution of the introduced cells to different cell types. Methods for producing chimeric animals are well known in the art and are described in U.S. Pat. No. 6,642,433, incorporated by reference herein.
[0048] Yet another method of confirming pluripotency is to observe cell differentiation into embryoid bodies and other differentiated cell types when cultured under conditions that favor differentiation (e.g., removal of fibroblast feeder layers).
[0049] The invention further provides iPS cells produced using the methods described herein, as well as populations of such cells. The reprogrammed cells of the present invention, capable of differentiation into a variety of cell types, have a variety of applications and therapeutic uses. The basic properties of stem cells, the capability to infinitely self-renew and the ability to differentiate into every cell type in the body make them ideal for therapeutic uses.
[0050] Accordingly, in one aspect the present invention further provides a method of treatment or prevention of a disorder and/or condition in a subject using induced pluripotent stem cells generated using the methods described herein. The method includes obtaining a somatic cell from a subject and reprogramming the somatic cell into an iPS cell using the methods described herein. The cell is then cultured under suitable conditions to differentiate the cell into a desired cell type suitable for treating the condition. The differentiated cell may then be introducing into the subject to treat or prevent the condition.
[0051] One advantage of the present invention is that it provides an essentially limitless supply of isogenic or synegenic human cells suitable for transplantation. The iPS cells are tailored specifically to the patient, avoiding immune rejection. Therefore, it will obviate the significant problem associated with current transplantation methods, such as, rejection of the transplanted tissue which may occur because of host versus graft or graft versus host rejection. Several kinds of iPS cells or fully differentiated somatic cells prepared from iPS cells from somatic cells derived from healthy humans can be stored in an iPS cell bank as a library of cells, and one kind or more kinds of the iPS cells in the library can be used for preparation of somatic cells, tissues, or organs that are free of rejection by a patient to be subjected to stem cell therapy.
[0052] The iPS cells of the present invention may be differentiated into a number of different cell types to treat a variety of disorders by methods known in the art. For example, iPS cells may be induced to differentiate into hematopoetic stem cells, muscle cells, cardiac muscle cells, liver cells, cartilage cells, epithelial cells, urinary tract cells, neuronal cells, and the like. The differentiated cells may then be transplanted back into the patient's body to prevent or treat a condition. Thus, the methods of the present invention may be used to treat a subject having a myocardial infarction, congestive heart failure, stroke, ischemia, peripheral vascular disease, alcoholic liver disease, cirrhosis, Parkinson's disease, Alzheimer's disease, diabetes, cancer, arthritis, wound healing, immunodeficiency, aplastic anemia, anemia, Huntington's disease, amyotrophic lateral sclerosis (ALS), lysosomal storage diseases, multiple sclerosis, spinal cord injuries, genetic disorders, and similar diseases, where an increase or replacement of a particular cell type/ tissue or cellular de-differentiation is desirable.
[0053] In various embodiments, the method increases the number of cells of the tissue or organ by at least about 5%, 10%, 25%, 50%, 75% or more compared to a corresponding untreated control tissue or organ. In yet another embodiment, the method increases the biological activity of the tissue or organ by at least about 5%, 10%, 25%, 50%, 75% or more compared to a corresponding untreated control tissue or organ. In yet another embodiment, the method increases blood vessel formation in the tissue or organ by at least about 5%, 10%, 25%, 50%, 75% or more compared to a corresponding untreated control tissue or organ. In yet another embodiment, the cell is administered directly to a subject at a site where an increase in cell number is desired either before or after differentiation of the cell to a desired cell type.
[0054] Methylome analysis of iPS cells allows for the indentification of such cells. As such, the present invention provides a method of identifying an iPS cell. The method includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of an iPS cell, wherein a similarity in methylation status is indicative of the putative cell being an iPS cell. The known methylation status of the one or more nucleic acid sequences of an iPS cell may include the R-DMRs set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4C-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
[0055] Alternatively, the method of identifying an iPS cell includes comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of a corresponding somatic cell from which the iPS cell is induced and/or an ES cell, wherein an alteration in methylation status is indicative of the putative cell being an iPS cell. As such, the one or more nucleic acid sequences may be DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
[0056] The invention further provides a plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequence is up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in the reprogramming of a somatic cell to generate an iPS cell. For example, the nucleic acid sequences are the DMR sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A- 4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene.
[0057] The invention further provides a plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the methylation status of the nucleic acid sequences is altered in an iPS cell as compared to an ES cell. For example, the nucleic acid sequences are the DMR sequences as set forth in Table 7, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene.
[0058] In various embodiments of the invention, the plurality of nucleic acid sequences may be utilized to provide a microarray for performing the methods described herein. One skilled in the art would appreciate the many techniques that are well known for attaching nucleic acids on a substrate that may be utilized along with the various types of substrates and configurations.
[0059] The invention further provides a method of characterizing the methylation status of the nucleic acid of an iPS cell. The method includes a) hybridizing labeled and digested nucleic acid of an iPS cell to a DNA microarray comprising at least 2000 nucleic acid sequences, with the proviso that the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island; and b) determining a pattern of methylation from the hybridizing of (a), thereby characterizing the methylation status for the iPS cell. In various embodiments, the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
[0060] Characterizing the methylation status of the nucleic acid of an iPS cell may further include comparing the methylation status profile to a methylation profile from hybridization of the microarray with labeled and digested nucleic acid from a parental somatic cell from which the iPS is induced or from an ES cell. In particular embodiments, the one or more nucleic acid sequences are DMR sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
[0061] In various aspects of the invention, methylation status is converted to an M value. As used herein an M value, can be a log ratio of intensities from total (Cy3) and McrBC- fractionated DNA (Cy5): positive and negative M values are quantitatively associated with methylated and unmethylated sites, respectively.
[0062] In various aspects of the invention DMR may be hypermethylated or
hypomethylated. Hypomethylation of a DMR is present when there is a measurable decrease in methylation of the DMR. In some embodiments, a DMR can be determined to be hypomethylated when less than 50% of the methylation sites analyzed are not methylated. Hypermethylation of a DMR is present when there is a measurable increase in methylation of the DMR. In some embodiments, a DMR can be determined to be hypermethylated when more than 50% of the methylation sites analyzed are methylated. Methods for determining methylation states are provided herein and are known in the art. In some embodiments methylation status is converted to an M value. As used herein an M value, can be a log ratio of intensities from total (Cy3) and McrBC-fractionated DNA (Cy5): positive and negative M values are quantitatively associated with methylated and unmethylated sites, respectively. M values are calculated as described in the Examples. In some embodiments, M values which range from -0.5 to 0.5 represent unmethylated sites as defined by the control probes, and values from 0.5 to 1.5 represent baseline levels of methylation.
[0063] Numerous methods for analyzing methylation status of a gene are known in the art and can be used in the methods of the present invention to identify either hypomethylation or hypermethylation of the one or more DMRs. In various embodiments, the determining of methylation status in the methods of the invention is performed by one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequenceing, single-strand conformation polymorphism (SSCP) analysis, restriction analysis, microarray technology, and proteomics. As illustrated in the Examples herein, analysis of methylation can be performed by bisulfite genomic sequencing. Bisulfite treatment modifies DNA converting unmethylated, but not methylated, cytosines to uracil. Bisulfite treatment can be carried out using the
METHYLEAS Y bisulfite modification kit (Human Genetic Signatures).
[0064] In some embodiments, bisulfite pyrosequencing, which is a sequencing-based analysis of DNA methylation that quantitatively measures multiple, consecutive CpG sites individually with high accuracy and reproducibility, may be used. Exemplary primers for such analysis are set forth in Table 11. [0065] It will be recognized that depending on the site bound by the primer and the direction of extension from a primer, that the primers listed above can be used in different pairs. Furthermore, it will be recognized that additional primers can be identified within the DMRs, especially primers that allow analysis of the same methylation sites as those analyzed with primers that correspond to the primers disclosed herein.
[0066] Altered methylation can be identified by identifying a detectable difference in methylation. For example, hypomethylation can be determined by identifying whether after bisulfite treatment a uracil or a cytosine is present a particular location. If uracil is present after bisulfite treatment, then the residue is unmethylated. Hypomethylation is present when there is a measurable decrease in methylation.
[0067] In an alternative embodiment, the method for analyzing methylation of the DMR can include amplification using a primer pair specific for methylated residues within a DMR. In these embodiments, selective hybridization or binding of at least one of the primers is dependent on the methylation state of the target DNA sequence (Herman et al., Proc. Natl. Acad. Sci. USA, 93:9821 (1996)). For example, the amplification reaction can be preceded by bisulfite treatment, and the primers can selectively hybridize to target sequences in a manner that is dependent on bisulfite treatment. For example, one primer can selectively bind to a target sequence only when one or more base of the target sequence is altered by bisulfite treatment, thereby being specific for a methylated target sequence.
[0068] Other methods are known in the art for determining methylation status of a DMR, including, but not limited to, array-based methylation analysis and Southern blot analysis.
[0069] Methods using an amplification reaction, for example methods above for detecting hypomethylation or hyprmethylation of one or more DMRs, can utilize a real-time detection amplification procedure. For example, the method can utilize molecular beacon technology (Tyagi et al., Nature Biotechnology, 14: 303 (1996)) or Taqman™ technology (Holland et al., Proc. Natl. Acad. Sci. USA, 88:7276 (1991)).
[0070] Also methyl light (Trinh et al., Methods 25(4):456-62 (2001), incorporated herein in its entirety by reference), Methyl Heavy (Epigenomics, Berlin, Germany), or SNuPE (single nucleotide primer extension) (see e.g., Watson et al., Genet Res. 75(3):269-74 (2000)) Can be used in the methods of the present invention related to identifying altered methylation of DMRs.
[0071] As used herein, the term "selective hybridization" or "selectively hybridize" refers to hybridization under moderately stringent or highly stringent physiological conditions, which can distinguish related nucleotide sequences from unrelated nucleotide sequences.
[0072] As known in the art, in nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (for example, relative GC:AT content), and nucleic acid type, for example, whether the oligonucleotide or the target nucleic acid sequence is DNA or RNA, can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter. Methods for selecting appropriate stringency conditions can be determined empirically or estimated using various formulas, and are well known in the art {see, e.g., Sambrook et al., supra, 1989).
[0073] An example of progressively higher stringency conditions is as follows: 2X SSC/0.1% SDS at about room temperature (hybridization conditions); 0.2X SSC/0.1% SDS at about room temperature (low stringency conditions); 0.2X SSC/0.1% SDS at about 42°C (moderate stringency conditions); and 0.1X SSC at about 68°C (high stringency conditions). Washing can be carried out using only one of these conditions, for example, high stringency conditions, or each of the conditions can be used, for example, for 10 to 15 minutes each, in the order listed above, repeating any or all of the steps listed.
[0074] The degree of methylation in the DNA associated with the DMRs being assessed, may be measured by fluorescent in situ hybridization (FISH) by means of probes which identify and differentiate between genomic DNAs, associated with the DMRs being assessed, which exhibit different degrees of DNA methylation. FISH is described, for example, in de Capoa et al. (Cytometry. 31 :85-92, 1998) which is incorporated herein by reference. In this case, the biological sample will typically be any which contains sufficient whole cells or nuclei to perform short term culture. Usually, the sample will be a sample that contains 10 to 10,000, or, for example, 100 to 10,000, whole cells. [0075] Additionally, as mentioned above, methyl light, methyl heavy, and array-based methylation analysis can be performed, by using bisulfite treated DNA that is then PCR- amplified, against microarrays of oligonucleotide target sequences with the various forms corresponding to unmethylated and methylated DNA.
[0076] The term "nucleic acid molecule" is used broadly herein to mean a sequence of deoxyribonucleotides or ribonucleotides that are linked together by a phosphodiester bond. As such, the term "nucleic acid molecule" is meant to include DNA and RNA, which can be single stranded or double stranded, as well as DNA/RNA hybrids. Furthermore, the term "nucleic acid molecule" as used herein includes naturally occurring nucleic acid molecules, which can be isolated from a cell, as well as synthetic molecules, which can be prepared, for example, by methods of chemical synthesis or by enzymatic methods such as by the polymerase chain reaction (PCR), and, in various embodiments, can contain nucleotide analogs or a backbone bond other than a phosphodiester bond.
[0077] The terms "polynucleotide" and "oligonucleotide" also are used herein to refer to nucleic acid molecules. Although no specific distinction from each other or from "nucleic acid molecule" is intended by the use of these terms, the term "polynucleotide" is used generally in reference to a nucleic acid molecule that encodes a polypeptide, or a peptide portion thereof, whereas the term "oligonucleotide" is used generally in reference to a nucleotide sequence useful as a probe, a PCR primer, an antisense molecule, or the like. Of course, it will be recognized that an "oligonucleotide" also can encode a peptide. As such, the different terms are used primarily for convenience of discussion.
[0078] A polynucleotide or oligonucleotide comprising naturally occurring nucleotides and phosphodiester bonds can be chemically synthesized or can be produced using recombinant DNA methods, using an appropriate polynucleotide as a template. In comparison, a polynucleotide comprising nucleotide analogs or covalent bonds other than phosphodiester bonds generally will be chemically synthesized, although an enzyme such as T7 polymerase can incorporate certain types of nucleotide analogs into a polynucleotide and, therefore, can be used to produce such a polynucleotide recombinantly from an appropriate template. [0079] In another aspect, the present invention includes kits that are useful for carrying out the methods of the present invention. The components contained in the kit depend on a number of factors, including: the particular analytical technique used to detect methylation or measure the degree of methylation or a change in methylation, and the one or more DMRs is being assayed for methylation status.
[0080] Accordingly, the present invention provides a kit for determining a methylation status of one or more DMRs of the invention. In some embodiments, the one or more DMRs are selected from one or more of the sequences as set forth in Tables 2, 6, 7, 9, Figures 1B- 1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof. The kit includes an oligonucleotide probe, primer, or primer pair, or combination thereof for carrying out a method for detecting hypomethylation, as discussed above. For example, the probe, primer, or primer pair, can be capable of selectively hybridizing to the DMR either with or without prior bisulfite treatment of the DMR. The kit can further include one or more detectable labels.
[0081] The kit can also include a plurality of oligonucleotide probes, primers, or primer pairs, or combinations thereof, capable of selectively hybridizing to the DMR with or without prior bisulfite treatment of the DMR. The kit can include an oligonucleotide primer pair that hybridizes under stringent conditions to all or a portion of the DMR only after bisulfite treatment. In one aspect, the kit can provide reagents for bisulfite pyrosequencing including one or more primer pairs set forth in Table 11. The kit can include instructions on using kit components to identify, for example, the presence of cancer or an increased risk of developing cancer.
[0082] To examine DNAm on a genome-wide scale, comprehensive high-throughput array-based relative methylation (CHARM) analysis, which is a microarray-based method agnostic to preconceptions about DNAm, including location relative to genes and CpG content was carried out. The resulting quantitative measurements of DNAm, denoted with M, are log ratios of intensities from total (Cy3) and McrBC-fractionated DNA (Cy5):
positive and negative M values are quantitatively associated with methylated and
unmethylated sites, respectively. For each sample, -4.6 million CpG sites across the genome of iPS cells, parental somatic cells and ES cells were analyzed using a custom-designed NimbleGen HD2 microarray, including all of the classically defined CpG islands as well as all nonrepetitive lower CpG density genomic regions of the genome. 4,500 control probes were included to standardize these M values so that unmethylated regions were associated, on average, with values of 0. CHARM is 100% specific at 90% sensitivity for known methylation marks identified by other methods (for example, in promoters) and includes the approximately half of the genome not identified by conventional region preselection . The CHARM results were also extensively corroborated by quantitative bisulfite pyrosequencing analysis.
[0083] Provided herein is a genome-wide analysis of DNA methylation addressing variation among iPS cells, somatic cells and ES cells, revealing several surprising differences and relationships among the cell types of epigenetic variation, supported by extensive bisulfite pyrosequencing and functional analysis. First, most cell-specific DNAm was found to occur, not at CpG islands, but at CpG island shores (sequences up to 2kb distant from CpG islands). The identification of these regions opens the door to functional studies, such as those investigating the mechanism of targeting DNAm to these regions and the role of differential methylation of shores.
[0084] IPS cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not peviously been analyzed on a genome-wide scale. Substantial
hypermethylation and hypomethylation of cytosine-phosphate-guanine (CpG) island shores in nine human iPS cell lines as compared to their parental fibroblasts was determined. The R- DMRs in the reprogrammed cells were significantly enriched in tissue-specific (T-DMRs; 2.6-fold, P < I Q-4) and cancer-specific DMRs (C-DMRs; 3.6-fold, P < 10"4). Notably, even though the iPS cells are derived from fibroblasts, their R-DMRs can distinguish between normal brain, liver and spleen cells and between colon cancer and normal colon cells. Thus, many DMRs are broadly involved in tissue differentiation, epigenetic reprogramming and cancer. Colocalization of hypomethylated R-DMRs with hypermethylated C-DMRs and bivalent chromatin marks, and colocalization of hypermethylated R-DMRs with
hypomethylated C-DMRs and the absence of bivalent marks were observed, suggesting two mechanisms for epigenetic reprogramming in iPS cells and cancer.
[0085] In one aspect of the invention, methylation density is determined for a region of nucleic acid. Density may be used as an indication of production of an iPS cell, for example. A density of about 0.2 to 0.7, about 0.3 to 0.7 , 0.3 to 0.6 or 0.3 to 0.4, or 0.3, may be indicative of generation of an iPS cell (the calculated DNA methylation density is the number of methylated CpGs divided by the total number of CpGs sequenced for each sample).
Methods for determining methylation density are well known in the art. For example, a method for determining methylation density of target CpG islands has been established by Luo et al. Analytical Biochemistry, Vol. 387:2 2009, pp. 143-149. In the method, DNA microarray was prepared by spotting a set of PCR products amplified from bisulfite- converted sample DNAs. This method not only allows the quantitative analysis of regional methylation density of a set of given genes but also could provide information of methylation density for a large amount of clinical samples as well as use in the methods of the invention regarding iPS cell generation and detection. Other methods are well known in the art (e.g., Holemon et al., BioTechniques, 43:5, 2007, pp. 683-693).
[0086] The following example is provided to further illustrate the advantages and features of the present invention, but are not intended to limit the scope of the invention. While they are typical of those that might be used, other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.
EXAMPLE
DIFFERENTIAL METHYLATION OF TISSUE AND CANCER SPECIFIC CpG ISLAND SHORES DISTINGUIAHES HUMAN iPS CELLS, ES CELLS AND
FIBROBLASTS
[0087] The following experimental protocols and materials were utilized.
[0088] Cell culture and isolation of RNA and genomic DNA from fibroblast, hES cells and iPS cells. iPS cell lines and their parental fibroblasts used were described in Park et al. (Nature (451)141-146 (2008)) and Park et al. Cell (134)877-886 (2008)).
[0089] MRC5 (14-week-old fetal lung fibroblast from the ATCC cell biology collection), Detroit 551 (551, fetal skin fibroblast from ATCC), hFib2 (adult dermal fibroblast), SBDS (DF250), DMD (GM04981 from Coriell), GD (GM00852A from Coriell), PD (AG20446 from Coriell), JDM (GM02416 from Coriell) and ADA (GM01390 from Coriell). Human ES cells BGOl, BG03 and H9 were used. Fibroblasts were grown in a-MEM containing 10% W 201
25 inactivated fetal serum, 50 U/ml penicillin, 50 mg/ml streptomycin and 1 mM L-glutamine. hES cells and iPS cells were cultured in hES medium (80% DMEM/F12, 20% KO Serum Replacement™, 10 ng/ml bFGF, 1 mM L-glutamine, 100 μΜ nonessential amino acids, 100 μΜ 2-mercaptoethanol, 50 U/ml penicillin and 50 mg/ml streptomycin). Total RNA and genomic DNA were isolated using RNeasy™ kit (Qiagen) with in-column DNase treatment and DNeasy™ kit (Qiagen), respectively, according to manufacturer's protocol.
[0090] CHARM DNA methylation analysis. For each sample, 5 μg of genomic DNA was digested, fractionated, labeled and hybridized to a CHARM microarray as described in Irizarry et al. (Nat. Genet. (41)178-186 (2009)) and Irizarry et al. {Genome Res. (18)780-790 (2008)).
[0091] CHARM microarrays were prepared using custom-designed NimbleGen™ HD2 microarrays as described in Irizarry et al. (Nat. Genet. (41)178-186 (2009)) and Irizarry et al. {Genome Res. (18)780-790 (2008)). For each probe, the averaged methylation ( ) values across the same cell type were computed and were used to find regions of differential methylation {AM) for each pairwise cell type comparison. The absolute area of each region was calculated by multiplying the number of probes by Δ For the first experiment {n = 6 for each cell type), false discovery rates (FDR) were computed and a cutoff of 5% was used to define the R-DMRs. The parental fibroblast lines for this experiment were MRC5, SBDS, DMD, GD, Detroit551 and PD, and they were compared to the iPS cell lines derived from them. For the second set of experiments {n = 3 for each cell type), an absolute FDR could not be calculated, so we used an absolute area cutoff of 10.0, which corresponded in magnitude to the 5% FDR cutoff of the first set of experiments. The parental fibroblast lines for the second experiment were JMD, ADA and hFib2 and were compared to the iPS cell lines derived from them, as well as to three ES cell lines, BGOl, BG03 and H9.
[0092] Overlap of R-DMRs with bivalent domains, transcription factor {POU5F1, NANOG, SOX2) binding sites, T-DMRs and C-DMRs. The number of overlapping regions for hypermethylated R-DMRs and hypomethylated R-DMRs were computed for overlaps with bivalent domains as in Bernstein et al. {Cell (125)315-326 (2006)) and Pan et al. {Cell Stem Cell (1)299-312 (2007)). The number of overlapping regions for hypermethylated R- DMRs and hypomethylated R-DMRs were computed for overlaps with POU5F1, NANOG and SOX2 binding sites as described in Boyer et al. {Cell (122)947-956 (2005)). The number of overlapping regions for hypermethylated R-DMRs and hypomethylated R-DMRs were computed for overlaps with tissue-specific differentially methylated regions (T-DMRs) as described in Irizarry et al. (Nat. Genet. (41)178-186 (2009)). The number of overlapping regions for hypermethylated R-DMRs and hypomethylated R-DMRs were computed for overlaps with cancer-specific differentially methylated regions (C-DMRs) as described in Irizarry et al. (Nat. Genet. (41)178-186 (2009)). To determine the significance of each overlap, randomly generated CHARM array regions equal to the number and lengths of the R-DMRs were generated and P values were calculated by 10,000 permutations. Random values were calculated as the average over all 10,000 permutations.
[0093] Unsupervised cluster analysis. Using the R-DMRs, we performed unsupervised cluster analysis to determine to what degree the methylation at these locations distinguished normal brain, liver and spleen as well as colon cancer from its matched counterpart. As a test of significance, we randomly generated 1,000 CHARM array regions of length and number equal to those of the R-DMRs and then assessed the median euclidean distance among samples of a given tissue type and the median euclidean distance among samples of different tissue types. This test was also applied to the cancer and normal samples.
[0094] Bisulfite pyrosequencing. For validation of DMRs, 500 ng of genomic DNA from each sample was treated with bisulfite using an EpiTect Kit (Qiagen) according to the manufacturer's specifications. Bisulfite-treated genomic DNA was PCR-amplified using unbiased nested primers and performed quantitative pyrosequencing using a PSQ HS96 (Biotage). The DNA methylation percentage at each CpG site was determined using the Q- CpG methylation software (Biotage). Control DNA was from the generally highly methylated HCT116 colon cancer cell line, as well as from a hypomethylated double DNA
methyltransf erase 1/3 B knockout somatic cell line derived from it. Table 1 1 provides the primer sequences used for the bisulfite pyrosequencing reactions, as well as the chromosomal coordinates in the University of California at Santa Cruz March 2006 human genome assembly for each CpG site interrogated. The annealing temperature used for all PCR reactions was 50 °C.
[0095] Affymetrix microarray expression analysis. Genome-wide gene expression analysis was done using Affymetrix U133 Plus 2.0™ microarrays. For each sample, 1 μg of high-quality total RNA was amplified, labeled and hybridized onto the microarray according to Affymetrix's specifications, and data were normalized as previously described in Irizarry et al. (Biostatistics (4)249-264 (2003)).
[0096] GO annotation. GO annotation was performed as described in Dennis et al.
{Genome Biol. 4, R60 (2003)) and Huang et al. {Nat. Protocols (4)44-57 (2009)).
[0097] Accession codes. NCBI GEO: Gene expression microarray data and CHARM microarray data have been submitted under accession number GSE18111.
[0098] URLs. A complete set of R-DMRs can be found at rafalab.jhsph.edu/r- dmrplots.pdf. A complete set of ES-iPS DMRs can be found at rafalab.jhsph.edu/es- ipsdmr.pdf.
[0099] IPS cells can be derived from somatic cells by introduction of a small number of genes: for example, POU5F1, MYC, KLF4 and SOX2. As direct derivatives of an individual's own tissue, iPS cells offer considerable therapeutic promise, avoiding both immunologic and ethical barriers to their use. iPS cells differ from their somatic parental cells epigenetically, and thus a comprehensive comparison of the epigenome in iPS and somatic cells would provide insight into the mechanism of tissue reprogramming. Although two previous targeted studies examined a subset of the genome, 7,000 (Ball et al. (Nat. Biotechnol. (27)485 (2009)) and 66,000 (Deng et al. (Nat. Biotechnol. (27)353-360 (2009))) CpG sites in a small cohort of three iPS-fibroblast pairs, a global assessment of genome- wide methylation has not yet been performed.
]0100] Recently, differential methylation patterns that distinguish among normal tissue types (T-DMRs) and patterns that can segregate colorectal cancer tissue from matched normal tissues (C-DMRs) were described. Unexpectedly, these two DMRs occur 13 -fold more frequently at CpG island 'shores', regions of comparatively low CpG density that are located near traditional CpG islands, than at the CpG islands themselves. Cancers showed approximately equal numbers of hypomethylated and hypermethylated regions, and 45% of C-DMRs overlapped T-DMRs, suggesting that epigenetic changes in cancer involve reprogramming of the normal pattern of tissue-specific differentiation.
[0101] Here differential methylation patterns in iPS cell reprogramming was explored, first comparing six human iPS cell lines to the fibroblasts from which they were derived using comprehensive high-throughput array-based relative methylation (CHARM) analysis as described in Irizarry et al. (Genome Res. (18)780-790 (2008)). This approach allows the interrogation of ~4.6 million CpG sites genome- wide using a custom designed NimbleGen™ HD2 microarray, including almost all CpG islands and shores in the human genome.
Genomic DNA from iPS cells, their parental fibroblasts and human embryonic stem (hES) cells was digested with the enzyme McrBC, fractionated, labeled and hybridized to a
CHARM array.
[0102] A total of 4,401 regions (including 96,404 CpG sites) were found to differ in iPS cell lines from the fibroblasts of origin (Tables 1 and 2) at a false discovery rate (FDR) of 5%; we term these regions R-DMRs. Of these R-DMRs, DMRs that were hypermethylated in iPS cells compared to fibroblasts predominated over hypomethylated DMRs (60%:40%). Of the 4,401 DMRs, 1,969 were within 2 kb of the transcriptional start site of a gene.
[0103] The genes that were associated with these R-DMRs showed functionally important features based on bioinformatic analyses. First, gene ontology (GO) annotation analysis of these genes revealed significant enrichment for genes involved in developmental and regulatory processes (Table 3). For example, 38% of the genes that were hypomethylated in iPS compared to fibroblasts (P = 3.56 x 10"60) and 22% of the genes that were
hypermethylated in iPS compared to fibroblasts (P = 1.73 χ 10-12) were involved in developmental processes. To further elucidate the functional significance of these R-DMRs, their overlap with bivalent domains, which mark developmental genes in ES cells was examined. Notably, 65% of the R-DMRs that were hypomethylated in iPS cells compared to fibroblasts showed significant association with bivalent domain marks (P < 0.0001 by 10,000 permutations), whereas only 18.6% of hypermethylated R-DMRs overlapped with these domains (P = 0.5699 by 10,000 permutations) (Table 4). Furthermore, when we observed the overlap of the R-DMRs with known binding sites for pluripotency markers such as POU5F1, NANOG and SOX2 as discussed in Boyer et al. (Cell (122)947-956 (2005)), we saw a similar relationship, in which the hypomethylated R-DMRs showed significant overlap (P < 0.0001 by 10,000 permutations) whereas the hypermethylated DMRs did not (P = 1 by 10,000 permutations; Table 5). These observations indicate that the sites of demethylation during reprogramming of fibroblasts to iPS cells are tightly linked to genes that are functionally important for pluripotency. [0104] The R-DMRs showed several noteworthy features. First, over 70% of the R-DMRs were associated with CpG island shores rather than with the associated CpG islands (Figure 1 A), regardless of whether the R-DMRs were hypermethylated or hypomethylated in iPS cells relative to fibroblasts (Figure 2A). Second, 56% of R-DMRs overlapped T-DMRs previously identified as distinguishing tissues representing the three germ cell lineages, namely, brain, liver and spleen (Table 1). This overlap was statistically significant (P < 0.0001 by 10,000 permutations). Furthermore, both hypermethylated and hypomethylated R- DMRs in iPS cells showed similar overlap with known T-DMRs, overlapping at 54% and 60%, respectively (Table 1). Thus, R-DMRs are heavily enriched in CpG island shores and largely overlap T-DMRs that are involved in normal development. There was also a 61% overlap of the gene-proximal R-DMRs with the T-DMRs.
[0105] Figure 1 details reprogramming differentially methylated regions (R-DMRs). Figure 1 A depicts enrichment of R-DMRs at CpG island shores. The CHARM array (left, labeled CpG regions) is enriched in CpG islands, and the R-DMRs (right, labeled R-DMR) show marked enrichment at CpG island shores. Islands are denoted as regions that include >50% of a CpG island or are wholly contained in an island, and overlap regions are denoted as regions that include 0.1-50% of a CpG island. Specific base intervals of regions not overlapping islands are indicated; (0-500) means from 1 to 500 bases. Percentage of the distribution ( axis) is given for the CpG regions (CHARM array, null hypothesis) and reprogramming differentially methylated regions (R-DMRs). Figures IB and C show examples of DMRs. The gene encoding bone morphogenetic protein 7 (BMP7) is indicated in B, and the gene encoding goosecoid (GSC) is indicated in C. In each case, the upper panels show a plot of methylation ( value; see Methods) versus genomic location, where the curve represents averaged smoothed M values; the location of CpG dinucleotides (black tick marks), CpG density, location of CpG islands (filled boxes along the x-axis (zero)), as well as the gene annotation are shown. The bottom panels show validation by bisulfite
pyrosequencing (mapping to unfilled box in upper panel). Bars represent the mean methylation (triplicate measurement) ± s.d. of iPS cells, fibroblasts and ES cells (BGOl, BG03 and H9) as well as the generally highly methylated HCTl 16 colon cancer cell line and a generally hypomethylated double DNA methyltransferase 1/3B double knockout line (DKO) derived from it. In each case, five separate CpG sites were assayed quantitatively, shown as differing shades. W 201
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[0106] Figure 2 depicts the distribution of distance of reprogramming differentially methylated regions (R-DMRs) from CpG islands. Islands are regions that are inside, cover, or overlap more than 50% of a CpG island. Overlap are regions that overlap 0.1-50% of a CpG island. Regions denoted by (0, 500] are regions located <500 bp but do not overlap an island. Regions denoted by (500, 1000] are regions located >500 bp and <1000 bp from an island. Regions denoted by (1000, 2000] are regions located >1000 bp and <2000 bp from an island. Regions denoted by (2000, 3000] are regions located >2000 bp and <3000 bp from an island. Regions denoted by >3000 are >3000 bp from an island. Percentage are given for the CpG regions (CHARM array, null hypothesis) and reprogramming differentially methylated regions (R-DMRs) as well as the R-DMRs subdivided into hypermethylation and
hypomethylation in iPS relative to fibroblast. Percentages of each class is given for (A) R- DMRs from the first experiment (n=6 for each cell type) (R-DMR panel is duplicated from Figure 1 A) and (B) R- DMRs from second experiment (n=3 for each cell type).
[0107] The CHARM analysis was then repeated on a separate set of three iPS cell lines and the fibroblasts from which they were derived, as well as three human ES cell lines. It was not possible to perform an FDR statistical test on this smaller number of lines, so a similar area cutoff in the curves was used that corresponded in magnitude to the 5% FDR cutoff of the previous experiment. In this second analysis, 2,179 R-DMRs were identified, with a slight excess of hypomethylated versus hypermethylated DMRs (55% compared to 45%) in iPS cells. Notably, 80% of the DMRs overlapped those found in the first experiment (see Table 6 for full list). As in the first analysis, there was a substantial enrichment for CpG island shores (78%, Figure 2B), and 60% of the R-DMRs overlapped T-DMRs (Table 1).
[0108] This second analysis provided insight into the methylome of iPS cells as compared to ES cells. Although the two cell types had very similar DNA methylation, 71 DMRs distinguished them, with 51 showing hypermethylation and 20 showing hypomethylation in iPS cells (Table 7). GO annotation of these DMRs showed significant enrichment of developmental processes in the genes that were hypermethylated in iPS cells as compared to ES cells (Table 8). In 32 of the DMRs that distinguish iPS cells from ES cells, the DMRs were near genes of interest, including HOXA9 and two genes that encode the zinc finger proteins ZNF568 and ZFP112. In some cases, the methylation in iPS cells was intermediate between differentiated fibroblasts and ES cells; this was true, for example, of TBX5, which encodes a transcription factor that is involved in cardiac and limb development. In other cases, methylation in iPS cells differed from both fibroblasts and ES cells, suggesting that the iPS cells occupy a distinct and possibly aberrant epigenetic state. An example was PTPRT, encoding a protein tyrosine phosphatase involved in many cellular processes including differentiation. For some ES-iPS differences, the methylation levels changed in the same direction as for ES cells compared to fibroblasts, but to a greater degree; for example, methylation of the homeobox gene HOXA9 was greater in iPS compared to ES, whose methylation at this gene was greater than in fibroblasts.
[0109] These data were validated in two ways. First the methylation results from CHARM were verified by bisulfite pyrosequencing of nine DMRs, examining 2-6 CpGs within each DMR. For all of these genes, the bisulfite pyrosequencing data confirmed the differential methylation data from CHARM (Figures IB and C; Figure 4).
[0110] Figure 4 includes examples of differential DNA methylation (upper panels) and confirmation by bisulfite pyrosequencing (lower panels). Upper panels are a plot of M value versus genomic location, where the curve represents averaged smoothed M values. Also shown in the upper panels are the locations of CpG dinucleotide (black tick marks on x axis), CpG density (smoothed black line) calculated across the region using a standard density estimator, location of CpG islands (filled boxes along the x-axis (zero)), as well as gene annotation indicating the transcript (thin outer gray line), coding region (thin inner gray line), exons (filled gray box) and gene transcription directionality on the y axis (sense marked as +, antisense as -). The lower panels represent the degree of DNA methylation as measured by bisulfite pyrosequencing. The unfilled box indicated on the x axis of the CpG density plot in the upper panel indicates the CpG sites that were measured. Reactions were done in triplicate; bars represent the mean methylation ±SD of iPS cells, fibroblasts, and ES cells (BGOl, BG03 and H9) as well as DKO (DNMT1 and DNMT3B Double KO cell line) and HCT116 (parental colon cancer cell line) for each individual CpG site measured. Figure A and B are DMRs found by comparison between iPS cells and fibroblast (n=6), (c-g) is a DMR found by comparison between iPS cells and ES cells (n=3). (A) TBX3 (T-box 3 protein), (B) HOXD3 (Homeobox D3), (C) POU3F4 (POU domain, class 3, transcription factor 4), (D) A2BP1 (ataxin 2-binding protein 1), (E) ZNF184 (zinc finger protein 184), (F) W
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IGF1R (insulin-like growth factor 1 receptor), (G) PTPRT (protein tyrosine phosphatase, receptor type, T).
[0111] Global gene expression analysis was also performed using the Affymetrix
HGU133 Plus™ 2.0 microarray. There was a strong inverse correlation between differential gene expression and differential DNA methylation at R-DMRs that are within 500 bp of the transcriptional start site (TSS) of a gene: P < 10-3 for both hypermethylation and
hypomethylation (Figure 5, Table 9). The significant association held true even when the R- DMR was within 1 kb of a TSS (P = 0.01 and P < 10-3 for hypermethylated and
hypomethylated R-DMRs, respectively, Figure 5). Moreover, this correlation was enhanced in DMRs that were in CpG island shores.
[0112] Figure 5 illustrates that gene expression strongly correlates with reprogramming differentially methylated regions (R-DMRs) at CpG island shores. Red circles represent R- DMRs that are within 2kb from a CpG island, blue circles represent those that are more than 2kb away from a CpG island, and black circles represent log ratios for all genes not within (A) 500bp or (B) lkb from the transcriptional start site (TSS) of an annotated gene. The log2 ratios of fibroblast to iPS expression were plotted against ΔΜ values (fibroblast minus iPS) for R-DMRs in which one of the two points had approximately no methylation. (A) DMRs that are within 500bp from a TSS of a gene. (B) DMRs that are within lkb from a TSS of a gene.
[0113] Furthermore, an unsupervised cluster analysis was performed using the R-DMRs to determine to what degree the methylation at these locations distinguished normal brain, liver and spleen from each other. Notably, there was complete separation of these three tissues, indicating that the sites of the methylation changes that occur during reprogramming normally distinguish these disparate tissues (Figure 3A). In addition, the R-DMRs could largely distinguish normal colonic mucosa from colorectal cancer, indicating that the R- DMRs are also involved in abnormal reprogramming in cancer (Figure 3B). As a test of significance, none of 1,000 randomly generated lists of the CHARM array regions of equal length and number clustered the tissues as well, as assessed either by whether they yielded a median euclidean distance among samples of a given tissue type at least as low as that found when using the R-DMRs, or yielded a median euclidean distance among samples of different tissue types at least as great as that found when using the R-DMRs. This was true both for the comparison between normal tissues and for the cancer-to-normal-tissue comparison.
[0114] Figure 3 shows that DNA methylation at R-DMRs distinguishes normal tissues from each other and colon cancer from normal colon. (A and B) The M values of all tissues from the 4,401 regions (FDR < 0.05) corresponding to R-DMRs (iPS cells compared to parental fibroblasts) were used for unsupervised hierarchical clustering comparing (A) normal brain, spleen and liver (denoted as Br, Sp and Lv, respectively) and (B) colorectal cancer and matched normal colonic mucosa (denoted as T and N, respectively). Notably, all of the normal brain, spleen and liver tissues are completely discriminated by the regions that differ between iPS cells and fibroblasts (R-DMRs). The major branches in the dendrograms correspond perfectly to tissue type. Furthermore, most of the colorectal cancer samples are discriminated from matched normal colonic mucosa by R-DMRs.
[0115] The R-DMRs were compared to those obtained in a genome-scale comparison of DNA methylation in colorectal cancer and matched normal colonic mucosa from the same individuals (C-DMRs) as discussed in Irizarry et al. (Nat. Genet. (41)178-186 (2009)).
Previously a much smaller number of C-DMRs than T-DMRs (2,707 compared to 16,379) were found, and 45% of the C-DMRs overlapped T-DMRs. Approximately 16% of the R- DMRs in the present study overlapped the C-DMRs of the previous study, whereas only 4.5% on average would be predicted by permutation analysis to overlap (P < 0.0001 based on 10,000 permutations) (Table 10). Notably, hypomethylated R-DMRs (iPS compared to fibroblasts) were associated with hypermethylated C-DMRs (cancer compared to normal, P < 0.0001 based on 10,000 permutations) (Table 10). Of the 294 DMRs found to overlap between hypomethylated R-DMRs and hypermethylated C-DMRs, 251 (85%) also overlapped bivalent chromatin marks. In contrast, hypermethylated R-DMRs were associated with hypomethylated C-DMRs (P < 0.0001 based on 10,000 permutations) (Table 10). Of the 293 DMRs found to overlap between hypermethylated R-DMRs and hypomethylated C- DMRs, only 37 (13%) also overlapped bivalent chromatin marks. Because bivalent chromatin marks are associated with recruitment of Polycomb group proteins, these data suggest that there are two independent epigenetic mechanisms for cell reprogramming and tumorigenesis. One mechanism involves decreased DNA methylation and chromatin modifications at bivalent sites during reprogramming and increased methylation in cancer. The other W
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mechanism involves increased methylation during reprogramming and loss of methylation in cancer.
[0116] In summary, it was determined that epigenetic reprogramming of human fibroblasts to iPS cells involves substantial changes in DNA methylation largely affecting the same CpG island shores in T-DMRs that mark normal differentiation. It is notable that the R- DMRs completely distinguish brain from liver from spleen tissues and largely distinguish colon cancer from normal colon tissue. These results provide compelling evidence of the importance of CpG island shores and T-DMRs in both normal development and somatic cell reprogramming. Indeed, the target loci for normal tissue programming, epigenetic reprogramming to pluripotency and aberrant programming of cancers largely overlap. A secondary finding is that certain loci in iPS cells remain incompletely reprogrammed, whereas others are aberrantly reprogrammed, thus establishing that the methylation pattern of iPS cells differs both from those of the parent somatic cells and from those of human ES cells.
[0117] These results contrast with prior studies that were primarily directed toward developing powerful new tools to analyze DNA methylation of targeted genomic regions rather than genome-scale studies of iPS cell methylation. The more extensive genome-scale analysis of nine paired sets of iPS cells and parental fibroblasts detected roughly equal levels of hypo-and hypermethylation and revealed the predominant involvement of CpG island shores over islands themselves. The present study reveals a host of loci that represent targets of epigenetic remodeling that are central to somatic cell reprogramming. These R-DMRs include both hypomethylated and hypermethylated regions and are a subset of the previously described T-DMRs and C-DMRs, indicating that these R-DMRs at CpG island shores are critical epigenetic targets for defining cell fate.
[0118] Finally, the colocalization of hypomethylated R-DMRs in iPS cells with hypermethylated C-DMRs in cancer and bivalent chromatin marks, and hypermethylated R- DMRs with hypomethylated C-DMRs and the absence of these marks, suggest two parallel mechanisms for epigenetic reprogramming in iPS cells and in cancer, one involving a loss of DNA methylation in iPS and a chromatin-dependent gain of DNA methylation in cancer and the other involving a gain of methylation in iPS and a chromatin-independent loss of DNA methylation in cancer. [0119] Table 1. Differentially methylated regions (DMRs) found by CHARM that overlap with tissue-specific differentially methylated regions (T-DMRs).
Figure imgf000036_0001
[0120] Table 2. Reprogramming differentially methylated regions (R-DMRs).
R-DMRs are regions that differ in DNA methylation between 6 iPS lines and the fibroblasts from which they were derived.
FDR is false discovery rate. R-DMRs were defined by using a FDR cutoff of 5%.
Columns are chromosome, start, end, fibroblast M value, iPS M value, absolute area, gene, distance to gene, relation to gene, distance to CGI, relation to CGI, and false discovery rate. chrl2 113615113 113620729 1.43448 0.0408 180.198 TBX3 8762 upstream 0 overlap 0.00951 chr20 55266497 55269993 -0.0051 1.84274 157.024 BMP7 4714 inside intron 2701 disjoint 0.00951 chr5 174085257 174089570 1.50878 0.23511 126.294 MSX2 1077 overlaps exon -287 disjoint 0.00952 upstream
chrl 219123936 219127011 1.73419 0.21292 125.485 HLX1 4555 overlaps 3' 0 cover 0.00952 chr4 1 11758431 111761769 1.46628 0.17657 124.17 PITX2 1933 overlaps two exons 0 cover 0.00952 chrl4 94307646 94310797 1.41713 -0.013 124.15 GSC 1395 promoter 0 cover 0.00952 chr6 137852236 137855776 1.29071 0.06637 122.374 OLIG3 1447 overlaps 3' 272 disjoint 0.00952 chr4 111780191 111783030 1.52351 0.0034 120.023 PITX2 2235 promoter 0 overlap 0.00952 chrl l 133790742 133793856 0.17983 1.92691 118.054 B3GAT1 3721 upstream -2613 disjoint 0.00952 chrl 5 34959195 34962542 1.30256 -0.0587 116.991 MEIS2 215252 downstream 0 cover 0.00952 chrl 2 113612415 113614457 2.08362 -0.0856 115.852 TBX3 6064 upstream 0 overlap 0.00952 chr9 14338796 14341545 1.64962 0.0227 115.082 NFIB 34852 upstream 0 cover 0.00952 chr2 70984357 70987408 1.82495 0.44225 107.406 VAX2 3130 inside intrpn 0 cover 0.00952 chr5 72631400 72634770 1.63421 0.43683 107.234 TMEM174 131571 downstream 0 overlap 0.00952 chrl2 79625531 79628584 1.43952 0.17467 105.759 MYF6 0 covers 0 cover 0.00952 chrl5 94691087 94693280 1.89489 0.0704 100.921 NR2F2 16138 downstream -666 disjoint 0.00952 chrlO 8140562 8143911 1.14432 0.09455 99.7919 GATA3 3890 overlaps exon 0 overlap 0.00953 downstream
chr7 4712239 4714574 1.82095 0.30258 99.6951 F0XK1 23784 inside intron 9754 disjoint 0.00953 chrl5 34962957 34965118 1,48228 -0.246 99.599 MEIS2 212676 downstream 1690 disjoint 0.00953 chr21 42054297 42057115 1.16873 -0.1064 98.9434 RIPK4 3202 inside intron 2234 disjoint 0.00953 chrl2 52730162 52732417 1.60816 -0.0132 96.5584 HOXC4 33254 inside intron 0 cover 0.00953 chr4 174673379 174677211 1.23246 0.22757 96.5248 HA D2 10741 downstream 0 cover 0.00953 chr5 149847304 149849876 0.15888 1.78167 95.4845 NDST1 30746 upstream -1073 disjoint 0.00953 chrlO 22661208 22663338 1.5285 -0.0903 95.1842 BMI1 11063 downstream 18 disjoint 0.00953 chr9 128417927 128420967 1.17239 -0.015 93.7972 LMX1B 1309 inside intron 0 overlap 0.00954 ohrl3 49599787 49601769 1.597 -0.0412 93.4964 KCNRG 1 12397 downstream 0 overlap 0.00954 chr6 101009618 101012415 1.40269 0.15833 93.2524 SIMl 5856 inside intron 0 cover 0.00954 chr7 25863763 25867905 1.4184 0.50635 92.7557 NFE2L3 290479 upstream 0 cover 0.00954 chrl2 113318995 113322771 1.19105 0.04824 92.6843 TBX5 3314 covers exon(s) 0 overlap 0.00954 chrl l 31799555 31804098 0.84544 0.10592 92.6827 PAX6 10101 upstream 0 overlap 0.00954 c r6 1550734 1553987 1.24149 0.18705 92.6491 FOXC1 1692 promoter 0 inside 0.00954 chrl9 36535982 36538597 1.25578 -0.0619 92.4183 TSHZ3 73968 upstream 0 overlap 0.00954 chrl l 2196101 2201145 0.02802 0.87106 91.0259 ASCL2 47612 downstream 45535 disjoint 0.00954 chrl4 69416701 69419462 0.12389 1.72241 90.3344 SMOC1 806 inside intron -421 disjoint 0.00954 chr8 847048 849973 0.32613 1.32521 87.9738 ERICH1 175823 upstream -6643 disjoint 0.00955 chrl5 34965493 34968087 1.16464 -0.1113 86.5124 MEIS2 209707 downstream 0 cover 0.00955 chrH 36198033 36200832 1.17994 0.05156 86.335 PAX9 0 overlaps 5' -8 disjoint 0.00955 chr4 54661928 54664948 1.25439 0.17391 86.3018 GSH2 974 overlaps 3' 0 overlap 0.00955 chr2 176736385 176738835 1.49822 0.18106 85.9965 HOXD3 0 overlaps 5' 0 cover 0.00955 chr9 963211 966271 0.967 -0.0035 84.5033 DMRT3 692 promoter 0 overlap 0.00956 chrl l 64947133 64949321 -0.0079 1.29292 84.4065 FKSG44 36435 downstream 0 cover 0.00956 chr2 28470918 28472912 0.0887 1.56392 83.9376 FOSL2 1636 inside intron -666 disjoint 0.00956 chr2 63126514 63128174 1.69 -0.0041 82.7999 EHBP1 339878 overlaps 3' 0 overlap 0.00956 chrl3 87125724 87127739 1.89333 0.41678 81.2646 SLITR 5 2854 inside exon 0 overlap 0.00957 chr4 174680723 174683340 1.37494 0.23767 80.6449 HAND2 4612 downstream -200 disjoint 0.00957 chr6 82515479 82518001 0.48063 1.69277 80.5519 FAM46A 1145 overlaps exon 0 overlap 0.00957 upstream
chrl 219127138 219130239 1.57176 0.40914 80.4969 HLX1 7757 downstream 0 cover 0.00957 chr3 140143032 140146287 1.34365 0.48166 80.0244 FOXL2 2203 overlaps 3' 118 disjoint 0.00957 chr9 14334559 14336992 1.20263 -0.0591 79.5231 NFIB 30615 upstream 0 overlap 0.00957 chrlO 21827602 21829056 1.7571 -0.2308 79.438 C10orfl l4 1406 promoter 0 overlap 0.00957 chr6 4717496 4720297 0.99067 -0.036 79.172 CDYL 66105 inside intron 0 overlap 0.00958 chrl l 128061957 128064927 1.25553 0.1253 78.452 FLU 4271 upstream 386 disjoint 0.00958 chr2 156889981 156892221 1.96851 0.54417 77.734 NR4A2 5224 covers exon(s) 414 disjoint 0.00958 chrl5 94706105 94708262 1.36777 0.07745 76.997 NR2F2 31156 downstream -51 disjoint 0.00958 chr8 72919481 72921712 1.39725 -0.1586 76.544 MSC 197 promoter -260 disjoint 0.00958 chrS 92934662 92936521 1.66838 0.1109 76.2362 NR2F1 8277 upstream -31 disjoint 0.00958 chrl 7 67622920 67625195 1.24987 -0.0704 75.4783 SOX9 3560 upstream 0 cover 0.00959 chrl l 128058857 128061859 1.07065 0.11786 75.3971 FLU 7339 upstream 3454 disjoint 0.00959 chr9 111119732 111121314 2.13998 0.06694 75.3391 EPB41L4B 1527 inside intron 0 overlap 0.00959 chrX 39836514 39838321 1.36168 -0.1442 75.2887 BCO 3278 inside intron 0 overlap 0.00959 chr4 54653182 54656622 1.787 0.03393 75.2454 GSH2 4332 upstream 0 overlap 0.00959 chr5 122456244 122458733 1.31255 0.1416 75.1185 PPIC 55921 upstream 0 overlap 0.00959 chrlQ 8138174 8140471 1.29619 0.09119 74.7691 GATA3 1502 overlaps exon 0 overlap 0.00959 upstream
chrl7 37864479 37865925 -0.2758 1.41859 73.5934 ATP6V0A1 92 overlaps exon 0 overlap 0.0096 downstream
chr4 81403269 81404930 1.62505 0.09892 73.2665 FGF5 1835 promoter 1588 disjoint 0.0096 chr3 32835387 32837002 1.76983 0.12357 73.2192 TRJ 71 874 overlaps exon 0 cover 0.0096 downstream
chr6 126108229 126110075 1.37534 0.04514 72.7901 HEY2 2349 promoter 340 disjoint 0.0096 chr5 92963067 92965516 1.25898 0.06708 72.6429 NR2F1 18269 downstream 35 disjoint 0.00961 chrl l 2320662 2324704 0.51413 1.40751 72.6294 TSPAN32 40149 downstream 30095 disjoint 0.00961 chrlO 35965449 35967529 1.23896 -0.0698 72.1141 FZD8 2838 overlaps 3' 978 disjoint 0.00961 chr7 96492786 96494518 1.42058 -0.0722 71.0536 DLX5 708 promoter -651 disjoint 0.00962 chr20 49847685 49850240 1.08139 -0.1639 71.0028 SALL4 2180 inside intron 479 disjoint 0.00962 chr7 27206734 27209251 1.3355 0.32095 70.9245 HOXA13 485 promoter 0 overlap 0.00962 chr4 174692854 174695567 1.09831 0.09691 70.2274 HA D2 4902 upstream 208 disjoint 0.00962 chr9 1036413 1039281 1.42296 0.26139 70.0508 DMRT2 2332 promoter -19 disjoint 0.00962 chr4 111778292 111780100 1.41679 0.09749 69.7088 PITX2 336 promoter 0 overlap 0.00963 chr6 52547447 52549152 0.40769 1.94488 69.2149 TRAM2 668 inside intron 76 disjoint 0.00963 chr5 172595175 172597606 1.32872 0.21327 68.8258 NKX2-5 308 promoter 0 cover 0.00964 chr6 10525565 10527225 1.57282 0.07069 68.3482 TFAP2A 557 inside intron 0 overlap 0.00964 chrl7 4788938 4791174 0.3473 1.61616 68.0349 PFN1 1395 overlaps 3' 513 disjoint 0.00964 chr6 26151595 26154569 0.19994 1.20549 67.9378 H1ST1H3C 0 covers 0 cover 0.00964 chrl7 7321594 7323042 0.3789 2.09997 67.7704 ZBTB4 5198 inside intron 0 overlap 0.00964 chr6 5944727 5947251 1.25419 0.15335 67.4658 NRN1 5380 inside intron 0 overlap 0.00965 chrl2 113607244 113609681 1.18972 0.11087 67.2052 TBX3 893 promoter 0 cover 0.00965 chr2 66662677 66664864 1.23022 0.13752 67.2046 MEIS1 146642 downstream 0 overlap 0.00965 chrX 39832051 39834193 1.12008 -0.1621 66.9246 BCOR 7406 inside intron 123 disjoint 0.00965 chr6 1339497 1342098 1.39629 0.37774 66.8716 FOXF2 4430 overlaps 3' -328 disjoint 0.00966 chr9 111849043 111850572 1.72984 -0.0343 66.7219 PALM2- 266634 inside intron 107 disjoint 0.00966
AKAP2
chrl5 94686085 94687818 1.33256 -0.0655 66.1928 NR2F2 11136 downstream -548 disjoint 0.00966 chrl4 64239302 64240573 1.82985 -0.0939 65.9892 PLE HG3 372 promoter 56 disjoint 0.00966 chrl6 71654610 71657245 1.01951 -0.0039 65.925 ATBF1 14836 upstream 0 overlap 0.00966 chrl2 128900598 128903997 0.11442 1.39687 65.8968 TMEM132D 50168 inside intron 1639 disjoint 0.00966 chrl2 6531060 6534095 0.50762 1.47267 65.1372 HOM-TES- 1394 inside intron 591 disjoint 0.00967
103
chr7 27108771 27111401 1.43041 0.32973 64.7024 HOXA2 0 overlaps 5' 0 cover 0.00967 chrX 39892632 39895474 0.99317 0.08119 64.6558 BCOR 51033 upstream 389 disjoint 0.00967 chrl6 56717685 56719709 -0.2587 1.1731 64.6029 C16orf80 1087 inside intron 546 disjoint 0.00967 chr3 159301979 159303873 1.61559 0.26972 64.4739 SHOX2 0 overlaps 5' 50 disjoint 0.00968 chr3 148619648 148621588 1.43016 0.17678 64.4629 ZIC1 9778 downstream 0 overlap 0.00968 chr9 137248246 137249687 0.27087 2.30976 63.9281 OLFMl 141255 downstream 26184 disjoint 0.00968 chr4 111768053 111770595 1.18817 0.21615 63.5604 PITX2 7361 inside intron 0 cover 0.00969 chrl5 94696690 94698221 1.74275 0.15249 63.5574 R2F2 21741 downstream 0 overlap 0.00969 chr8 61996185 61997897 1.3558 -0.0145 63.1492 CHD7 242293 downstream 0 overlap 0.00969
Figure imgf000039_0001
chr9 21978825 21980586 1.19067 -0.0463 56.4994 CDKN2A 3903 inside intron 0 cover 0.0098 chrl2 113316530 113318351 1.45736 0.1834 56.4495 TBX5 7734 covers exon(s) 0 overlap 0.0098 chrl6 49141142 49143727 0.34147 1.16101 56.4337 KD1 1401 inside intron -176 disjoint 0.0098 chr5 72775112 72777080 1.19247 0.06924 56.3592 F0XD1 3027 downstream 0 cover 0.00981 chrX 142546718 142548898 0.10972 1.07845 56.269 SLITRK4 1786 inside intron 178 disjoint 0.00981 chr8 37675489 37677287 1.35389 0.16439 56.0782 ZNF703 3031 overlaps 3' 0 overlap 0.00981 chr7 158068383 158070253 0.66736 1.81877 56.0767 PTPRN2 2925 inside intron 1836 disjoint 0.00981 chr2 200041154 200044204 1.02361 0.25864 55.9753 FLJ32063 0 overlaps 5' 0 cover 0.00982 chrlO 3813870 3815492 0.00644 1.26678 55.7484 KLF6 1962 overlaps exon 0 overlap 0.00982 upstream
chrl l 114876746 114878334 1.74804 0.51166 55.6546 IGSF4 1990 inside intron 450 disjoint 0.00982 chrl3 20185184 20187236 0.36726 1.43634 55.6478 IL17D 9703 inside intron 6375 disjoint 0.00982 chr5 77181062 77182901 1.73579 0.60298 55.4367 TBCA 73122 upstream 0 overlap 0.00983 chrX 39750776 39752664 1.16205 0.02782 55.3684 BCOR 88935 downstream 0 inside 0.00983 chrlO 94440466 94442754 0.99776 0.10224 55.3418 HHEX 787 covers exon(s) 0 cover 0.00983 chr8 4841642 4843066 0.58209 1.86405 55.3406 CS D1 1907 promoter -1599 disjoint 0.00983 chrl 196155703 196157454 1.25401 0.05546 55.2972 LHX9 2564 covers exon(s) 0 cover 0.00983 chrl 75365070 75367347 0.56096 1.5762 55.2219 LHX8 0 overlaps 5' 1054 disjoint 0.00983 chrl 7 599301 15 59931897 -0.439 0.92545 55.1608 DDX5 971 covers exon(s) 44 disjoint 0.00984 chrlO 73438670 73440692 0.43014 1.43035 55.155 CHST3 44545 inside exon -285 disjoint 0.00984 chr2 66658293 66660266 1.23847 0.09146 54.5373 MEIS1 142258 downstream 0 overlap 0.00985 chrl2 84195829 84197592 1.22379 0.11766 54.4783 CART1 423 promoter 417 disjoint 0.00986 chrl 8 13859288 13861718 -0.0466 0.93388 54.4326 MC2R 43816 downstream -262 disjoint 0.00986 chrl l 19692927 19694024 0.18092 2.13556 54.2561 NAV2 1440 inside intron -1031 disjoint 0.00986 chr3 159297680 159299809 1.10678 0.16564 53.8348 SHOX2 3710 overlaps exon 0 cover 0.00988 upstream
chr7 42233206 42234299 1.65379 -0.2001 53.741 GLI3 3787 upstream 0 overlap 0.00988 chr5 92954197 92956167 1.37442 0.23729 53.6982 NR2F1 9399 overlaps 3' 0 cover 0.00989 chrlO 100985942 100987462 1.19301 -0.0202 53.6075 HPSE2 334 promoter -1764 disjoint 0.00989 chrl 3 111906549 111908881 -0.0368 0.86201 53.5765 SOX1 136636 downstream -9327 disjoint 0.00989 chrl2 121002249 121004619 0.23984 1.19255 53.5592 MLXIP 1107 inside intron -659 disjoint 0.00989 chrlO 21836151 21837774 1.57209 0.12323 53.4981 FLJ45187 16842 downstream 0 overlap 0.00989 chr5 140599551 140601126 0.55697 1.84686 53.4415 PCDHB15 4204 upstream 0 overlap 0.0099 chrX 128919355 128921597 1.04538 0.04537 53.3685 BCORL1 22752 upstream -46 disjoint 0.0099 chrl l 62230533 62231948 1.33551 0.02605 53.2764 BSCL2 0 overlaps 5' 0 overlap 0.0099 chrl 212223691 212225235 1.46707 0.10706 53.1784 PROXl 3247 upstream 114 disjoint 0.0099 chr7 27139140 27140714 1.60669 0.46243 52.9903 HOXA4 2217 promoter -1977 disjoint 0.00991 chrl 7 44157441 44159979 0.35211 1.07851 52.8932 HOXB13 1130 overlaps exon 0 cover 0.00991 upstream
chr22 26528421 26530163 1.32306 0.03409 52.7837 M 1 936 promoter 0 overlap 0.00992 chrl 9 3314942 3316440 2.01568 0.17507 52.4622 NFIC 4327 inside intron 1303 disjoint 0.00993 chrl5 35183438 35184463 1.64539 -0.1365 52.2805 MEIS2 2647 upstream -1898 disjoint 0.00994 chr2 174905608 174907523 1.25848 0.16283 52.2489 FLJ46347 3016 overlaps 3' 186 disjoint 0.00994 chr5 115934805 115936290 1.35644 0.05542 52.229 SEMA6A 2107 inside intron 6 disjoint 0.00994 chrl5 94667566 94669626 1.08425 0.03879 52.22 R2F2 5323 upstream 0 overlap 0.00994 chr20 2436261 2437534 -0.2219 1.43188 52.1949 ZNF343 243 overlaps exon 0 overlap 0.00994 downstream
chr4 174664434 174666750 1.5136 0.35561 52.1861 HAND2 21202 downstream 0 cover 0.00994 chrl 112853554 112854782 1.61085 0.09865 51.8868 NT2B 166 overlaps exon 0 overlap 0.00995 downstream chr9 102276338 102277667 1.71233 0.25285 51.8343 TMEFF1 801 inside intron 0 overlap 0.00995 chr22 36S28744 36530199 1.21846 -0.0042 51.8264 H1F0 860 promoter 419 disjoint 0.00995 chrl9 16049883 16051512 -0.1787 1.11299 51.5279 TPM4 1559 inside intron -608 disjoint 0.00996 chrl 154961985 154963849 0.75971 1.95945 51.4944 ISG20L2 479 overlaps exon 886 disjoint 0.00997 downstream
chrl 232809675 232810844 0.04085 1.59277 51.4714 IRF2BP2 1049 overlaps exon 55 disjoint 0.00997 upstream
chrl 63558079 63560262 1.02026 0.20334 51.4319 FOXD3 1055 promoter 0 inside 0.00997 chrl 7 8868117 8869432 1.1291 -0.3653 51.3635 NTN1 2534 inside intron -472 disjoint 0.00997 chr7 157223669 157225153 0.6357 1.99499 51.1943 PTPRN2 848025 inside intron -4167 disjoint 0.00998 chrl l 65377239 65378964 0.76123 1.73521 51.0459 FLJ30934 19254 overlaps 3' 2107 disjoint 0.00998 chr3 148623313 148624902 1.21214 0.06867 50.8782 ZIC1 13443 downstream 0 overlap 0.00999 chrX 48659428 48660766 1.37332 -0.0828 50.841 PM2 461 covers exon(s) 0 overlap 0.00999 chrl l 2454351 2458944 0.5673 1.53775 50.7595 CNQ1 .15092 inside intron -30957 disjoint 0.01 chr4 4916646 4917818 1.81875 0.35551 50.7099 MSX1 4347 downstream 0 cover 0.01 chrl9 36538760 36539881 1.57239 -0.2933 50.5547 TSHZ3 76746 upstream 0 overlap 0.01001 chrl 6 85104214 85106488 0.78389 -0.1565 50.3582 F0XF1 2581 overlaps 3' -81 disjoint 0.01002 chr5 146810975 146812734 1.2388 0.12592 50.2454 DPYSL3 718 inside intron 19 disjoint 0.01002 chr20 48161089 48162228 -0.1279 1.42541 50.1698 UBE2V1 888 inside intron 447 disjoint 0.01003 chrl 7 73467252 73468526 1.43173 -0.1873 50.1518 FLJ45079 75489 upstream 0 overlap 0.01003 chr2 121212263 121214242 1.15321 0.21032 50.1503 GLI2 52084 upstream -559 disjoint 0.01003 chrlO 80872601 80873991 0.24961 1.77503 50.1405 C10orf56 1394 inside intron 467 disjoint 0.01003 chrl9 4861736 4863369 0.31062 1.47856 50.0095 UHRF1 171 overlaps exon -480 disjoint 0.01003 downstream
chr2 172654276 172657216 0.83084 0.17064 49.9914 MAP1D 81227 downstream 0 cover 0.01003 chr8 49631687 49633069 0.45079 1.66032 49.9832 EFCAB1 177274 downstream -175 disjoint 0.01003 chr8 104453246 104454370 0.11138 1.80831 49.8895 CTHRC1 285 inside intron 0 overlap 0.01004 chrl 3 29319130 29320231 0.04784 1.69931 49.6246 UBL3 1928 inside intron 1690 disjoint 0.01005 chrl 4 68511652 68513866 0.3418 1.79059 49.5043 ACTN1 1842 inside intron 526 disjoint 0.01006 chrll 64949337 64950620 -0.1418 1.33801 49.4702 F SG44 38639 downstream -1703 disjoint 0.01006 chrl l 111314453 111315784 0.06384 1.42598 49.3854 DKDC1 1317 inside intron -1040 disjoint 0.01006 chrl5 35173578 35174610 1.6618 -0.1706 49.3361 ME1S2 3184 covers exon(s) 68 disjoint 0.01006 chr7 27100171 27101400 1.69482 0.30412 49.3096 HOXAl 749 overlaps exon 0 cover 0.01006 upstream
chrl5 65142450 65144358 1.57196 0.15905 49.3052 SMAD3 890 promoter 35 disjoint 0.01006 chrl 24615289 24616878 0.29523 1.41359 49.2588 NPAL3 385 inside intron 0 overlap 0.01007 chrl 2 88272358 88274228 1.74752 0.49034 49.2357 DUSP6 1932 promoter -83 disjoint 0.01007 chr9 21994772 21996026 1.61604 -0.0545 49.163 CDKN2B 3285 inside exon 0 overlap 0.01007 chrlO 45192522 45194063 0.09116 1.42715 48.9679 ALOX5 2888 inside intron -2360 disjoint 0.01008 chrl6 55197586 55199577 -0.0886 1.43578 48.8995 MT2A 434 promoter 53 disjoint 0.01008 chr21 46384247 46386486 2.01393 0.35303 48.8469 FTCD 13422 inside intron 3227 disjoint 0.01009 chr2 85215427 85217577 1.46325 0.64813 48.7075 TCF7L1 1183 inside intron 0 overlap 0.01009 chrl 9 62041705 62043172 0.52591 1.69129 48.439 PEG3 703 inside intron 0 cover 0.0101 1 chr20 44314659 44316212 0.42488 1.51891 48.2876 CDH22 919 promoter -964 disjoint 0.01012 chr4 54669050 54671099 1.24745 0.25919 48.2833 GSH2 8096 downstream 0 cover 0.01012 chrl 7 75364760 75365932 1.49355 -0.028 48.2296 CBX2 655 promoter 41 disjoint 0.01012 chr6 10512897 10514243 1.44595 0.08679 48.2178 TFAP2A 6349 overlaps exon 0 overlap 0.01012 upstream
chr5 154218603 154220032 -0.0008 1.40761 48.18 CNOT8 213 inside intron -48 disjoint 0.01012 chr7 71437052 71438389 0.62399 2.02807 48.1647 CALM 1506 inside intron 304 disjoint 0.01012 chrl4 68326043 68327713 0.04711 1.20255 48.0164 ZFP36L1 1824 overlaps exon 0 cover 0.01013 upstream
chr20 56237388 56238774 1.34383 -0.0655 47.9763 PPP4R1L 79126 downstream 0 overlap 0.01013 chrl l 63284462 63286480 1.50289 0.18033 47.845 RTN3 78965 downstream 0 overlap 0.01014 chr3 148587710 148589395 1.12131 0.12533 47.814 ZIC4 17701 overlaps exon 1803 disjoint 0.01015 upstream
chrl9 51166677 51168019 0.13824 1.49481 47.7333 N0VA2 477 inside intron -18334 disjoint 0.01015 chr7 26159244 26160595 1.38347 0.02639 47.7309 NFE2L3 860 inside intron 0 overlap 0.01015 chr2 85967189 85968460 0.63764 1.88003 47.7097 ST3GAL5 1207 inside intron 641 disjoint 0.01015 chr7 2619831 2621420 0.65493 1.68829 47.708 IQCE 54674 downstream -7540 disjoint 0.01015 chrl6 85161572 85162895 1.29119 -0.0094 47.6848 F0XC2 3130 downstream -1422 disjoint 0.01015 chr4 100795321 100796316 0.43582 2.17144 47.6842 TTP 80318 downstream -1644 disjoint 0.01015 chrl8 33316010 33317572 0.00331 1.29611 47.6371 BRUNOL4 82368 inside intron 1465 disjoint 0.01016 chrl 144218454 144219982 0.31996 1.4043 47.6362 RBM8A 0 overlaps 5' 0 cover 0.01016 chr5 140836087 140837886 0.28333 1.53292 47.5866 PCDHGC3 335 inside exon 0 overlap 0.01016 chrl 3 21139884 21141497 1.23723 0.12315 47.5639 FGF9 2377 promoter 0 overlap 0.01016 chrl l 65947076 65948629 1.07597 2.15596 47.5296 NPAS4 2026 covers exon(s) -1103 disjoint 0.01016 chrl l 128065552 128067519 0.99249 0.03186 47.4057 FLU 1679 promoter 0 overlap 0.01017 chr2 119322444 119323646 1.54282 0.22197 47.1231 E 1 216 promoter 0 cover 0.01019 chrl 9 35406456 35407967 1.08313 -0.1992 47.1117 ZNF536 147200 upstream 0 cover 0.01019 chr5 42985056 42986927 0.8512 1.80006 47.1079 LOC389289 89170 downstream 0 overlap 0.01019 chrl6 25612389 25613926 -0.1962 0.94681 47.1047 HS3ST4 1542 inside intron -257 disjoint 0.01019 chrl 8 2643078 2645111 0.92297 -0.189 46.9281 NTC2 81474 downstream 0 overlap 0.0102 chrl 8 11839761 11841153 -0.2831 0.99285 46.7679 GNAL 97576 inside intron 56 disjoint 0.01021 chr6 136911271 136912368 1.7301 0.36581 46.6875 MAP7 1116 inside intron 151 disjoint 0.01022 chrl8 74370980 74372432 0.64784 1.81046 46.6361 SALL3 468830 upstream -3539 disjoint 0.01022 chr22 38247466 38249243 0.02116 1.74166 46.4535 ATF4 952 overlaps 3' -327 disjoint 0.01023 chrl2 31366318 31368093 1.01934 -0.0392 46.383 FAM60A 2246 inside intron 0 overlap 0.01024 chr5 139470739 139472466 1.21865 0.18537 46.2995 PURA 1425 promoter 441 disjoint 0.01024 chr4 77351885 77353546 0.24803 1.32244 46.2718 SCARB2 512 inside intron 44 disjoint 0.01024 chrlS 94688398 94689954 1.15518 0.10023 46.2105 NR2F2 13449 downstream 0 cover 0.01025 chrl 219130962 219132836 1.58279 0.50041 46.1769 HLX1 11581 downstream 0 cover 0.01025 chr2 102603564 102606728 0.39989 1.55903 46.0904 SLC9A2 967 inside intron -578 disjoint 0.01026 chrl 219117308 219118671 1.43318 0.1014 46.0126 HLX1 710 promoter 0 overlap 0.01026 chrlO 126417881 126419316 1.55824 0.32551 45.9617 FAM53B 3603 inside intron 1988 disjoint 0.01026 chrlO 76835584 76837101 1.47141 0.37149 45.9483 ZNF503 4154 upstream 0 inside 0.01026 chrl l 2459860 2461470 1.11527 2.27987 45.8205 KCNQ1 20601 inside intron -36466 disjoint 0.01027 chrl 219121580 21912352S 1.33706 0.30553 45.8027 HLX1 2199 covers exon(s) 0 cover 0.01027 chr6 28661906 28664051 0.98678 0.12685 45.7764 ZNF452 0 overlaps 5' 0 cover 0.01027 chr6 1329630 1331219 1.27957 0.29247 45.6819 F0XF2 3848 upstream 0 overlap 0.01028 chr3 148607740 148609393 1.04585 0.08319 45.6565 ZIC1 477 promoter 282 disjoint 0.01028 chrl 21373594 21374664 -0.0773 1.44373 45.6307 EIF4G3 1262 inside intron 1038 disjoint 0.01028 chrl3 112671693 112673042 -0.0106 1.29128 45.5867 MCF2L 31026 upstream -32 disjoint 0.01028 chrl 8 18006348 18007622 1.49016 0.23787 45.5428 GATA6 2935 inside intron 0 overlap 0.01028 chrl7 56834728 56836686 1.11734 0.09083 45.5135 TBX2 2690 covers exon(s) 0 inside 0.01029 chrl l 2094292 2096809 0.02455 0.85209 45.4979 IGF2 19970 downstream 13800 disjoint 0.01029 chrl 7 697181 15 69719966 1.849 0.49108 45.4751 RPL38 6726 downstream 103 disjoint 0.01029 chrl2 128952367 128953608 -0.0689 1.29665 45.4605 TMEM132D 557 inside intron 0 overlap 0.01029 chrl 6 53921949 53923469 1.33392 0.21606 45.3147 IRX6 5978 overlaps 3' 0 cover 0.0103 chr7 90486175 96488318 0.96648 0.17523 45.2871 DLX5 3760 overlaps 3' 0 overlap 0.0103 chrl9 40306476 40307366 0.4186 2.28008 45.2641 FXYD3 7838 overlaps 3' 0 overlap 0.0103 chrl 4 60188120 60189818 0.94113 -0.0077 45.2593 SKI 2188 promoter -1815 disjoint 0.0103 chr22 44842676 44844235 -0.1443 1.01606 45.249 C22or£26 13989 upstream 405 disjoint 0.0103 chr7 96488760 96490171 1.28929 0.15148 45.2277 DLX5 1907 covers exon(s) 0 overlap 0.0103 chrl2 128961185 128962628 0.14092 1.64136 45.1851 TMEM132D 7020 upstream -6093 disjoint 0.01031 chr5 178980948 178982027 -0.0266 1.56215 45.1434 HNRPH1 1248 overlaps exon 394 disjoint 0.01031 upstream
chrl8 52963741 52965315 -0.0673 2.05326 45.079 WDR7 494128 downstream -23549 disjoint 0.01031 chr2 63132869 63134574 1.39985 0.39203 44.9938 OTX1 1401 covers exon(s) 0 overlap 0.01032 chr6 101020166 101021773 1.17303 0.13573 44.8811 SMI 1895 promoter 0 overlap 0.01033 chrlO 102485639 102487566 0.86061 0.0674 44.8699 PAX2 7755 upstream 0 overlap 0.01033 chr8 68139975 68141466 0.2847 1.56861 44.8163 CSPP1 819 inside intron 0 overlap 0.01033 chr2 100088245 100089913 1.14828 0.28393 44.6781 AFF3 35555 covers exon(s) -1072 disjoint 0.01034 chrl2 121944829 121946259 0.36106 1.45902 44.6737 VPS37B 405 inside intron 27 disjoint 0.01034 chrl l 65839109 65840137 0.59089 2.06085 44.5593 CD248 953 inside exon 11 disjoint 0.01035 chrlO 124217984 124218979 0.07493 1.74217 44.5166 HTRA1 6938 inside intron -5754 disjoint 0.01036 chrll 2255031 2256440 0.29168 1.50243 44.5164 ASCL2 6274 upstream -5523 disjoint 0.01036 chrl8 22385090 22386161 1.2951 -0.2049 44.5075 CTD1 88144 inside intron 0 overlap 0.01036 chr3 148595418 148596664 1.29336 0.00524 44.4691 ZIC4 10432 overlaps exon 0 overlap 0.01036 downstream
chr7 27106893 27108098 1.38657 0.1236 44.446 HOXA2 820 overlaps exon 1608 disjoint 0.01036 upstream
chrl7 44032842 44034189 1.21791 0.07811 44.2628 HOXB6 3143 inside intron -2254 disjoint 0.01038 chrl5 91430517 91432119 0.64264 1.66107 43.8966 RGMA 1317 inside intron 313 disjoint 0.01041 chrl7 41332227 41334492 0.4412 1.53568 43.8828 MAPT 4604 inside intron -1391 disjoint 0.01041 chrl9 61846610 61847539 0.41423 2.20962 43.8581 BC37295J 28518 downstream 0 overlap 0.01041 chrl4 60179443 60180892 1.00185 -0.1265 43.856 SKI 5040 downstream 0 overlap 0.01041 chr2 176693206 176694483 1.33241 0.15382 43.8386 HOXD10 3469 downstream 187 disjoint 0.01041 chr4 174658869 174660227 1.80427 0.64075 43.8051 HAND2 27725 downstream 0 overlap 0.01041 chr2 10140898 10142002 0.71531 2.1407 43.5682 CYS1 2910 upstream -2431 disjoint 0.01044 chr3 148612483 148614283 1.15974 0.12741 43.4782 ZIC1 2613 covers exon(s) 0 cover 0.01044 chrl 226337893 226339239 0.10945 1.32534 43.4704 ARF1 420 inside intron 0 overlap 0.01044 chr5 11954677 11956181 0.52735 1.82393 43.4335 CTN D2 928 inside intron 369 disjoint 0.01045 chr9 97316427 97317424 1.6997 -0.0294 43.4224 PTCH1 5776 upstream 525 disjoint 0.01045 chrl4 100421431 100422503 0.38961 1.72367 43.3543 FLJ41170 118894 upstream -1818 disjoint 0.01046 chr5 16235250 16237106 0.09221 1.63234 43.3422 FBXL7 681946 downstream -1830 disjoint 0.01046 chr2 200038503 200039607 1.45609 0.05881 43.2151 FLJ32063 3256 upstream -577 disjoint 0.01047 chrl 8 18000005 18002227 0.62113 -0.0968 43.1511 GATA6 1186 promoter 0 inside 0.01048 chrlO 364830 365864 0.27044 1.79583 43.1495 D1P2C 359741 covers exon(s) -1671 disjoint 0.01048 chrl4 22377894 22378994 0.21578 1.94591 43.1494 MMP14 2262 inside intron -1041 disjoint 0.01048 chr9 93221086 93222437 0.01925 1.36027 42.8922 NFIL3 3527 inside intron 791 disjoint 0.0105 chrl l 2083522 2085639 0.35196 1.3237 42.8903 IGF2 31140 downstream 24970 disjoint 0.0105 chr6 108548088 108549767 1.48137 0.34872 42.8653 NR2E1 44187 upstream -187 disjoint 0.0105 chr7 152249022 152250823 0.18013 2.26507 42.8326 ACTR3B 161239 downstream 2026 disjoint 0.0105 chr2 156887086 156888744 1.32301 0.37998 42.6987 NR4A2 8701 downstream -1494 disjoint 0.01052 chr5 172128592 172129940 0.25061 1.61067 42.5641 DUSP1 868 covers exon(s) 148 disjoint 0.01053 chr4 175371182 175372843 0.91501 0.09409 42.5446 FBX08 69133 downstream 0 cover 0.01053 chr8 102575528 102576610 1.67529 0.13477 42.5191 G HL2 1367 inside intron 0 overlap 0.01053 chr7 27193622 27195131 1.26244 0.26489 42.3805 H0XA11 2263 promoter 0 overlap 0.01055 chrl 7 44011443 44013237 0.82209 -0.0397 42.3208 HOXB4 702 promoter 710 disjoint 0.01055 chr5 131588689 131589828 0.27587 1.71751 42.2544 P4HA2 1005 inside intron 1165 disjoint 0.01056 chrl9 36534725 36535858 1.18744 -0.0912 42.0956 TSHZ3 72711 upstream 0 overlap 0.01058 chrl l 6632319 6633173 0.12562 1.806 42.0898 DCHS1 476 inside intron 0 overlap 0.01058 chr9 127546747 127548067 0.36219 1.53293 42.0559 PBX3 1419 promoter 75 disjoint 0.01058 chr20 3614657 3615955 0.27093 1.97596 42.0283 SIGLECl 19819 overlaps 3' -3470 disjoint 0.01058 chr9 101626732 101628042 1.30229 0.12471 42.0049 NR4A3 2775 covers exon(s) 0 overlap 0.01058 chr5 175019341 175020506 0.77754 2.31933 41.9102 HRH2 21811 upstream -979 disjoint 0.01059 chr2 45020211 45021965 1.12191 0.21817 41.9081 S1X3 575 promoter -140 disjoint 0.01059 chr7 96469441 96470935 1.26733 0.18407 41.876 DLX6 2290 promoter 0 overlap 0.01059 chrl6 52874059 52875660 1.18767 0.15643 41.8137 IRX3 2218 overlaps 3' 0 inside 0.0106 chrl l 62064168 62066467 0.62419 1.67007 41.7957 AHNAK 4440 inside intron 3391 disjoint 0.0106 chr2 24566005 24567024 2.25344 0.56666 41.7419 NCOA1 93825 upstream 190 disjoint 0.01061 chr3 148589491 148590632 1.3465 0.05478 41.7359 ZIC4 16464 inside intron 566 disjoint 0.01061 chr5 140593852 140595195 0.27731 1.68325 41.6801 PCDHB14 10591 downstream 380 disjoint 0.01061 chr2 45012649 45013792 1.38201 0.10621 41.6787 SK3 8748 upstream 0 cover 0.01061 chr22 38380505 38384729 0.58223 1.59126 41.6556 CACNA1I 83802 covers exon(s) 3158 disjoint 0.01061 chr5 174090464 174091807 1.27887 0.15333 41.6377 MSX2 6284 overlaps 3' 0 overlap 0.01062 chrl2 56522327 56524562 0.34479 1.31772 41.6284 CTDSP2 2451 inside intron 545 disjoint 0.01062 chrl2 107774108 107775136 0.16425 1.59017 41.5861 SSH1 343 inside intron 198 disjoint 0.01062 chr6 3403467 3404909 1.61211 0.34822 41.4782 C6orf85 13251 upstream -505 disjoint 0.01063 chr8 65652483 65654003 0.90668 -0.1352 41.4705 BHLHB5 1364 promoter 0 cover 0.01063 chr5 140582954 140584599 0.04349 0.98875 41.3638 PCDHB14 0 overlaps 5' 38 disjoint 0.01064 chr8 49995012 49996167 -0.0331 1.2553 41.2278 SNAI2 373 overlaps exon 2373 disjoint 0.01066 upstream
ehrl7 26911860 26913311 0.1525 1.14231 41.2138 RAB11FIP4 169093 downstream -370 disjoint 0.01066 chrlO 21843789 21845417 0.78013 -0.2957 41.2013 FLJ45187 9199 inside exon 0 overlap 0.01066 chrlO 85947519 85948923 0.61014 1.97987 41.1634 PCDH21 3023 covers exon(s) -2236 disjoint 0.01067 chr4 142274147 142275533 0.16617 1.37429 41.1539 RNF150 82 promoter -96 disjoint 0.01067 chr5 92960059 92961324 1.25343 0.06305 41.1326 NR2F1 15261 downstream -3473 disjoint 0.01067 chr4 151722068 151723752 1.25692 0.14422 41.1325 MAB21L2 0 overlaps 5' 0 overlap 0.01067 chrl2 33481603 33482952 0.39929 1.51302 41.1177 SYT10 1068 inside intron 78 disjoint 0.01067 chrl4 92649334 92650885 1.3384 0.56075 40.8955 ΓΓΡΚ1 1094 inside intron 0 overlap 0.0107 chr5 43055099 43056561 1.18682 0.15051 40.7996 LOC389289 19536 downstream -674 disjoint 0.01071 chrl7 34081606 34083158 1.08359 -0.0203 40.7946 MLLT6 32242 upstream 60 disjoint 0.01071 chr5 158454922 158456752 1.42502 0.50981 40.7457 EBF1 2594 covers exon(s) 0 overlap 0.01071 chr5 92950347 92951623 1.38288 0.25877 40.7425 NR2F1 5549 inside intron -94 disjoint 0.01071 chrl 2151726 2153465 0.30301 1.19418 40.7048 SKI 1733 inside intron -693 disjoint 0.01071 chr4 151719147 151721384 0.88977 0.15766 40.6926 LRBA 434714 inside intron 0 cover 0.01072 chrH 60177484 60178791 1.28526 0.11843 40.6851 SKI 7141 downstream 0 overlap 0.01072 chrl 153332249 153333791 0.53221 1.64972 40.681 EFNA3 14278 downstream -7569 disjoint 0.01072 chrl 14092541 14093954 0.87338 2.00679 40.5273 PRD 2 188605 downstream -217 disjoint 0.01073 chrl l 44291089 44292576 1.16817 0.04798 40.5162 ALX4 2798 upstream 1697 disjoint 0.01074 chr2 222866029 222867565 1.14836 0.13529 40.4134 PAX3 4378 overlaps 3' 404 disjoint 0.01075 chr7 1250362 1251934 1.25982 0.31793 40.393 ZFAND2A 84039 upstream 0 cover 0.01075 chr8 124353201 124354868 0.11616 0.94936 40.3805 ZHX1 859 inside intron 522 disjoint 0.01075 chr8 143641112 143642674 1.77903 3.0107 40.3418 BAI1 98734 downstream 0 overlap 0.01076 chr8 98857940 98859531 1.54903 0.08209 40.2483 LAPTM4B 956 inside intron 0 overlap 0.01077 chr8 10502847 10503905 0.48821 1.96814 40.2163 RP1L1 46121 inside exon 3300 disjoint 0.01077 chr8 145906695 145908094 0.24476 1.28553 40.148 ZNF34 68374 downstream 1207 disjoint 0.01078 chr9 108660922 108662603 1.28277 0.11675 40.1363 ZNF462 2595 upstream 0 overlap 0.01078 chr2 45030986 45032557 1.32331 0.18107 39.9246 SDG 8446 downstream -218 disjoint 0.01081 chr7 100401572 100403451 0.67643 1.56597 39.8515 MUC17 46632 upstream -5059 disjoint 0.01082 chr3 148614644 148615960 1.04213 -0.0236 39.847 ZIC1 4774 inside exon -624 disjoint 0.01082 chr22 26520905 26522019 1.22272 -0.2684 39.7985 MN1 5466 inside intron 774 disjoint 0.01082 chr20 44094989 44097515 0.20185 1.22891 39.7555 SLC12A5 3745 covers exon(s) -634 disjoint 0.01083 chr3 73753052 73755720 0.30221 1.6001 39.7533 PDZRN3 1041 inside intron 197 disjoint 0.01083 chrS 134853320 134855179 1.08723 0.2283 39.733 C5orf20 42384 upstream 0 overlap 0.01083 chr22 46984494 46985879 0.43917 1.52577 39.6472 LOC388915 69030 downstream -323 disjoint 0.01085 chrl 215380037 215381312 1.37441 0.22506 39.5903 ESRRG 50439 upstream -1641 disjoint 0.01085 chrl l 1976903 1978269 1.65339 0.62395 39.5713 MRPL23 51790 downstream -464 disjoint 0.01086 chr5 174091829 174093575 1.19614 0.29535 39.5382 MSX2 7649 downstream 0 overlap 0.01086 chr 118489681 118491029 0.21852 1.50273 39.4159 TRM32 252 inside intron -93 disjoint 0.01087 chrl6 50228057 50229193 1.73537 0.25675 39.3539 SALL1 485405 upstream -480296 disjoint 0.01088 chrl 7 58135932 58137150 1.1015 -0.144 39.2812 RNF190 102276 covers exon(s) -266 disjoint 0.01088 chrlO 132997345 132999071 0.03844 0.93349 39.2626 TCERG1L 902 covers exon(s) 112 disjoint 0.01089 chr9 134807029 134809290 0.03507 0.85225 39.2283 TSC1 550 inside intron 57 disjoint 0.01089 chrl l 32869188 32870223 1.34516 -0.1033 39.1553 QSER1 1144 promoter 342 disjoint 0.0109 chrl 47672083 47674387 1.17925 0.32331 39.1185 F0XD2 0 overlaps 5' 0 cover 0.0109 chrlO 112248499 112249707 1.23622 0.15638 39.1002 DUSP5 885 inside intron 0 overlap 0.01091 chrl 6 7076622 7077449 -0.099 1.7391 39.0474 A2BP1 1067490 inside intron 216885 disjoint 0.01091 chr4 151723846 151725012 1.39314 0.19975 39.0414 AB21L2 1094 inside exon 0 overlap 0.01091 chrl2 109959973 109961693 0.63884 1.45376 39.0321 CUTL2 3762 inside intron -348 disjoint 0.01092 chrlO 102750534 102751247 0.11114 2.02117 38.9655 LZTS2 3580 inside intron -746 disjoint 0.01092 chr6 30525270 30526796 0.44254 1.50658 38.9552 HLA-E 38453 upstream 27 disjoint 0.01092 chr4 154075001 154076524 1.34272 0.11445 38.938 KIAA1727 7060 upstream 38 disjoint 0.01093 chrlO 120958275 120959771 0.06236 1.0578 38.9138 GRK5 1089 inside intron -662 disjoint 0.01093 chr5 140206443 140207435 0.20457 1.62685 38.8475 PCDHA8 5353 inside intron 878 disjoint 0.01094 chrl 162810850 162812191 1.77442 0.61415 38.819 PBX1 15290 inside intron 0 overlap 0.01094 chrl l 61198697 61200132 0.08916 1.08036 38.8038 Cl lorfll 4353 upstream 4043 disjoint 0.01094 chr2 176745452 176746590 1.40867 0.13565 38.772 HOXD3 8402 overlaps 3' 0 overlap 0.01095 chrl2 52727647 52728611 1.36481 -0.0388 38.7676 HOXC4 30739 inside intron 0 overlap 0.01095 chr2 156894396 156895491 1.72109 0.47179 38.7569 NR4A2 1954 overlaps two exons 0 overlap 0.01095 chrX 39835006 39835901 1.29091 -0.3274 38.725 BCOR 5698 inside intron 0 overlap 0.01095 chr4 111771023 111772570 1.12853 0.20757 38.6728 PITX2 5386 inside intron 0 overlap 0.01096 chr20 30814996 30816575 1.06788 -0.0398 38.6589 DNMT3B 1145 inside intron -72 disjoint 0.01096 chr5 43080225 43081358 1.43833 0.26194 38.5694 LOC389289 4128 upstream -991 disjoint 0.01097 chrl2 113587900 113589921 1.09176 0.23519 38.5677 TBX3 16430 downstream 0 overlap 0.01097 chrl4 72427020 72428292 1.84662 0.07985 38.5541 DPF3 2301 inside intron 250 disjoint 0.01097 chr2 176686753 176688199 1.35789 0.20286 38.5341 HOXD10 1538 promoter 812 disjoint 0.01098 chrlO 118880692 118882737 0.75249 0.06562 38.5044 VAX1 5064 covers exon(s) 0 cover 0.01098 chr20 47329693 47331033 0.78629 -0.2734 38.4783 ZNFX1 1685 promoter -1087 disjoint 0.01098 chrl 166463289 166464283 0.60191 2.04872 38.4773 SFT2D2 1420 inside intron -826 disjoint 0.01098 chr5 68747086 68748117 1.46612 0.10138 38.4506 MARVELD2 377 inside intron 0 overlap 0.01099 chrl6 51139176 51140443 1.06034 -0.0743 38.4191 CHD9 506002 upstream -65 disjoint 0.01099 chr9 36811822 36812759 0.36578 2.10625 38.354 PAX5 211716 downstream 59191 disjoint 0.011 chrl4 23089148 23090035 1.15005 -0.336 38.3518 THTPA 5035 upstream 0 overlap 0.011 chrl8 71046179 71047460 1.03034 -0.2613 38.3019 ZADH2 2644 inside intron 0 overlap 0.011 chr3 55497870 55499430 1.26531 0.22187 38.2748 WNT5A 1500 promoter 0 overlap 0.01101 chr4 78960871 78961788 0.03104 1.56294 38.1327 CN0T6L 1304 promoter -292 disjoint 0.01103 chr!9 54067836 54069153 0.15324 0.96061 38.0919 PPP1R1SA 347 overlaps exon -96 disjoint 0.01103 upstream
chr4 81329335 81331039 1.25772 0.40574 38.067 PRDM8 4873 inside intron 0 overlap 0.01104 chr3 2116385 2117443 0.48319 1.75727 38.0497 CNTN4 0 overlaps 5' 0 overlap 0.01104 chr8 75388529 75389720 0.28868 1.46731 38.0232 JPH1 6396 overlaps exon 176 disjoint 0.01 104 downstream
chr2 119324413 119325418 1.46144 0.12115 38.0017 EN1 2185 promoter -33 disjoint 0.01105 chr21 46471032 46472171 0.25726 1.46415 37.933 LSS 947 covers exon(s) 448 disjoint 0.01106 chr7 142691474 142692970 1.84376 0.81518 37.9312 TMEM139 0 overlaps 5' 2199 disjoint 0.01106 chrl3 111753183 111754945 0.13224 1.05697 37.8799 S0X1 14968 upstream 860 disjoint 0.01107 chr7 113510693 113511796 1.24298 0.02266 37.8656 PPP1R3A 164394 upstream 364 disjoint 0.01107 chr21 45115931 45117025 0.39441 1.92466 37.843 PTTG11P 1143 inside intron 146 disjoint 0.01108 chr7 27247106 27248568 1.10705 0.04805 37.8423 EVX1 120 promoter 43 disjoint 0.01108 chr8 1089642 1090952 0.28144 1.39328 37.8115 DLGAP2 346023 upstream 1538 disjoint 0.01108 chr8 1388977 1390469 0.56455 1.57482 37.79 DLGAP2 46506 upstream 1822 disjoint 0.01108 chr5 76150933 76152517 1.07658 0.17056 37.7814 F2RL1 324 inside intron 0 cover 0.01109 chr2 3730279 3732512 0.32712 1.20509 37.7633 ALLC 10194 downstream -477 disjoint 0.01109 chrX 128895347 128896412 1.2981 0.01716 37.7604 UTP14A 27508 downstream -439 disjoint 0.01109 chr9 83495230 83496609 1.68738 0.48896 37.7167 TLE1 1815 promoter -409 disjoint 0.01109 chrl 146255765 146257981 1.28365 0.37911 37.6895 NBPF1 1146655 inside intron 0 cover 0.0111 chr6 10523611 10525546 1.10341 0.18275 37.6863 TFAP2A 2236 inside intron 0 overlap 0.0111 chrl 2 1623604 1625210 0.57647 1.71461 37.6161 WNT5B 14932 inside intron 48 disjoint 0.01111 chr6 134540510 134541505 0.27637 1.98596 37.6023 SGK 2816 upstream -1061 disjoint 0.01111 chr4 47181803 47183461 0.098 0.97298 37.5614 ATP10D 0 overlaps 5' -21227 disjoint 0.01111 chr6 170325183 170330016 0.47794 1.89242 37.5522 DLL1 111605 downstream 0 overlap 0.01112 chrl 2 24945810 24947103 1.36109 0.27184 37.5266 BCAT1 46395 covers exon(s) 0 overlap 0.011 12 chr3 64404333 64405446 0.09124 1.40784 37.4921 ADAMTS9 242958 downstream 176 disjoint 0.01112 chr20 54635424 54636825 0.93624 -0.1054 37.4569 TFAP2C 939 promoter 0 inside 0.01113 chr5 72563687 72564980 1.33661 0.28716 37.4408 TMEM174 63858 downstream 0 overlap 0.01113 chrl 2 119419267 119420682 -0.0735 0.94988 37.327 DYNLL1 1026 overlaps 3' -171 disjoint 0.01115 chr4 113651724 113652617 1.55186 0.05283 37.3179 NEUROG2 4159 downstream 0 overlap 0.01115 chr8 1494748 1496055 0.66482 1.79756 37.2992 DLGAP2 57773 inside intron 1202 disjoint 0.01115 chr3 161424439 161425541 1.82187 0.67369 37.2835 IFT80 174472 downstream 66 disjoint 0.01115 chr8 819298 820365 0.95379 2.38215 37.2386 ERICH1 148073 upstream 1879 disjoint 0.01116 chr5 98138671 98139704 0.11329 1.42468 37.2375 RGMB 5772 inside intron -464 disjoint 0.01116 chrl9 39954334 39955434 0.11966 1.56482 37.2144 ZNF599 514 covers exon(s) 54 disjoint 0.01116 chr4 124541651 124543101 0.52931 1.3997 37.1769 SPRY1 1519 overlaps exon -2203 disjoint 0.01117 upstream
chr3 4997378 4999158 0.21926 1.13892 37.1701 BHLHB2 1171 covers exon(s) -155 disjoint 0.01117 chr4 174667570 174669252 1.48981 0.49152 37.1108 HAND2 18700 downstream -134 disjoint 0.01118 chr6 31777467 31778888 -0.1092 0.71282 37.0848 BAT5 178 covers exon(s) 0 overlap 0.01 118 chrl4 103935048 103937957 0.18051 1.60718 37.048 LOC400258 179143 upstream 28992 disjoint 0.01119 chrl7 74915087 74916508 0.47516 1.48744 37.0215 LOC146713 15057 inside intron 55332 disjoint 0.01119 chrl3 92675166 92676682 1.04767 0.1 36.941 GPC6 413 promoter 564 disjoint 0.0112 chr7 81911773 81912703 1.67283 0.24077 36.9356 CACNA2D1 807 promoter -317 disjoint 0.0112 chr2 12713ΰ970 127132630 0.11555 1.05352 36.9266 GYPC 817 inside intron -329 disjoint 0.01121 chrl2 129470674 129471865 0.46427 1.60679 36.9236 R BP2 96497 inside intron 2865 disjoint 0.01121 chrl4 76567803 76568984 0.04615 1.1376 36.8749 C14orf4 3017 upstream 0 overlap 0.01122 chrl6 23221847 23223901 0.52924 1.42354 36.7787 SCNN1B 707 inside intron -400 disjoint 0.01 123 chrlO 101932883 101933842 -0.0525 1.35632 36.7743 SPFH1 1550 covers exon(s) 1719 disjoint 0.01123 chr5 168658530 168659838 0.34427 1.56 36.7459 SLIT3 715 inside intron 169 disjoint 0.01124 chrl5 24570773 24572559 0.55642 1.42044 36.6869 GABRB3 754 promoter -737 disjoint 0.01125 chrl7 35473694 35475396 -0.098 1.02775 36.6793 THRA 1106 inside intron -288 disjoint 0.01125 chrl l 2646034 2647827 1.05163 1.85502 36.671 KCNQ1 206775 inside intron 29159 disjoint 0.01125 chr3 54133429 54134743 0.48306 1.57379 36.6655 CACNA2D3 1697 inside intron -1364 disjoint 0.01125 chr9 19118195 19120085 1.91769 0.02064 36.6207 ADFP 623 promoter -315 disjoint 0.01126 chrl9 4406171 4408176 0.42975 1.18319 36.6002 UBXD1 613 inside intron 317 disjoint 0.01126 chrl4 37141243 37142700 0.61742 1.57975 36.5848 FOXA1 7004 upstream -2285 disjoint 0.01127 chr2 200039917 200040984 1.49279 0.2304 36.5718 FLJ32063 1879 promoter 948 disjoint 0.01127 chr9 14306422 14307922 1.18428 0.24592 36.561 FEB 2478 promoter -1071 disjoint 0.01127 chr6 168976802 168979285 0.97377 2.66133 36.5162 SMOC2 391923 downstream 5397 disjoint 0.01127 chr5 72546172 72547380 1.29745 0.1156 36.5045 TMEM174 46343 downstream 96 disjoint 0.01128 chrl7 34159709 34161124 0.92001 -0.107 36.452 PSMB3 1403 promoter 0 overlap 0.01129 chr20 39677712 39679423 -0.0031 0.83727 36.4491 CHD6 1123 inside intron 336 disjoint 0.01 129 chr4 125850864 125852360 0.12005 1.07723 36.4352 ANKRD50 0 overlaps 5' 480 disjoint 0.01129 chr8 10956020 10957608 0.84107 1.84807 36.3975 XKR6 138676 inside intron -1513 disjoint 0.0113 chrl2 107646995 107648200 -0.1713 0.88326 36.3608 COR01C 1223 inside intron 153 disjoint 0.0113 chr6 117690142 117691299 0.39178 1.58802 36.3234 VGLL2 2114 promoter 0 overlap 0.01131 chrl2 52962113 52963584 0.45572 1.69926 36.2069 H RPA1 1359 covers exon(s) -858 disjoint 0.01133 chrll 31774696 31775917 1.19997 0.10151 36.1578 PAX6 13516 inside intron 719 disjoint 0.01134 chr3 198959502 198960777 0.23002 1.47317 36.1559 FYTTD1 302 promoter 0 overlap 0.01134 chrl l 94522141 94523838 1.25607 0.10373 36.1257 SESN3 80055 downstream 0 cover 0.01134 chrl 152794931 152796794 0.10098 0.93237 35.992 UBE2Q1 949 covers exon(s) 511 disjoint 0.01137 chr3 171555291 171556181 1.53382 0.09563 35.9377 SKIL 2028 promoter 1296 disjoint 0.01138 chr7 35266150 35267955 0.9413 -0.0678 35.8777 TBX20 6384 upstream 0 overlap 0.01139 chrl2 47812143 47813501 0.13522 1.23111 35.8649 K-ALPHA-1 573 promoter -384 disjoint 0.01139 chr9 132579802 132580887 -0.0927 1.25665 35.86 ABL1 714 inside intron -1080 disjoint 0.01139 chrlO 62161484 62162843 1.00682 -0.0428 35.8396 CDC2 45398 upstream 0 overlap 0.0114 chrl 3 78078830 78080779 0.67871 -0.0764 35.8066 POU4F1 3135 upstream 0 cover 0.0114 chrll 9737352 9738420 0.18438 1.52431 35.7888 SWAP70 95149 downstream -306 disjoint 0.0114 chrX 132945296 132946741 0.8084 -0.1577 35.7679 GPC3 590 inside intron 0 cover 0.01141 chrl 168895983 168897263 1.27136 0.22113 35.7669 PRRX1 2673 upstream 0 overlap 0.01141 chrl 6 4101996 4103117 0.45972 1.65912 35.7603 ADCY9 3069 inside intron 1692 disjoint 0.01141 chr2 45025538 45027494 1.05241 0.19023 35.753 SDO 2998 overlaps 3' -150 disjoint 0.01141 chr4 154898738 154900269 1.5188 0.25251 35.7235 RNF175 567 inside intron 0 overlap 0.01142 chr2 934402 935653 1.24738 0.25635 35.6892 SNTG2 901 promoter 33 disjoint 0.01143 chr6 35418842 35420016 0.12629 1.35678 35.6836 PPARD 530 inside intron -178 disjoint 0.01143 chrl 5 69193324 69194701 1.74296 0.79305 35.6819 THSD4 26140 upstream 9 disjoint 0.01143 chrl 5 38359518 38360966 1.11326 0.14101 35.6089 PA 6 40151 downstream 0 overlap 0.01144 chr3 49671540 49672637 0.44209 1.67285 35.5677 BSN 104615 inside intron -6207 disjoint 0.01145 chrX 105857129 105858125 1.23753 -0.0725 35.5452 NF128 580 overlaps exon 0 overlap 0.01146 downstream
chrl 219132891 219134317 1.59316 0.56218 35.5397 HLX1 13510 downstream 0 overlap 0.01146 chrl l 78824768 78825997 2.19338 0.90995 35.5096 NARS2 861402 upstream 9 disjoint 0.01146 chr20 20298579 20299623 0.91592 -0.3398 35.366 INSM1 1815 overlaps 3' 0 overlap 0.0115 chrX 136484560 136485975 0.82593 -0.1279 35.3609 ZIC3 8549 downstream 0 overlap 0.0115 chrl 8 11136670 11137964 1.3688 0.28077 35.34 FAM38B 448857 upstream 343 disjoint 0.0115 chrl l 20581723 20582577 -0.0712 1.27792 35.3073 SLC6A5 4202 covers exon(s) -1748 disjoint 0.01151 ehrl6 372784 375975 1.05332 0.31041 35.3016 LOC441743 773 promoter 0 overlap 0.01151 chrl l 27448101 27449663 0.95637 0.02314 35.2704 LGR4 1205 inside intron 553 disjoint 0.01152 chr4 36920124 36921653 0.36503 1.41043 35.244 C4orfl9 340596 upstream 0 overlap 0.01152 chrl 9 47441742 47443567 0.31753 1.06712 35.2202 ERF 7545 overlaps 3' -627 disjoint 0.01153 chr6 132311629 132313173 0.05906 0.96391 35.2061 CTGF 1037 covers exon(s) 0 overlap 0.01153 chrl2 54406696 54407868 0.67682 1.89293 35.1539 CD63 1308 covers exon(s) 416 disjoint 0.01153 chrl 7 44151753 44153432 0.7865 -0.2722 35.1258 PRAC 1448 close to 3' 0 overlap 0.01154 chrl 6 47403413 47404571 -0.0014 1.39902 35.0722 N4BP1 201793 upstream -648 disjoint 0.01155 chrl 3 49604309 49605448 1.27364 0.03633 35.0592 KCNRG 116919 downstream 138 disjoint 0.01155 chrl2 88267227 88268834 0.93364 -0.0088 35.0409 DUSP6 1592 overlaps two exons 465 disjoint 0.01155 chrl 2 52061339 52062794 0.09409 1.2043 35.0154 SP1 1094 covers exon(s) -469 disjoint 0.01156 chr4 184255173 184255919 1.98472 0.35473 34.9787 FLJ30277 1426 inside exon 0 overlap 0.01156 chrl 5 41906504 41907907 0.1976 1.40192 34.9494 WDR76 5 covers exon(s) 0 overlap 0.01157 chr7 150694354 150695473 0.16188 1.65017 34.9076 NUB1 24564 covers exon(s) 13922 disjoint 0.01158 chrl 9 13811803 13813118 0.16329 1.17953 34.9023 ZSW 4 44530 downstream 1104 disjoint 0.01158 chrlO 102480940 102482441 1.19264 0.0619 34.8781 PAX2 12880 upstream 0 overlap 0.01159 chr5 132972969 132974280 0.57623 1.54269 34.8571 FSTL4 1841 inside intron 363 disjoint 0.01159 chrl2 106691543 106693035 0.25898 1.10063 34.8051 ASCL4 0 overlaps 5' 81 disjoint 0.0116 chr7 27195534 27196866 1.17843 0.20502 34.7894 H0XA11 4175 upstream 0 overlap 0.0116 chrl 47678180 47679696 1.06729 0.24461 34.7438 FOXD2 3905 overlaps 3' -75 disjoint 0.01161 chrl 2029221 17 202924106 0.25158 1.14324 34.7094 LRRN5 898 promoter -609 disjoint 0.01162 chr6 33050057 33051032 -0.1029 1.24684 34.6393 BRD2 5643 covers exon(s) -1125 disjoint 0.01163 chrl 7 77090773 77092548 0.26983 1.27614 34.5962 ACTG1 1873 overlaps 3' 282 disjoint 0.01164 chr9 136348232 136349967 0.33653 1.41531 34.5852 RXRA 8263 upstream 6916 disjoint 0.01165 chrl 7 71646291 71647388 1.06165 -0.0801 34.5706 FOXJ1 772 inside intron 129 disjoint 0.01165 chrl 146292385 146293862 1.29385 0.27142 34.5589 NBPF1 1110774 inside intron 0 cover 0.01165 chrX 13864472 13865782 0.71831 -0.1647 34.5418 GP 6B 969 inside intron 289 disjoint 0.01165 chr20 34524559 34528534 0.23632 1.18661 34.4661 DLGAP4 1004 inside intron -1147 disjoint 0.01167 chrl 8 18011169 18012835 1.12862 0.23116 34.4186 GATA6 7756 inside intron -91 disjoint 0.01168 chr7 157605825 157607309 0.66776 1.49025 34.393 PTPRN2 465869 inside intron 4156 disjoint 0.01168 chrl l 2648827 2650700 0.00128 0.71622 34.3089 CNQ1 209568 inside intron 26286 disjoint 0.0117 chr2 45010752 45012040 0.96962 0.03028 34.2899 SIX3 10500 upstream -199 disjoint 0.0117 chrl 9 9980147 9981037 0.25904 1.62596 34.2882 COL5A3 1109 inside intron 713 disjoint 0.0117 chrl 6 601 1044 6012383 0.0281 1.12559 34.287 A2BP1 1912 inside intron -642 disjoint 0.0117 chr6 39868512 39869858 0.35331 1.25524 34.2849 DAAM2 0 overlaps 5' -108 disjoint 0.01171 chrl l 124868827 124870281 0.73262 -0.1245 34.2403 FEZ1 1051 inside intron 66 disjoint 0.01171 chr21 17904600 17905851 -0.1058 0.95731 34.2032 BTG3 1181 inside intron 25 disjoint 0.01172 chr8 128877152 128878297 1.50154 0.47199 34.1957 MYC 59655 downstream -1071 disjoint 0.01172 chr4 41574155 41575813 1.18574 0.20859 34.1854 TMEM33 56112 upstream 0 cover 0.01172 chr5 134392542 134393676 1.05797 0.00042 34.1327 PITX1 4210 overlaps exon 0 overlap 0.01173 upstream
chrlO 71835049 71836544 0.70135 1.69766 34.061 EIF4EBP2 1122 inside intron -470 disjoint 0.01175 chrX 44619102 44620837 -0.2177 0.51671 34.048 UTX 1378 inside intron -892 disjoint 0.01175 chrl5 94695171 94696248 1.47464 0.27809 34.0355 NR2F2 20222 downstream 62 disjoint 0.01175 chrl4 98803697 98805208 1.47478 0.63594 34.0338 BCL11B 2366 inside intron 585 disjoint 0.01175 chrS S0297048 50298438 1.25553 0.29271 34.0179 PARP8 298479 downstream 2404 disjoint 0.01176 chr20 30410772 30412250 -0.0389 1.04985 34.0093 ASXL1 959 inside intron -78 disjoint 0.01176 chrlO 59943664 59944834 0.05593 1.03526 33.9825 TFA 128483 downstream -202 disjoint 0.01176 chrl 47466118 47468088 1.0207 0.25787 33.9808 TALI 0 overlaps 5' 1003 disjoint 0.01176 chrlO 73704958 73706016 0.27423 1.44485 33.8792 DDIT4 1276 overlaps 3' -254 disjoint 0.01179 chr9 125817665 125819536 0.99808 0.14175 33.8753 LHX2 3956 inside intron 0 inside 0.01179 chrll 75205375 75206334 -0.0233 1.16628 33.872 UVRAG 1516 inside intron -801 disjoint 0.01179 chrl6 83763074 83764707 0.488 1.41213 33.8468 FAM92B 59460 upstream -542 disjoint 0.0118 chrl 6 11978744 11980053 0.05885 1.41216 33.8267 RU DC2A 642 inside intron -373 disjoint 0.0118 chrl 51214288 51215628 1.02464 0.11502 33.8 CD N2C 6059 downstream 271 disjoint 0.01181 chrl 64710792 64712328 1.08518 0.04997 33.7691 CACHD1 1729 inside intron -1590 disjoint 0.01182 chr22 24128732 24130420 0.12593 1.25823 33.7597 LRP5L 40209 upstream 134 disjoint 0.01182 chr2 70976456 70978189 1.09034 0.43679 33.7448 VAX2 3038 upstream 2039 disjoint 0.01182 chrl5 34958026 34958784 1.82984 0.13942 33.7443 MEIS2 219010 downstream 981 disjoint 0.01182 chrlO 26541114 26542366 -0.1069 1.02576 33.7388 MY03A 277913 overlaps 3' 0 overlap 0.01182 chrl 2 113362343 113363974 1.21125 0.36201 33.7107 TBX5 31714 upstream 0 cover 0.01183 chr3 135608725 135609660 1.45887 0.13177 33.6573 AMOTL2 32630 upstream -167 disjoint 0.01184 chr8 966720 968141 0.83772 1.86806 33.6474 ERICH1 295495 upstream -962 disjoint 0.01185 chrl 9 12756002 12757024 1.12378 2.30809 33.6217 JUNB 6285 upstream -906 disjoint 0.01185 chr2 17924560 17925530 2.03695 0.62621 33.61 KCNS3 1135 inside intron -159 disjoint 0.01185 chrl 154984887 154986160 0.06944 1.19388 33.5747 HDGF 1999 inside intron 1211 disjoint 0.01186 chrl 46538961 46539989 0.25279 1.55153 33.5661 LRRC41 1635 inside intron 23 disjoint 0.01186 chrl2 2939709 2940808 1.25518 0.06828 33.5575 TEAD4 487 inside intron -4 disjoint 0.01186 chrl 2 49919269 49920589 0.57683 2.00439 33.5479 DAZAP2 377 covers exon(s) 0 overlap 0.01187 chrlO 3818572 3819574 1.74929 0.35802 33.5366 KLF6 1118 promoter -446 disjoint 0.01187 chrlO 43388640 43389600 0.24349 1.48488 33.5133 ZNF239 4728 upstream 0 overlap 0,01187 chrl 8 68357323 68359114 0.54948 1.30469 33.4825 CBLN2 3427 inside intron 840 disjoint 0.01188 chrl2 127319542 127320778 0.14193 1.53426 33.4524 SLC15A4 553715 downstream -438 disjoint 0.01188 chr4 81341228 81342375 1.47584 0.33463 33.3183 PRDM8 16766 covers exon(s) 157 disjoint 0.01191 chr4 4913970 4915429 1.59536 0.50857 33.3034 MSX1 1671 overlaps exon 0 overlap 0.01191 upstream
chr20 17242918 17244114 0.25547 1.59439 33.2963 PCS 2 87288 inside intron 11 disjoint 0.01192 chr8 100029988 100031334 0.9688 0.09808 33.2893 0SR2 4127 covers exon(s) 0 overlap 0.01192 chrl l 31784573 31785984 0.65216 -0.134 33.2793 PAX6 3449 covers exon(s) -76 disjoint 0.01192 chrl 8 27517018 27518154 1.48814 0.20172 33.2552 B4GALT6 471 inside intron 547 disjoint 0.01192 chrl l 2265220 2266404 0.81537 2.00033 33.2389 TSPAN32 13414 upstream -15712 disjoint 0.01193 chr3 55492715 55494125 1.32504 0.24907 33.1902 WNT5A 2245 inside intron 0 overlap 0.01194 chr2 119310305 1 19311393 1.40798 0.12679 33.185 EN1 10835 downstream 0 overlap 0.01194 chrl2 8955819 8957656 0.24367 -0.3753 33.1647 PHC1 926 promoter 557 disjoint 0.01195 chr20 6462584 6463175 -0.4077 1.71341 33.0826 BMP2 233569 upstream 232877 disjoint 0.01197 chrl9 6016955 6017881 0.47581 1.50461 33.0713 RFX2 43672 inside intron -25727 disjoint 0.01197 chr4 111756694 111757509 1.41904 -0.0388 33.0653 ΡΓΓΧ2 6193 downstream 1168 disjoint 0.01197 chr2 222862100 222863716 0.79569 0.05389 33.05 PAX3 8227 inside intron 254 disjoint 0.01198 chr20 49852331 49853047 1.48452 -0.1703 33.0319 SALL4 0 overlaps 5' 0 overlap 0.01198 chrlO 8S945784 85947359 0.62805 1.30858 33.0306 PCDH21 1288 covers exon(s) -501 disjoint 0.01198 chr4 109311333 109312541 1.01674 0.0077 33.0262 LEF1 2307 promoter 0 cover 0.01199 chrl l 15053377 15054819 0.25956 1.07805 32.9212 CALCB 1656 inside intron -929 disjoint 0.01201 chr22 44848360 44849214 0.2177 1.46332 32.9045 FLJ27365 11332 upstream -1168 disjoint 0.01201 chr9 125821398 125823966 1.412 0.24161 32.8899 LHX2 7689 covers exon(s) -624 disjoint 0.01202 chrl4 60194028 60195337 0.90573 -0.0035 32.8657 SKI 8096 upstream 0 overlap 0.01202 chr6 134255598 134257001 1.0401 0.13231 32.8325 TCF21 3629 overlaps exon 0 cover 0.01203 upstream
chr21 37003795 37005534 0.78931 -0.1059 32.808 SI 2 9935 inside intron -92 disjoint 0.01204 chr4 13970754 13971680 0.70291 1.99933 32.8041 CPEB2 642939 upstream 501926 disjoint 0.01204 chr8 30363325 30364571 0.95111 -0.0755 32.7994 RBPMS 1840 inside intron -905 disjoint 0.01204 chr3 148603915 148605183 1.50174 0.54921 32.7907 ZIC4 1913 inside intron 4492 disjoint 0.01205 chrl l 87882192 87883295 1.95753 0.6501 32.7676 GRM5 537542 overlaps exon 0 overlap 0.01205 upstream
chr5 153832767 153834602 0.89118 0.14781 32.74 HAND1 3414 downstream 0 cover 0.01206 chr9 70927135 70928280 1.70588 0.15874 32.7334 FX 86972 downstream 0 overlap 0.01206 chrl2 45510421 45511424 1.38263 0.19487 32.7189 SLC38A4 4420 upstream 0 overlap 0.01206 chrl 177981311 177983431 0.43071 1.47908 32.7129 Clorf76 2391 inside intron -737 disjoint 0.01206 chrlO 17312624 17313758 -0.0468 1.15337 32.7068 VIM 1321 covers exon(s) -1 disjoint 0.01206 chr5 122450942 122452118 1.17173 0.21452 32.6893 PPIC 50619 upstream 118 disjoint 0.01207 chr2 201385610 201386475 0.15855 1.50378 32.6888 BZW1 719 covers exon(s) -59 disjoint 0.01207 chr4 111773566 111774594 1.34548 0.21818 32.6833 PITX2 3362 overlaps exon 0 overlap 0.01207 upstream
chr6 90175931 90177228 1.09319 0.21848 32.6636 RRAGD 1255 inside intron 365 disjoint 0.01207 chrl 8 40515677 40517029 0.63523 -0.3169 32.6485 SETBP1 18437 upstream -884 disjoint 0.01208 chrl 7 61730764 61732089 1.07481 0.01508 32.6094 PR CA 1377 inside intron -685 disjoint 0.01209 chr8 50054217 50055544 -0.1512 0.88596 32.5755 SNAI2 57677 upstream -790 disjoint 0.0121 chrlO 112250170 112251165 0.1479 1.42781 32.5442 DUSP5 2556 inside intron -1496 disjoint 0.01211 chrl4 51849417 51850462 0.19043 1.36825 32.5171 PTGER2 400 promoter 0 overlap 0.01212 chrl l 20577621 20579252 0.02174 0.82707 32.4356 SLC6A5 100 overlaps two exons 44 disjoint 0.01215 chr20 25124888 25126168 1.25254 0.15993 32.4199 ENTPD6 517 inside intron 0 overlap 0.01215 chr20 13147349 13148688 1.32194 0.07517 32.364 C20orf38 209503 downstream 0 overlap 0.01216 chrl 180290461 180291940 0.58461 1.5889 32.3487 ZNF648 5529 inside exon 287 disjoint 0.01217 chrl4 60189942 60190908 1.32693 -0.2421 32.3031 SKI 4010 upstream 2458 disjoint 0.01218 chrl3 49598457 49599558 1.0769 -0.0152 32.2682 KCNRG 111067 downstream 0 inside 0.01219 chr5 79414556 79415608 0.27347 1.62176 32.2573 THBS4 47810 overlaps 3' -47312 disjoint 0.01219 chr6 108594757 108596081 1.18483 0.2034 32.2244 NR2E1 803 inside intron 0 inside 0.0122 chr2 176659495 176661802 1.05319 0.30623 32.2237 HOXD13 3975 upstream 0 cover 0.0122 chrl 35428773 35429804 -0.0147 1.10372 32.2065 SFPQ 1517 covers exon(s) 250 disjoint 0.01221 chrlO 129973472 129974437 0.75679 1.8983 32.2051 M I67 158828 upstream -19204 disjoint 0.01221 chrl 50660079 50661308 1.10863 0.18313 32.1811 FAF1 537215 downstream 0 inside 0.01222 chr5 134395235 134396212 1.29572 0.13334 32.1731 PITX1 1674 inside intron 0 overlap 0.01222 chrl5 43188922 43190028 0.40146 1.44952 32.1618 DUOX2 3622 covers exon(s) 512 disjoint 0.01222 chrX 24299244 24300694 0.93504 0.05914 32.1553 PDK3 92780 upstream -8657 disjoint 0.01222 chrl 9 61711327 61712169 -0.0515 1.51331 32.1205 ZNF471 304 inside intron -9 disjoint 0.01223 chrl 47670613 47671746 1.41273 0.44947 32.0381 FOXD2 2529 upstream 0 overlap 0.01225 chr2 36320900 36321588 0.22562 1.91241 32.0197 CRIM1 115312 upstream 114313 disjoint 0.01226 chrlO 104395964 104397209 -0.1065 0.94317 31.9965 TRIM8 1609 inside intron -1006 disjoint 0.01226 chr4 6694038 6695375 0.05625 1.19084 31.9806 MRFAP1 693 overlaps 3' 0 overlap 0.01227 chrl6 9094367 9095777 -0.1009 0.92247 31.9132 C16orf72 1330 inside intron -177 disjoint 0.01229 chr3 148597985 148599139 1.18932 0.21304 31.905 ZIC4 7957 inside intron 0 cover 0.01229 chrlO 101757650 101758910 1.13015 31.8957 CPN1 72673 downstream 56041 disjoint 0.0123 chr8 1032896 1033954 0.37105 1.53346 31.8878 ERICH1 361671 upstream 2012 disjoint 0.0123 chrl4 56928059 56929090 0.36646 1.37675 31.8554 NAT12 1036 overlaps exon 0 overlap 0.01231 downstream
chrl2 120728026 120729107 0.01485 1.08421 31.8534 RHOF 12050 upstream -253 disjoint 0.01231 chr2 201434189 201436953 0.03122 1.07212 31.8293 CLK1 713 covers exon(s) 184 disjoint 0.01232 chrlO 104669314 104670494 0.9997 0.01097 31.8062 C NM2 1211 overlaps exon -12 disjoint 0.01232 downstream
chr22 44847221 44848033 -0.2923 1.22205 31.8016 FU27365 12513 upstream -29 disjoint 0.01233 chrlO 134526926 134527738 0.62295 2.37384 31.7989 C10or©2 5701 upstream -4332 disjoint 0.01233 chrl l 115953394 115954911 0.23579 1.51445 31.7909 BUD13 194002 downstream 958 disjoint 0.01233 chrX 153280464 153281350 -0.1522 1.15317 31.7778 RPL10 553 covers exon(s) 0 overlap 0.01234 chr9 126570897 126572049 0.78274 -0.2369 31.7655 NR6A1 1347 inside intron 0 overlap 0.01234 chr4 78034283 78035653 0.40995 1.26731 31.6957 AN RD56 2372 overlaps 3' 1386 disjoint 0.01236 chrl l 44295178 44296361 0.99431 0.00467 31.6642 ALX4 6887 upstream 0 overlap 0.01236 chr22 38768893 38770072 0.64174 1.83362 31.6167 TNRC6B 694 promoter 726 disjoint 0.01237 chr21 36996016 36997471 0.69442 -0.2267 31.603 SIM2 2156 inside intron -255 disjoint 0.01238 chr2 171384559 171386002 1.22607 0.29676 31.5471 GAD1 3114 inside intron 0 cover 0.01239 chrX 39748046 39749278 0.84121 -0.1452 31.522 BCOR 92321 downstream 191 disjoint 0.0124 chrl 154896679 154897932 0.5283 1.47483 31.5125 BCA 18316 downstream -2479 disjoint 0.0124 chr5 140568353 140569426 0.47752 1.57099 31.5035 PCDHB12 0 overlaps 5' 502 disjoint 0.01241 chrl l 1976657 1978203 1.80884 0.62957 31.5023 MRPL23 51544 downstream -218 disjoint 0.01241 chr8 58218718 58220223 0.60857 1.46224 31.4503 IMPADl 149762 upstream 0 overlap 0.01242 chrl 7 44052055 44053494 0.92294 0.0792 31.4436 HOXB9 5339 downstream 0 cover 0.01243 chr2 151048780 151050032 0.00583 1.23397 31.4374 RND3 2393 inside intron 0 overlap 0.01243 chrS 72767341 72768195 1.54697 0.1981 31.3713 FOXD1 11912 downstream 0 cover 0.01245 chrl 8 33397571 33398671 0.25426 1.2605 31.3663 BRUNOL4 1269 inside intron 234 disjoint 0.01245 chr4 154930259 154931462 1.20709 0.14607 31.3587 SFRP2 582 promoter 0 overlap 0.01245 chr9 93748388 93749977 0.20945 0.90167 31.3489 ROR2 2287 inside intron 961 disjoint 0.01246 chrl 7 75384018 75385068 1.12423 -0.0374 31.3336 CBX8 416 covers exon(s) 199 disjoint 0.01246 chr3 161957342 161958653 0.92556 0.07043 31.326 PPM1L 653 inside intron -164 disjoint 0.01246 chrl 196148961 196150238 1.00479 0.13308 31.3016 LHX9 704 inside intron -701 disjoint 0.01247 chr3 57555368 57557029 0.30636 1.2042 31.2392 ARF4 1088 inside intron 1031 disjoint 0.01248 chr8 509871 18 50988689 0.25665 0.98312 31.2357 SNTG1 0 overlaps 5' -1705 disjoint 0.01249 chr6 106547307 106548443 1.09008 0.02797 31.23 PRDM1 92444 upstream 236 disjoint 0.01249 chrl 8 9007266 9008153 -0.1249 1.16217 31.2136 DUFV2 84571 upstream 84263 disjoint 0.01249 chr2 74916636 74918283 1.07119 0.22148 31.2036 H 2 3347 inside intron -464 disjoint 0.0125 chrl 8 33320171 33321618 0.25398 1.39443 31.1425 BRUNOL4 78322 inside intron -625 disjoint 0.01251 chrl 6 23756770 23758087 0.22668 1.40851 31.0559 PR CB1 1948 inside intron -1167 disjoint 0.01254 chr4 3764167 3765419 0.14412 1.36942 30.986 ADRA2C 26074 downstream -20307 disjoint 0.01256 chr4 85635441 85637068 1.06273 0.1608 30.9857 NKX6-1 1342 covers exon(s) 0 overlap 0.01256 chrX 74059646 74060484 0.03283 1.3786 30.9464 KIAA2022 1224 inside intron 93 disjoint 0.01257 chrl6 19994111 19995794 0.10012 1.1199 30.9383 GPR139 1511 promoter -1305 disjoint 0.01257 chrl 3 34951054 34951668 1.58888 -0.188 30.9286 NBEA 536599 inside intron 0 overlap 0.01257 chr6 134216952 134218445 0.94873 0.16586 30.9068 TCF21 33524 upstream -15910 disjoint 0.01258 chr7 31341062 31341982 0.47336 1.50649 30.8789 NEUR0D6 5080 downstream 388 disjoint 0.01259 chr20 34633173 34634797 1.03406 0.11373 30.8664 TGIF2 639 promoter 0 overlap 0.01259 chr3 153467976 153468929 0.26976 1.31323 30.861 MB L1 0 overlaps 5' 85 disjoint 0.01259 chrl8 55085941 55086864 1.00053 -0.1696 30.8543 RAX 4740 overlaps 3' 0 inside 0.0126 chrl5 91248894 91249959 0.04022 1.11297 30.8278 CHD2 4472 inside intron -67 disjoint 0.01261 chrX 39901201 39902219 1.00878 -0.1913 30.8183 BCOR 59602 upstream -54 disjoint 0.01261 chi8 956251 957357 0.6659 1.70495 30.8121 ERICH1 285026 upstream -1646 disjoint 0.01261 chr2 45029099 45030409 1.27581 0.48502 30.8084 SK3 6559 downstream 0 overlap 0.01261 chr6 88935361 88936416 0.50511 1.70358 30.8029 CNR1 23587 upstream -1193 disjoint 0.01261 chr6 10506649 10507479 1.56765 0.21813 30.801 TFAP2A 13113 overlaps exon 0 overlap 0.01261 upstream
chrl 4617771 4618661 0.49857 1.63574 30.7485 AJAP1 2807 inside intron -1356 disjoint 0.01263 chr8 29260747 29261964 1.08479 0.20565 30.737 DUSP4 276 overlaps exon 0 overlap 0.01263 downstream
chr6 1337085 1338113 1.38343 0.16406 30.6708 FOXF2 2018 inside intron 0 overlap 0.01265 chr5 135442454 135444013 1.29931 0.52658 30.6448 TGFBI 49858 downstream 0 cover 0.01266 chr9 97306266 97307536 1.26938 0.34104 30.6351 PTCH1 3115 inside intron 760 disjoint 0.01266 chr2 164301826 164302647 1.53352 0.17075 30.6314 FIGN 1068 promoter -69 disjoint 0.01266 chrl 154732131 154733736 0.66064 1.61112 30.6289 MEF2D 3416 inside intron 2505 disjoint 0.01267 chrl5 78856558 78857621 0.24645 1.26565 30.6258 KIAA1199 1145 promoter 701 disjoint 0.01267 chrl 9 38981450 38982634 1.39735 0.55534 30.6236 KCTD15 1844 overlaps exon -475 disjoint 0.01267 downstream
chr7 19151445 19152404 1.22461 0.14464 30.6206 FERD3L 0 overlaps 5' 0 overlap 0.01267 chrl 3 99424212 99425349 0.81434 -0.3079 30.6134 ZIC5 2034 promoter -1863 disjoint 0.01267 chrl l 64238875 64240350 0.45371 1.56647 30.6066 NRXN2 6885 inside intron -955 disjoint 0.01267 chrl l 114880816 114882099 1.3534 0.19926 30.5972 IGSF4 492 promoter 0 overlap 0.01268 chr2 217208366 217209782 1.12842 0.35236 30.5947 IGFBP2 1995 inside intron -1274 disjoint 0.01268 chrX 129080186 129081047 0.42609 2.04085 30.5945 ELF4 8040 upstream 1118 disjoint 0.01268 chr5 162865671 162867401 0.17856 1.09415 30.5748 MAT2B 509 inside intron -147 disjoint 0.01268 chr6 41636886 41638101 1.3499 0.31303 30.5461 FOXP4 14745 inside intron -8 disjoint 0.01269 chrl 8 23017295 23018470 -0.0824 0.88823 30.5395 CHST9 808 inside intron 479 disjoint 0.0127 chr3 13293369 13294675 0.38748 1.32697 30.5376 NUP210 142133 downstream 3763 disjoint 0.0127 chrl 27210387 27211486 1.08888 0.11972 30.5264 FAM46B 427 overlaps exon 0 overlap 0.0127 downstream
chr3 170859956 170861077 1.14634 0.06248 30.507 MDS1 3090 inside intron 1051 disjoint 0.0127 chrl l 2633626 2635172 -0.0055 1.29767 30.4969 KCNQ1 194367 inside intron 41814 disjoint 0.01271 chr8 25954089 25955259 1.1411 0.10693 30.4833 EBF2 3049 covers exon(s) 0 overlap 0.01271 chrl6 52882030 52882650 1.57609 -0.2812 30.4621 IRX3 4152 upstream 0 overlap 0.01272 chrl3 36147435 36148563 0.71401 1.64309 30.4424 LOC400120 1387 inside intron -972 disjoint 0.01272 chr3 97976873 97978229 0.45287 1.38323 30.4189 ARL6 988055 upstream 75 disjoint 0.01273 chr2 19423679 19424735 1.43151 0.38681 30.4177 OSR1 1827 promoter 0 overlap 0.01273 chrl2 48020605 48021720 1.23165 0.0474 30.3709 C1QL4 3368 upstream 266 disjoint 0.01274 chrl l 133289456 133290736 0.71499 1.92741 30.353 SPATA19 68855 upstream 2445 disjoint 0.01275 chr8 118032349 118033443 0.72321 2.09471 30.3497 LOC441376 12686 downstream -12209 disjoint 0.01275 chrl 181077272 181078882 0.38102 1.16508 30.3419 DHX9 2199 covers exon(s) -1527 disjoint 0.01276 chrl 6 85155874 85156824 1.36996 0.13769 30.3249 FOXC2 1618 promoter 32 disjoint 0.01276 chrlO 3812098 3812988 0.56723 1.91561 30.3169 KLF6 4466 covers exon(s) 801 disjoint 0.01277 chr5 92956293 92957267 1.35506 0.25761 30.2986 NR2F1 11495 downstream 0 overlap 0.01277 chr5 168656240 168657250 0.88966 1.94333 30.2633 SLIT3 3303 inside intron 2757 disjoint 0.01278
Figure imgf000053_0001
chr4 30333497 30334390 1.63628 0.43399 29.3569 PCDH7 2363 inside exon 0 overlap 0.01312 chr6 32223942 32225190 1.42794 0.45888 29.3292 PRRT1 2507 overlaps 3' 0 overlap 0.01313 chr2 174911679 174912744 1.0638 0.00381 29.3206 FLJ46347 1140 promoter 345 disjoint 0.01313
ChrlO 124756222 124757589 -0.1513 0.79435 29.3203 D ZF5 714 covers exon(s) 159 disjoint 0.01313 chrl 18304910 18306232 0.53992 1.52209 29.3095 IGSF21 594 promoter 460 disjoint 0.01314 chr20 39378188 39378940 -0.1735 1.24695 29.2799 ZHX3 16036 upstream 68 disjoint 0.01315 chr5 87990795 87991904 1.19875 0.20529 29.2362 MEF2C 222875 downstream 0 cover 0.01316 chrl 4 94853971 94855140 1.9086 0.99277 29.202 CLMN 814 inside intron 365 disjoint 0.01318 chr3 16528474 16529216 0.10127 1.44734 29.1891 RFT 1 1009 inside intron 115 disjoint 0.01318 chr9 78826374 78827660 0.77183 -0.1824 29.1692 FOXB2 1984 close to 3' 0 overlap 0.01319 chr9 23812593 23813553 1.03663 0.04786 29.1098 ELAVL2 2509 inside intron 0 overlap 0.01321 chr7 27211702 27212559 1.48712 0.29092 29.1042 H0XA13 5453 upstream 0 overlap 0.01321 chr2 176746720 176747616 1.16182 0.05818 29.0949 H0XD3 9670 downstream 181 disjoint 0.01322 chr6 134251392 134252647 1.07104 0.1476 29.0943 TCF21 0 overlaps 5' 0 overlap 0.01322 chr6 1325519 1326619 1.43132 0.26761 29.0771 F0XF2 8448 upstream 123 disjoint 0.01322 chrl 6 67975469 67976809 -0.1456 0.77528 29.0753 TERF2 564 covers exon(s) 8 disjoint 0.01322 chrl l 20839300 20840410 0.29425 1.51499 29.0471 NELL1 191589 inside intron -190879 disjoint 0.01324 chii 26333740 26334489 1.99919 0.65086 29.0068 HIST1H3E 379 overlaps 3' 0 overlap 0.01325 chr2 1 19325769 119326721 1.23596 0.0726 29.0055 EN1 3541 upstream 1045 disjoint 0.01325 chrl 9 18621903 18622826 0.25371 1.39088 28.9941 KLHL26 13066 inside intron 0 cover 0.01326 chrl 9 47107473 47108396 0.46571 1.41387 28.9941 ARHGEF1 27188 downstream 436 disjoint 0.01326 chrl l 14950663 14951913 0.03988 0.98385 28.9764 CALCA 256 promoter 0 overlap 0.01326 chr4 914642 915463 0.30645 1.53516 28.9207 GA 511 inside intron 117 disjoint 0.01328 chr5 172604347 172605856 1.44204 0.3927 28.9028 NKX2-5 9480 upstream 0 cover 0.01329 chrX 39846016 39847287 1.10673 0.34276 28.8975 BCOR 4417 upstream 0 inside 0.01329 chr2 63134875 63135837 1.22967 0.16699 28.862 OTX1 3407 inside intron -24 disjoint 0.01331 chrl 39812705 39813772 0.47175 1.40745 28.8492 PABPC4 1230 inside intron 132 disjoint 0.01331 chr2 96666287 96667361 0.31349 1.39777 28.8456 FLJ10081 448 covers exon(s) 278 disjoint 0.01331 chrlO 76859938 76861143 1.05835 0.23101 28.8138 ZNF503 28508 upstream 0 overlap 0.01333 chr4 11 1763988 1 11764874 1.25486 0.09135 28.805 ΡΓΓΧ2 13082 inside intron -75 disjoint 0.01333 chrl 7 75376786 75377876 1.33828 -0.0361 28.8012 CBX2 10199 downstream 83 disjoint 0.01333 chr7 153213687 153214504 0.07717 1.38708 28.7925 DPP6 847 promoter 0 overlap 0.01334 chr2 78860830 78861951 0.10373 1.50051 28.7815 REG3G 244382 upstream 211749 disjoint 0.01334 chr9 109293331 109294438 1.32537 0.18446 28.7419 KLF4 1756 promoter -850 disjoint 0.01336 chrl 5 88092039 88093841 1.20204 0.57732 28.7229 MESP1 1703 close to 3' 384 disjoint 0.01337 chr7 157947632 157948447 0.60624 1.95719 28.7226 PTPRN2 124731 inside intron -4374 disjoint 0.01337 chr5 172588973 172590547 1.49292 0.71187 28.6963 NKX2-5 4320 downstream -165 disjoint 0.01337 chrl3 76797150 76798474 0.07529 1.07229 28.6937 MYCBP2 703 inside intron 31 disjoint 0.01338 chrl3 25520732 25522210 0.09897 0.7932 28.6791 TMEM46 987 inside intron 515 disjoint 0.01338 chr20 61029844 61030871 0.7797 -0.1247 28.6659 DIDOl 8847 inside intron 7 disjoint 0.01339 chrl 4 53499564 53500859 1.28522 0.51232 28.6301 BMP4 6203 upstream 0 cover 0.0134 chrl5 39006073 39007137 1.22907 0.12157 28.6165 ΌΙΛΑ 1701 promoter 0 inside 0.01341 chr7 27197241 27198513 1.37465 0.60484 28.6138 HOXA13 7736 downstream 0 overlap 0.01341 chrlO 102796497 102797808 1.03579 0.32518 28.5948 SFXN3 15512 downstream 0 overlap 0.01341 chr8 59732566 59733633 0.20174 1.12725 28.5711 NSMAF 1306 inside intron 524 disjoint 0.01343 chr4 81325458 81326417 1.25193 0.1 1365 28.532 PRD 8 996 inside intron -907 disjoint 0.01344 chrl 143641476 143642742 0.41606 1.23327 28.5149 PDE4DIP 646 overlaps exon 0 overlap 0.01345 downstream chr7 100397150 100398324 0.35792 1.72427 28.5089 MUC17 51759 upstream -637 disjoint 0.01345 chr22 43472731 43473669 0.2566 1.49555 28.505 P R5 21380 inside intron 2750 disjoint 0.01345 chrl5 29567744 29569264 0.22268 0.88359 28.4689 0TUD7A 165569 inside intron -3464 disjoint 0.01347 chr7 100271505 100272257 1.54372 0.05049 28.4656 EPHB4 8427 upstream 661 disjoint 0.01347 chrl8 58535461 58536735 0.48311 -0.333 28.4527 PHLPP 1748 overlaps exon -110 disjoint 0.01348 downstream
chr5 177950458 177951605 0.29623 1.50425 28.4307 COL23A1 297 promoter • -182 disjoint 0.01349 chr5 88213307 88214646 -0.0044 0.85351 28.4306 MEF2C 133 overlaps exon 976 disjoint 0.01349 downstream
chrl7 45397045 45398146 0.89496 0.0275 28.3989 DLX4 3416 upstream 0 overlap 0.0135 chrl3 76359319 76360417 1.49075 0.49838 28.3715 CTD12 794 promoter -219 disjoint 0.01351 chrl4 96515619 96516161 0.00233 1.94824 28.3207 VRK1 182183 downstream 53197 disjoint 0.01353 chr7 42862804 42864055 0.78072 1.68209 28.2864 C7or£25 54126 downstream 53686 disjoint 0.01354 chrll 2230035 2232285 0.35467 0.88707 28.286 ASCL2 16472 downstream 14395 disjoint 0.01354 chr20 35470034 35471314 0.77051 1.81137 28.2041 SRC 62064 downstream -1417 disjoint 0.01358 chrlO 101279333 101280673 0.73948 0.00881 28.1815 NKX2-3 2026 promoter 0 cover 0.01358 chr7 27252981 27253871 1.3012 0.09268 28.1646 EVX1 4293 downstream -219 disjoint 0.01359 chr3 185784623 185785447 1.54251 0.32372 28.1608 EPHB3 22343 downstream 0 overlap 0.01359 chrl l 303520 304360 1.3021 0.06213 28.1033 MTM1 0 overlaps 5' 1379 disjoint 0.01362 chr22 16230862 16231785 0.97294 -0.1357 28.0899 CECR1 160084 upstream -129 disjoint 0.01362 chrl l 2041606 2043468 0.00892 0.58177 28.0758 IGF2 73311 downstream -51039 disjoint 0.01363 chrlO 126835482 126836564 0.78658 -0.1162 28.0734 CTBP2 2449 inside intron 650 disjoint 0.01363 chrl l 2655963 2657675 -0.053 0.79316 27.989 KCNQ1 216704 inside intron 19311 disjoint 0.01366 chr8 1303610 1306652 0.91808 2.0346 27.957 DLGAP2 130323 upstream 1987 disjoint 0.01367 chr7 107431462 107432667 1.68962 0.68706 27.9269 LAMB1 423 promoter -168 disjoint 0.01369 chrl l 64839953 64841499 0.27146 1.28632 27.9119 CDC42EP2 1047 inside intron -44 disjoint 0.0137 chr20 55270645 55271935 1.33515 0.3797 27.8866 BMP7 2772 inside intron 759 disjoint 0.01371 chrl6 49535316 49535858 0.27909 2.09775 27.875 CYLD 201787 downstream -102493 disjoint 0.01371 chr6 30050571 30052040 1.09915 0.28729 27.8745 HCG9 0 overlaps 5' 341 disjoint 0.01371 chr6 125725250 125726280 1.27024 0.44935 27.8592 HDDC2 60270 upstream 0 overlap 0.01372 chrl9 1306822 1308150 0.34904 1.25788 27.8577 MUM1 813 covers exon(s) -472 disjoint 0.01372 chrl9 56897591 56898940 1.00814 0.08662 27.8557 LOC147650 9187 covers exon(s) 0 cover 0.01372 chrl3 34949969 34950896 1.26756 0.09714 27.8478 NBEA 535514 inside intron 0 overlap 0.01372 chr2 216655231 216656193 1.9029 0.88541 27.8301 TMEM169 345 inside intron -252 disjoint 0.01373
Chr4 108174284 108175890 0.28681 1.09068 27.8124 DK 2 1011 inside intron 114 disjoint 0.01374 chr5 78842898 78844247 1.13889 0.14148 27.8103 HOMERl 1208 inside intron 856 disjoint 0.01374 chrl 4561137 4562165 0.68295 1.7884 27.8052 AJAPl 52799 upstream 51684 disjoint 0.01374 chrl2 128899028 128900186 0.10549 0.97756 27.8014 T EM132D 53979 inside intron 5450 disjoint 0.01374 chrl5 59024276 59025319 0.78531 1.74745 27.7866 RORA 283474 inside intron 281594 disjoint 0.01374 chr2 86701715 86702593 0.16967 1.32327 27.7686 RNF103 1895 inside intron 960 disjoint 0.01375 chr2 235527786 235528886 1.76376 0.89059 27.7585 SH3BP4 2420 inside intron -1331 disjoint 0.01376 chrl 7 44038859 44039760 2.14882 0.83131 27.7454 HOXB7 3621 overlaps 3' 483 disjoint 0.01377 chrl 219980062 219981570 -0.0635 0.6888 27.7162 DUSP10 513 inside intron 527 disjoint 0.01378 chr2 119307923 119309084 1.19217 0.24894 27.7141 EN1 13144 downstream 0 overlap 0.01378 chrl 7 14153652 14154812 1.20769 0.02172 27.7068 HS3ST3B1 8422 inside intron -139 disjoint 0.01378 chrl 7 76991781 76992822 0.48924 1.42987 27.7045 T EM105 72713 upstream 0 cover 0.01379 chrl 8 74254146 74254962 0.68984 2.0023 27.6709 SALL3 586300 upstream -1627 disjoint 0.0138 chr7 27130736 27131713 1.47264 0.34062 27.6485 HOXA3 1450 inside intron -113 disjoint 0.01381 chr2 237837984 237838628 0.30276 1.83069 27.6431 COL6A3 148930 downstream 106586 disjoint 0.01381 chrl l 64944919 64946097 0.07358 1.00854 27.6219 FKSG44 34221 downstream 0 overlap 0.01382 chr7 4194956 4196201 0.22744 1.66242 27.5438 SDK1 887351 inside intron -58677 disjoint 0.01386 chr5 50301491 50302450 1.08109 0.09321 27.5323 PARP8 302922 downstream 0 overlap 0.01386 chr3 144319532 144320839 1.64909 0.85947 27.5322 CHST2 518 promoter 0 overlap 0.01386 chr7 27137559 27138479 1.39625 0.32927 27.524 H0XA4 636 promoter -396 disjoint 0.01387 chrl4 53483448 53484423 1.29663 0.03017 27.5233 BMP4 6596 downstream 0 overlap 0.01387 chrX 46963879 46964694 0.28119 1.71352 27.5187 PCT 1 821 inside intron -298 disjoint 0.01387 chr9 97314045 97315004 0.75307 -0.2483 27.5162 PTCH1 3394 upstream -316 disjoint 0.01387 chrll 82120072 82120854 1.3143 0.0638 27.511 GC33846 1699 overlaps 3' 229 disjoint 0.01387 chr20 44367099 44368121 0.20742 1.08179 27.5014 SLC35C2 58349 downstream 1218 disjoint 0.01387 chr4 189190243 189190914 2.18435 0.6204 27.4984 ZFP42 36325 downstream -36373 disjoint 0.01387 chrl 212236443 212237264 0.88089 2.07794 27.4966 PR0X1 7961 inside exon -7083 disjoint 0.01388 chrl2 116284747 116285869 0.60539 1.40996 27.4947 NOS1 783 promoter -916 disjoint 0.01388 chr8 53636408 53637154 0.57402 2.00561 27.4831 UNQ9433 3410 inside intron 2943 disjoint 0.01388 chr3 129686362 129687617 1.46092 0.40164 27.4615 GATA2 7100 overlaps exon 565 disjoint 0.01389 downstream
chrl 7 7997255 7998440 0.48129 1.59402 27.4237 PERI 829 promoter -695 disjoint 0.01391 chrl 6 2997644 2998742 0.91559 -0.0311 27.3961 CLDN9 3464 upstream -3328 disjoint 0.01392 chr5 133587087 133588292 0.2225 1.06644 27.3504 PPP2CA 1556 inside intron 747 disjoint 0.01394 chrl9 6483163 6484392 2.10618 0.46047 27.3478 TNFSF9 1127 covers exon(s) -611 disjoint 0.01394 chr4 77726086 77727358 1.29768 0.52349 27.3472 SHROOM3 150810 inside intron 0 cover 0.01394 chr5 95095666 95096529 -0.0788 1.18047 27.3411 RHOBTB3 3061 inside intron -2098 disjoint 0.01394 chr9 123537075 123538347 1.17654 0.2666 27.3135 DAB2IP 167856 inside intron 0 overlap 0.01396 chrll 133789012 133790474 0.26192 1.13916 27.2891 B3GAT1 1991 promoter -883 disjoint 0.01397 chr7 113515080 113515766 1.61759 0.10504 27.2783 PPP1R3A 168781 upstream -49 disjoint 0.01397 chrl2 56444197 56445162 1.48162 0.42778 27.2561 CYP27B1 2080 covers exon(s) 0 overlap 0.01398 chr2 45251164 45252133 1.62121 0.64817 27.2435 SIX2 161139 upstream 0 overlap 0.01399 chrl2 116279449 116280675 1.34972 2.29382 27.2426 NOS1 3289 inside intron 1784 disjoint 0.01399 chrl 3477695 3478672 0.41846 1.63286 27.2399 MEGF6 39246 inside intron 11090 disjoint 0.01399 chr7 36161647 36162639 0.59673 1.65181 27.2184 IAA1706 2287 inside intron -1688 disjoint 0.014 chrlO 32258780 32259842 -0.1028 0.95504 27.2006 ARHGAP12 1005 promoter -382 disjoint 0.01401 chrX 142544143 142545033 0.56487 1.53385 27.1699 SLITRK4 5651 inside exon 4043 disjoint 0.01402 chrl 3 111804027 111805226 0.83255 1.72828 27.1492 SOX1 34114 downstream 1373 disjoint 0.01403 chrl 6 2902719 2903748 0.59951 1.89273 27.1201 FLYWCH1 739 inside intron -186 disjoint 0.01405 chrl 3 34948736 34949770 0.94053 -0.0866 27.0848 NBEA 534281 inside intron -577 disjoint 0.01407 chrl 7 6859256 6859972 -0.0207 1.35444 27.0798 C17orf49 409 covers exon(s) 0 Overlap 0.01408 chrl 7 7423183 7424283 0.49475 1.4964 27.0549 CD68 0 overlaps 5' 2726 disjoint 0.01409 chrl 6 56327520 56328725 -0.2297 0.71948 27.0536 KATNB1 360 covers exon(s) -46 disjoint 0.01409 chrl 2 105169365 105170288 0.50971 1.64723 27.0526 CKAP4 3523 upstream -2861 disjoint 0.01409 chr7 92075312 92076050 1.75689 0.21711 26.9913 CDK6 225097 inside exon -17503 disjoint 0.01411 chrl 4 37127167 37128482 0.71367 -0.0587 26.9825 FOXA1 5757 downstream 0 overlap 0.01412 chrl l 113433492 1 13434448 1.38664 0.43635 26.9622 ZBTB16 1192 promoter 395 disjoint 0.01413 chrl 6 47864683 47866117 0.18672 1.17195 26.9464 CBLN1 7066 downstream 507 disjoint 0,01414 chrl l 133163180 133164361 0.20945 1.33558 26.9217 SPATA19 56240 downstream 43901 disjoint 0.01416 chrl l 2671310 2672452 1.41699 0.39592 26.9179 CNQ1 232051 inside intron 4534 disjoint 0.01416 chr21 36988761 36990054 0.53717 -0.2407 26.9063 SI 2 3806 upstream 9 disjoint 0.01416 chr9 135461474 135462784 0.39718 1.16225 26.8841 DBH 28521 upstream 1207 disjoint 0.01418
Figure imgf000057_0001
chrl7 56885838 56886530 1.33683 -0.0955 26.1209 TBX4 2058 promoter 0 overlap 0.01456 chr8 22609589 22611225 1.58366 0.93202 26.0804 EGR3 2830 upstream -217 disjoint 0.01458 chrl8 10445439 10446257 -0.2668 0.95285 26.0344 APCDD1 815 inside intron -171 disjoint 0.0146 chrl8 41937962 41939477 -0.1315 0.66534 26.0153 CCDC5 0 overlaps 5' 0 cover 0.01462 chr8 98726668 98727570 -0.0523 0.95472 26.0048 MTDH 1086 inside intron -262 disjoint 0.01462 chrU 62450002 62450889 0.96448 -0.0866 25.9794 CHRM1 4415 upstream 0 inside 0.01464 chr7 153219606 153220325 0.60203 1.8533 25.972 DPP6 4255 inside intron -3007 disjoint 0.01464 chrl3 34943551 34944657 0.91092 -0.0292 25.9457 NBEA 529096 overlaps exon 0 cover 0.01465 upstream
chr2 406957 408132 0.85799 1.66006 25.9414 LOC285016 129121 upstream 1919 disjoint 0.01465 chr8 65456164 65457300 0.09603 0.94453 25.937 BHLHB5 198067 upstream -2664 disjoint 0.01466 chrl6 78193690 78194682 0.176 1.08662 25.9295 AF 1579 promoter -652 disjoint 0.01466 chrl9 55521981 55523045 -0.2287 0.60029 25.8954 CNC3 1400 inside intron 221 disjoint 0.01468 chrl2 27375621 27376716 -0.1903 0.84223 25.883 ARNTL2 538 promoter 234 disjoint 0.01469 chr8 1 19188905 119189628 0.12078 1.43956 25.8829 EXT1 3610 inside intron 3527 disjoint 0.01469 chrl9 61968460 61969101 1.01344 2.42177 25.8807 ZIM2 74785 downstream 0 overlap 0.01469 chrl 19844653 19845573 0.54938 1.56572 25.8716 NBL1 1259 inside intron -143 disjoint 0.01469 chrl 62434341 62437362 1.28672 0.5256 25.8493 L1TD1 1218 covers exon(s) -807 disjoint 0.01471 chr7 153216658 153217865 0.70827 1.52516 25.8338 DPP6 1307 inside intron -59 disjoint 0.01471 chr2 119314778 119315719 1.23346 0.20014 25.7739 EN1 6509 downstream 0 overlap 0.01474 chrl 152848220 152849088 1.80421 0.17987 25.7654 ADAR 17972 inside intron -799 disjoint 0.01475 chrl4 104654929 104656258 0.36634 1.38987 25.7467 JAG2 49947 downstream -4508 disjoint 0.01476 chr9 86216204 86216868 0.54403 1.96095 25.7308 SLC28A3 42972 upstream 256130 disjoint 0.01477 chrl 5 37662574 37663449 0.48636 1.65865 25.7234 THBS1 2003 covers exon(s) -1715 disjoint 0.01477 chr7 130439023 130439772 1.04505 2.26999 25.7073 M LN1 223405 upstream 1126 disjoint 0.01478 chrl2 12402011 12403036 -0.0173 0.9324 25.6863 LOH12CR1 690 inside intron -316 disjoint 0.01479 chrl 48230173 48231135 0.99973 2.03348 25.6815 SLC5A9 229855 upstream 1264 disjoint 0.01479 chrl 8 44727478 44728758 -0.0999 0.80814 25.658 SMAD7 2320 overlaps exon 171 disjoint 0.01481 downstream
chrlO 93381686 93382700 -0.2161 0.97686 25.6467 PPP1R3C 137 overlaps exon 0 overlap 0.01481 downstream
chr20 58416735 58417484 0.26583 1.49687 25.6466 LOC284757 90704 downstream -320380 disjoint 0.01481 chrl 2 131467604 131469715 1.533 2.65053 25.6218 GALNT9 211079 upstream -603 disjoint . 0.01482 chr2 45023651 45024882 1.38075 0.36797 25.5978 SDG 1111 inside intron 0 inside 0.01484 chrl 9 45663927 45664709 0.62859 1.98691 25.5779 SPTBN4 256 promoter 0 inside 0.01485 chrlO 22805427 22806280 1.00918 -0.0515 25.5651 SPAG6 131023 downstream 0 inside 0.01485 chrl 219116260 219117012 1.32586 0.16554 25.5632 HLX1 2369 promoter 59 disjoint 0.01486 chr20 2678521 2679130 1.49414 -0.0095 25.5624 CPXM1 50151 downstream 0 overlap 0.01486 chrl 8 74624116 74624970 0.71612 1.77525 25.5369 SALL3 216292 upstream 17165 disjoint 0.01487 chr5 141469289 141470179 -0.3771 0.52778 25.4938 DFIP1 782 inside intron -186 disjoint 0.0149 chr7 5534758 5535645 0.42358 1.77625 25.4611 ACTB 1101 covers exon(s) 0 overlap 0.01492 chrl 9 55833457 55834275 0.64564 1.75718 25.4459 SYT3 344 promoter 0 overlap 0.01493 chrl 6 85160839 85161517 1.0695 -0.2228 25.4301 FQXC2 2397 close to 3' -689 disjoint 0.01493 chrl 7 44448194 44449251 0.50932 1.65148 25.3984 IGF2BP1 18422 inside intron -984 disjoint 0.01495 chrX 136474076 136475466 0.68381 -0.0409 25.3764 ZIC3 545 promoter 0 overlap 0.01496 chrl 7 7084355 7085414 0.44381 1.38492 25.3538 GABARAP 1062 overlaps 3' -560 disjoint 0.01498 chr5 140509530 140510381 0.88014 2.10703 25.352 PCDHB6 0 overlaps 5' 960 disjoint 0.01498 chrlO 90739545 90740380 -0.1478 0.86925 25.3515 FAS 0 overlaps 5' 0 overlap 0.01498 chr6 30537842 30539254 0.79153 1.50667 25.3486 HLA-E 25995 upstream 287 disjoint 0.01498 chr4 111775105 111776005 1.06246 -0.068 25.3399 PITX2 1951 inside intron -152 disjoint 0.01498 chr7 103757776 103758627 0.30773 1.52382 25.3379 LHFPL3 1437 inside intron -581 disjoint 0.01499 chrl8 51596590 51597805 0.81252 -0.1386 25.3229 TCF4 190150 upstream 267 disjoint 0.01499 chrl4 32476163 32477307 0.97126 0.15336 25.3128 PAS3 902 promoter -2333 disjoint 0.015 chr5 1825348 1826202 1.12674 2.11315 25.3008 MRPL36 26743 downstream -2653 disjoint 0.01501 chrl l 33715038 33716268 0.37467 1.42099 25.2803 CD59 439 promoter -340 disjoint 0.01502 chr20 21641340 21642560 0.91465 0.1348 25.2771 PAX1 6977 inside intron 0 overlap 0.01502 chrl8 2838366 2839491 -0.0124 0.90519 25.2637 E ILIN2 1339 inside intron -191 disjoint 0.01503 chr8 139576964 139577962 0.45236 1.25831 25.2602 C80RFK32 284 inside intron 15 disjoint 0.01503 chrl7 11086186 11087247 0.95083 1.71908 25.2325 FLJ45455 416 inside intron -45 disjoint 0.01504 chrlO 102980589 102981335 1.33066 0.16997 25.2027 LBX1 1883 promoter -536 disjoint 0.01506 chrl2 105053893 105054860 0.18798 1.10479 25.1923 NUA 1 3080 inside intron 1376 disjoint 0.01506 chrl9 43447568 43448251 2.00945 0.39201 25.1884 SPINT2 527 inside intron -29 disjoint 0.01507 chrl9 63528728 63530011 0.25849 1.73664 25.1685 ZSCAN22 185 promoter 0 overlap 0.01508 chrH 59264311 59265246 0.15248 1.22464 25.1612 RTN1 142063 inside intron -256 disjoint 0.01509 chrll 77466651 77467266 0.45142 1.89158 25.1498 NDUFC2 1312 inside intron 860 disjoint 0.01509 chrl l 117362678 117363607 0.27267 1.41545 25.1472 IL10RA 360 inside intron -170 disjoint 0.0151 chrl8 74598724 74599296 0.5064 2.07784 25.1431 SALL3 241966 upstream -10872 disjoint 0.0151 chrl2 94392859 94394124 0.07154 1.03776 25.1379 METAP2 907 covers exon(s) -709 disjoint 0.0151 chr3 32838509 32839315 1.26682 -0.0242 25.1297 TRI 71 3996 inside intron -90 disjoint 0.01511 chr20 50155875 50156749 1.28058 0.20269 25.1236 ZFP64 85181 inside intron -556 disjoint 0.01511 chrl5 30111374 30112303 0.71609 1.65893 25.1179 CHR A7 1357 inside intron -1022 disjoint 0.01511 chrl4 60182434 60183290 1.26869 0.01824 25.1036 SKI 2642 overlaps 3' 565 disjoint 0.01512 chrll 71467424 71468965 0.75469 1.75813 25.1005 NUMA1 255 inside intron 68 disjoint 0.01512 chr7 45925262 45926449 0.10738 1.01577 25.0954 IGFBP3 946 inside intron 213 disjoint 0.01513 chrl8 19065352 19066036 0.24992 1.53869 25.0943 CABLES 1 75566 inside intron -94283 disjoint 0.01513 chrl9 45006214 45007242 0.42027 1.3423 25.0577 DYR 1B 9438 downstream 0 cover 0.01515 chrl8 42748275 42750080 1.21013 0.5648 25.026 PIAS2 1383 inside intron 828 disjoint 0.01516 chrl l 12655706 12656356 -0.0692 1.31942 25.0083 TEAD1 85944 upstream -2149 disjoint 0.01517 chr7 96474559 96475276 1.22069 -0.0251 25.0044 DLX6 1334 covers exon(s) -874 disjoint 0.01517 chrl 224253757 224254644 0.41747 1.3794 24.9979 Clorf55 103 promoter 0 overlap 0.01518 chrl8 55087799 55089179 0.3144 -0.3934 24.9882 RAX 2425 inside intron 0 overlap 0.01519 chr2 74581772 74582905 1.55011 0.71884 24.9879 LBX2 1045 inside intron 2 disjoint 0.01519 chrl 6221407 6222763 1.40447 0.52572 24.9793 ICMT 2777 upstream 1519 disjoint 0.01519 chrl 4 23083610 23084392 1.84772 0.5563 24.9673 THTPA 10678 upstream 5450 disjoint 0.0152 chr2 176748340 176749299 0.91208 0.02858 24.9595 HOXD3 11290 downstream -143 disjoint 0.0152 chr9 130047380 130048066 0.37815 1.84071 24.9531 DNM1 41897 inside intron 4209 disjoint 0.0152 chr6 10995074 10996149 1.16464 0.32063 24.9334 NO 145 25 overlaps exon 0 cover 0.01522 downstream
chr2 201690124 201691350 0.26951 1.27673 24.9221 CFLAR 990 inside intron 93 disjoint 0.01522 chrl2 129493822 129495155 0.66136 1.54279 24.9216 RIMBP2 73207 inside intron 6510 disjoint 0.01522 chr8 29258861 29260023 1.17557 0.389 24.9183 DUSP4 2217 overlaps exon 1560 disjoint 0.01522 upstream
chrl2 52624026 52625571 0.13364 0.79154 24.9114 HOXC13 5184 overlaps exon 0 cover 0.01523 upstream
chr3 66001449 66002508 0.38287 1.42294 24.9104 MAGI1 1901 promoter -817 disjoint 0.01523 chrl2 41267825 41268987 0.06871 0.86251 24.8958 PRICKLEl 757 inside intron 112 disjoint 0.01524 chrX 24929408 24930111 1.57711 -0.0284 24.8903 ARX 13663 downstream 47 disjoint 0.01524 chr2 172659211 172660285 1.01468 0.16884 24.8651 DLX1 758 inside intron 0 overlap 0.01525 chr8 76480805 76481827 0.84606 0.00103 24.8574 H F4G 132930 upstream 178 disjoint 0.01526 chr7 89677688 89678738 1.16171 0.20215 24.8241 STEAP2 197 promoter 11 disjoint 0.01528 chr20 56699039 56699653 0.10322 1.46718 24.8191 NPEPL1 1614 promoter 1280 disjoint 0.01528 chrl8 33091257 33092452 0.39148 1.23978 24.8186 BRUNOL4 307488 inside intron -2653 disjoint 0.01528 chr7 154954292 154956173 0.23521 0.81399 24.8146 EN2 12117 downstream -128 disjoint 0.01528 chr8 75396619 75397600 0.01101 1.05031 . 24.811 JPH1 503 promoter 0 overlap 0.01528 chrX 23264565 23265432 -0.1544 0.87131 24.7931 PTCHD1 1550 inside intron -1005 disjoint 0.01529 chrl8 27557995 27559071 0.4S486 1.2158 24.7822 MCART2 35625 downstream 0 overlap 0.01531 chr7 29271301 29272621 0.82592 1.57638 24.7809 CHN2 70656 inside intron -69730 disjoint 0.01531 chrl4 68794896 68796027 2.37338 1.00705 24.7804 GALNTL1 640 promoter 0 overlap 0.01531 chr2 172487203 172488023 0.13214 1.15963 24,7438 HAT1 0 overlaps exon 0 overlap 0.01533 downstream
chr2 120821861 120823201 1.18834 0.35783 24.7397 INHBB 2393 overlaps exon 215 disjoint 0.01533 upstream
chr7 1211336 1217288 0.35764 1.49613 24.6947 ZFAND2A 45013 upstream 64 disjoint 0.01536 chr3 23827608 23828323 1.56665 0.29326 24.6927 UBE2E1 5166 covers exon(s) -96 disjoint 0.01536 chr2 66507641 66508824 1.03808 0.25835 24.6902 EIS1 7211 upstream 0 overlap 0.01536 chrl4 32470952 32471839 1.16315 0.21217 24.6837 NPAS3 6370 upstream 6 disjoint 0.01536 chr8 37713884 37714843 -0.0991 0.84445 24.6659 SPFH2 524 covers exon(s) -23 disjoint 0.01537 chrl2 52606401 52607519 0.02767 0.80968 24.6581 HOXC13 11323 upstream 49 disjoint 0.01538 chrl6 53920914 53921861 1.40413 0.39116 24.6576 IRX6 4943 overlaps exon -126 disjoint 0.01538 upstream
chrl l 69230364 69231690 0.6234 1.54718 24.6407 FGF19 2078 promoter -1254 disjoint 0.01539 chr4 186369034 186369714 1.5353 0.22333 24.6373 SNX25 757 inside intron -144 disjoint 0.01539 chrl6 48746197 48747408 0.02412 0.8348 24.6372 PAPD5 629 inside intron -88162 disjoint 0.01539 chr8 29266401 29267621 0.96596 0.12048 24.6272 DUSP4 2298 promoter 0 cover 0.0154 chrl7 45990271 45991506 1.18615 0.19106 24.6075 CACNA1G 1941 promoter 0 overlap 0.01541 chr3 15114165 15115540 0.27217 1.30372 24.6024 ZFYVE20 118 covers exon(s) 0 overlap 0.01541 chr8 132987378 132988616 0.02249 0.66462 24.5843 KIAA0143 32713 upstream -1136 disjoint 0.01542 chrl7 18030116 18030820 0.2877 1.63448 24.5673 ALKBH5 2103 inside intron -1031 disjoint 0.01543 chr6 41623896 41625068 1.14678 0.36037 24.5282 FOXP4 1755 inside intron 0 overlap 0.01547 chrl6 24172989 24173927 0.3659 1.39677 24.5121 CACNG3 449 promoter 614 disjoint 0.01548 chr2 45092581 45093264 2.01499 0.71953 24.5105 SK2 2556 upstream 612 disjoint 0.01548 chr2 219536269 219537705 -0.1255 0.60049 24.5051 CDK5R2 3628 downstream 0 overlap 0.01548 chr4 169638218 169638967 0.05941 1.11541 24.5015 PALLD 15824 upstream 0 overlap 0.01549 chrl9 3920026 3921580 -0.1668 0.66735 24.5004 DAPK3 0 overlaps 5' 0 overlap 0.01549 chrl7 74626071 74627670 0.56931 1.39089 24.4968 FLJ21865 43458 downstream 11330 disjoint 0.01549 chr2 177064022 177064669 0.19537 1.66408 24.4931 MTX2 221640 downstream -251 disjoint 0.01549 chrl 25589792 25590943 1.18072 0.28681 24.4856 SLC6A4 2962 upstream -2480 disjoint 0.0155 chr9 73571566 73572354 1.22381 24.4759 TMEM2 873 inside intron 543 disjoint 0.01551 chr8 1623222 1624361 0.46031 1.24032 24.4613 DLGAP2 186247 inside intron 2937 disjoint 0.01552 chr4 175375667 175376384 1.48091 0.23234 24.4523 FBX08 65592 downstream -3596 disjoint 0.01553 chr5 89806822 89808231 1.19935 0.20596 24.4512 POLR3G 386 inside intron -210 disjoint 0.01553 chrlO 124904668 124905628 0.32402 1.24344 24.4483 BUB3 809 covers exon(s) 0 overlap 0.01553 chr21 46293355 46294209 0.14302 1.39157 24.4446 COL6A1 67265 downstream -11188 disjoint 0.01554 chr7 27135137 27136029 1.58223 0.36514 24.4243 HOXA4 894 overlaps exon 68 disjoint 0.01555 upstream
chrl5 62853047 62853829 1.40265 0.2866 24.4182 RBPMS2 993 inside intron 140 disjoint 0.01555 chi5 157103864 157104511 0.08089 1.56545 24.4095 LSM11 532 inside intron 0 overlap 0.01556 chrl 27687239 27688914 -0.1938 0.61941 24.3897 WASF2 341 inside intron 15 disjoint 0.01557 chr7 27122168 27122917 1.38876 0.18203 24.3668 H0XA3 2821 inside intron -217 disjoint 0.01559 chrl4 103738579 103739610 0.86554 1.60147 24.3545 TDRD9 231893 downstream 17300 disjoint 0.0156 chrl9 12910898 12912013 0.19681 1.36384 24.3509 CALR 476 covers exon(s) -89 disjoint 0.0156 chrl l 613S4378 61355606 0.50708 1.29417 24.3455 FADS2 2090 inside intron -1092 disjoint 0.0156 chr2 129374108 129375491 0.40029 1.56863 24.3368 HS6ST1 581387 upstream 278 disjoint 0.01561 chrl 1700503 1701918 1.34753 0.49883 24.3239 NADK 735 promoter -61 disjoint 0.01562 chrl8 71047479 71048517 0.76611 -0.1175 24.2893 ZADH2 1587 inside intron 385 disjoint 0.01564 chrlO 27186912 27188355 0.12381 0.75669 24.2868 ABI1 1609 inside intron 817 disjoint 0.01564 chrl4 49766139 49767249 0.13382 0.84096 24.2815 S0S2 501 inside intron 301 disjoint 0.01565 chr20 48242857 48244287 0.20786 1.05595 24.2773 CEBPB 2075 close to 3' -428 disjoint 0.01565 chrl 7 73547890 73548536 -0.1409 1.32533 24.2737 TNRC6C 8052 upstream 133 disjoint 0.01566 chrl 7 29935644 29936578 -0.0406 0.88515 24.2543 TMEM132E 3764 inside intron -2238 disjoint 0.01567 chr3 50102142 50102993 -0.0303 0.84413 24.2269 RBM5 771 covers exon(s) 0 overlap 0.01569 chrl2 60870056 60871073 0.88816 0.06135 24.2026 FAM19A2 1744 inside intron 0 overlap 0.0157 chrl l 19323876 19324554 -0.2576 1.47109 24.202 E2F8 104794 upstream 0 inside 0.0157 chr8 1640944 1642272 1.11972 1.9083 24.1935 DLGAP2 203969 inside exon -3778 disjoint 0.0157 chrX 101656865 101657878 0.06479 1.08585 24.1851 TMSL8 476 inside intron 115 disjoint 0.01571 chrl7 11088391 11089635 0.60406 1.35155 24.179 FLJ45455 2621 inside intron -2250 disjoint 0.01571 chrX 106903493 106904860 1.30823 0.5758 24.1702 TSC22D3 812 inside intron 402 disjoint 0.01572 chrl 238841218 238842631 0.26982 0.86439 24.1647 GREM2 0 overlaps 5' -117875 disjoint 0.01573 chrl 4 36194933 36196159 0.87167 0.14659 24.1509 PAX9 4496 upstream 0 cover 0.01573 chr7 19149528 19150523 1.35647 0.29482 24.1467 FERD3L 1045 close to 3' 223 disjoint 0.01574 chr4 111754619 111755634 1.13962 0.13709 24.1238 PITX2 8068 downstream -1779 disjoint 0.01575 chr2 19425177 19426753 0.04839 0.72634 24.0972 OSR1 3325 upstream 0 cover 0.01577 chrl 6 10180085 10180732 0.45141 1.77645 24.0943 GRIN2A 3379 inside intron 712 disjoint 0.01578 chr4 40447329 40448484 1.15832 0.11385 24.0913 NSUN7 631 covers exon(s) 0 cover 0.01578 chr6 32202746 32203633 0.49557 1.59409 24.0759 CREBL1 361 covers exon(s) 2165 disjoint 0.01579 chr2 40530621 40531884 0.17824 1.24834 24.0627 SLC8A1 19674 upstream 97 disjoint 0.0158 chrl5 34968280 34969149 0.93826 -0.1053 24.0516 MEIS2 208645 downstream -1206 disjoint 0.01581 chr6 85532542 85533471 1.31831 0.35545 24.0443 KIAA1009 538510 upstream -1691 disjoint 0.01582 chr4 174689355 174690314 1.02822 0.09098 24.0217 HAND2 1403 promoter 0 overlap 0.01583 chrl 6 55227263 55228705 0.90034 0.02555 24.0128 MT1A 1373 promoter -35 disjoint 0.01584 chrl 9 63407589 63408471 2.29627 1.04725 24.0094 ZNF274 21382 inside intron 0 overlap 0.01584 chrl 7 17569348 17570514 0.80527 0.04425 24.0069 RAI1 43837 inside intron -123 disjoint 0.01584 chrlO 3499404 3500060 0.13852 1.93847 23.9932 PITRM1 294402 upstream -8828 disjoint 0.01585 chrlO 102035372 102036295 -0.0082 0.79718 23.9579 BLOC1S2 0 overlaps 5' 0 overlap 0.01587 chr5 92932803 92934223 0.9986 0.32296 23.9287 NR2F1 10575 upstream 0 inside 0.01589 chr20 38753645 38754565 1.40109 0.34194 23.8991 MAFB 2356 promoter 138 disjoint 0.0159 chrX 51168458 51169192 0.07768 1.2485 23.8921 LOC340602 1952 close to 3' -807 disjoint 0.01591 chrlO 121761885 121762565 0.54542 1.9077 23.8735 SEC23IP 119673 downstream -472 disjoint 0.01592 chr8 133563765 133564934 0.39803 1.64251 23.8602 KCNQ3 1580 promoter -997 disjoint 0.01593 chr9 102832271 102833053 0.59834 1.66581 23.8518 PRG-3 1420 inside intron -277 disjoint 0.01594 chr5 140532162 140532975 0.9366 2.14407 23.8317 PCDHB7 0 overlaps 5' 890 disjoint 0.01594 chrl 2 28015165 28016172 1.01602 0.04459 23.8305 PTHLH 10 overlaps exon -125 disjoint 0.01595 downstream
chrlO 26264471 26266406 0.27575 0.97024 23.8259 MY03A 1270 covers exon(s) -443 disjoint 0.01595 chrl4 92460706 92462209 0.28844 1.34755 23.8137 CHGA 1462 inside intron -1054 disjoint 0.01595 chr3 171240759 171241541 0.75819 1.81464 23.7874 GPR160 1363 inside intron -1221 disjoint 0.01597 chr6 150501895 150502887 0.30216 1.19675 23.7868 PPP1R14C 3038 upstream 2577 disjoint 0.01597 chrl5 65601462 65602211 -0.1765 0.92526 23.7578 MAP2K5 19863 upstream -227 disjoint 0.01599 chr21 37000964 37001823 0.96679 -0.096 23.7463 SIM2 7104 inside intron 0 overlap 0.016 chrl l 35399388 35400170 1.69269 0.78247 23.7325 SLC1A2 1708 promoter -930 disjoint 0.01601 chr2 120019854 120020363 0.09081 1.75213 23.7324 GC33657 1338 covers exon(s) -929 disjoint 0.01601 chr5 140199544 140200600 0.20547 0.92465 23.7297 PCDHA7 5392 inside intron 591 disjoint 0.01601 chrl 36624899 36626079 0.24319 1.49379 23.7153 STK40 828 promoter -439 disjoint 0.01602 chr7 157652761 157654593 0.22495 1.07633 23.6933 PTPRN2 418585 inside intron -2727 disjoint 0.01604 chrl3 99427732 99428704 1.37536 0.3686 23.689 ZIC2 3615 upstream 1049 disjoint 0.01604 chr6 30540906 30542081 0.40575 1.20128 23.6888 HLA-E 23168 upstream 0 overlap 0.01604 chrl6 86461341 86462950 1.20693 0.36209 23.687 SLC7A5 741 promoter -380 disjoint 0.01604 chr2 127691838 127692833 1.43086 0.40462 23.6705 FLJ 16008 12026 upstream 26 disjoint 0.01606 chr20 42371931 42372890 -0.0022 0.93691 23.6566 R3HDML 26149 upstream 0 overlap 0.01607 chr9 130838923 130840220 0.08948 0.94412 23.653 FAM73B 0 overlaps 5' 0 overlap 0.01607 chrl 4 20561657 20562621 1.83144 0.63558 23.6461 NDRG2 482 inside intron 0 overlap 0.01607 chr3 14616414 14617668 1.14868 1.96133 23.64 C3orfl9 50588 upstream 1054 disjoint 0.01608 chr3 126255030 126255920 0.37461 1.18886 23.6317 SLC12A8 158352 downstream 1013 disjoint 0.01608 chrl l 2654100 2655338 -0.0949 0.61077 23.6312 CNQ1 214841 inside intron 21648 disjoint 0.01608 chrl l 35398373 35399313 1.29007 -0.006 23.631 SLC1A2 693 promoter 0 overlap 0.01608 chr3 148622168 148623185 1.09294 0.19021 23.6051 Z1C1 12298 downstream 0 overlap 0.0161 chrl5 94702050 94702937 1.3468 0.43232 23.5945 NR2F2 27101 downstream -402 disjoint 0.0161 1 chr7 43117433 43118539 0.03216 0.76647 23.5624 HECW1 183 promoter 6 disjoint 0.01613 chrl 8 44753874 44754650 2.2351 1.13172 23.5573 S AD7 22796 upstream 972 disjoint 0.01614 chrl2 33484972 33485790 0.12823 1.28803 23.5477 SYT10 952 promoter -655 disjoint 0.01614 chr5 1314942 1315665 0.90346 2.06603 23.525 TERT 32496 inside intron -4720 disjoint 0.01615 chrl3 23743628 23744225 0.07069 1.45151 23.5141 SPATA13 110742 inside intron 35873 disjoint 0.01616 chrl 154256172 154257128 0.75337 1.93118 23.5007 SSR2 253 covers exon(s) 0 overlap 0.01617 chr7 50317790 50318774 0.47911 1.34126 23.4735 IKZFl 2867 inside intron -2725 disjoint 0.01619 chrl5 39738621 39739440 1.37577 0.30668 23.4609 TYR03 100098 downstream 387 disjoint 0.01619 chr2 56002649 56003424 1.79085 0.65177 23.4569 EFEMP1 435 covers exon(s) 420 disjoint 0.0162 chrlO 125029804 125030729 0.28915 1.35179 23.4468 BUB3 125945 downstream -125088 disjoint 0.0162 chr2 111590128 1 11591020 0.36031 1.34363 23.4434 FLJ44006 1896 promoter 657 disjoint 0.0162 chrl l 63364275 63365201 -0.1722 0.75734 23.4333 MARK2 805 inside intron -225 disjoint 0.01621 chr6 27677523 27679237 1.24864 0.34339 23.4196 ZNF184 128666 upstream 27429 disjoint 0.01622 chrl 3 24215341 24216093 0.48712 1.59838 23.4015 RNF17 20207 upstream 1575 disjoint 0.01623 chr3 4883264 4884083 0.48624 1.50732 23.3987 ITPR1 373129 downstream 879 disjoint 0.01623 chr8 21963796 21965137 0.95335 0.22175 23.3862 FGF17 7423 downstream -2093 disjoint 0.01624 chrl4 103381847 103382992 1.27569 0.25516 23.3707 PPP1R13B 562 inside intron 0 overlap 0.01625 chrX 19441074 19442138 0.44789 1.35815 23.3243 SH3KBP1 373501 downstream 786 disjoint 0.01628 chrl 7 25588690 25589671 1.16801 0.09105 23.3138 SLC6A4 1860 promoter -1378 disjoint 0.01629 chr7 30686516 30687579 0.84115 1.69615 23.307 CRHR2 841 inside intron 318 disjoint 0.01629 chr6 26162285 26163244 0.32238 1.21033 23.3054 HIST1H1C 1433 close to 3' 902 disjoint 0.01629 chr22 19191935 19193907 -0.0682 0.48813 23.3036 PCQAP 50 overlaps exon 0 overlap 0.0163 downstream
chrl 9 51059637 51060566 0.76015 -0.1311 23.3017 F0XA3 280 inside intron 0 overlap 0.0163 chrl l 75599754 75600641 2.01195 0.65958 23.2902 WNT11 4533 upstream 0 cover 0.0163 chrl 117007880 117008875 0.60167 1.47881 23.2896 IGSF3 2961 inside intron 2472 disjoint 0.0163 chrX 53129275 53130273 0.26251 0.96542 23.2885 TSPYL2 989 inside intron -534 disjoint 0.0163 chr6 91377978 91379140 1.11499 0.33277 23.2883 MAP3 7 24351 upstream -38 disjoint 0.0163 chr4 4910517 4911529 1.36056 0.5542 23.2776 MSX1 770 promoter 0 cover 0.01631 chr3 151961175 151962284 0.54722 1.28724 23.2742 SIAH2 1668 inside intron 137 disjoint 0.01632 chrlO 134771623 134772618 0.03316 1.01241 23.2724 GPR123 37201 inside intron -2658 disjoint 0.01632 chr9 21959811 21960716 1.01038 0.11545 23.2619 CDKN2A 4321 inside intron 197 disjoint 0.01632 chrl 158520001 158521672 0.14485 0.60178 23.2613 PEX19 0 overlaps 5' -20926 disjoint 0.01632 chr2 70165546 70166718 1.42284 0.24201 23.2613 PCBP1 1486 promoter 0 overlap 0.01632 chr2 219143162 219144124 0.06128 1.12741 23.2545 RQCD1 1241 inside intron -963 disjoint 0.01633 chr2 85407474 85408262 0.44459 1.3357 23.2511 TGOLN2 622 inside exon 0 overlap 0.01633 chrl l 2033558 2034919 0.56854 1.12713 23.2133 IGF2 81860 downstream -42991 disjoint 0.01636 chr20 9768497 9769246 0.23902 1.35446 23.1931 PAK7 976 promoter -636 disjoint 0.01638 chr6 101024068 101025061 1.60027 0.49712 23.1771 SIM1 5797 upstream 0 overlap 0.01639 chr6 27755857 27757160 1.10253 0.45333 23.1709 HIST1H2BL 126527 downstream 0 overlap 0.01639 chr2 190154525 190155740 0.94628 0.17434 23.1681 SLC40A1 668 promoter -297 disjoint 0.01639 chrl5 77362749 77364320 0.46783 1.34953 23.1506 T ED3 26225 upstream 0 cover 0.01641 chr3 188869372 188870572 0.69689 1.53012 23.141 SST 322 overlaps 3' 33 disjoint 0.01641 chr5 140843995 140845397 0.67995 0.08341 23.1398 PCDHGC3 8243 inside intron 0 cover 0.01642 chrlS 28302409 28303467 0.26279 1.00946 23.129 FAM59A 977 inside intron 646 disjoint 0.01642 chr5 43053057 43053716 1.31641 0.05369 23.1217 LOC389289 22381 downstream 9 disjoint 0.01643 chr5 140241052 140241870 0.4963 1.51267 23.1117 PCDHA12 5938 inside intron 198 disjoint 0.01644 chrl 6 55224610 55226920 1.17798 0.41567 23.1085 T1M 538 overlaps 3' 0 overlap 0.01644 chr5 1258544 1259820 0.79524 1.49688 23.0983 SLC6A19 3779 inside intron 225 disjoint 0.01645 chr3 18459643 18460468 1.42494 0.47418 23.0896 SATB1 19300 upstream 0 overlap 0.01645 chr9 73952498 73953630 0.61999 2.0961 23.065 GDA 482 promoter 431 disjoint 0.01647 chr4 183299788 183300705 1.46397 0.26927 23.0513 DCTD 774918 downstream 0 overlap 0.01648 chr9 88706845 88707680 1.14082 -0.0054 23.018 GAS1 44243 downstream 42724 disjoint 0.01651 chrl 224252595 224253728 0.07986 0.78984 23.0047 Clorf55 0 overlaps 5' 0 overlap 0.01652 chr2 54049034 54050390 0.02365 0.61301 23.0018 PSME4 963 inside intron 890 disjoint 0.01652 chr7 157227404 157228342 1.28543 2.14956 22.9875 PTPRN2 844836 inside intron -7902 disjoint 0.01653 chr4 52597757 52598360 0.11702 1.7271 22.9722 SGCB 842 inside intron 851 disjoint 0.01654 chrlO 28075465 28076555 0.88868 -0.0817 22.9641 KX 713 promoter -248 disjoint 0.01655 chrl5 50870748 50871691 0.95859 0.12996 22.95 ONECUT1 1248 promoter 0 overlap 0.01656 chrl l 85454542 85456026 -0.1068 0.61278 22.945 PICAL 1729 inside intron 1347 disjoint 0.01656 chr5 77981275 77982129 1.54069 0.68722 22.9413 LHFPL2 872 promoter -299 disjoint 0.01656 chrl4 90351236 90351946 0.45787 1.74516 22.9298 TTC7B 567 inside intron 34 disjoint 0.01657 chr7 1093227 1094312 0.33645 1.34682 22.9256 GPR30 259 overlaps exon 0 overlap 0.01658 downstream
chr2 236753384 236754720 0.1219 0.87875 22.8877 GBX2 11994 upstream -182 disjoint 0.0166 chrX 79166175 79166819 0.06753 1.30568 22.8614 TBX22 1778 covers exon(s) 310557 disjoint 0.01662 chr20 56841054 56842160 1.06523 2.01167 22.8601 GNAS 6029 upstream 5830 disjoint 0.01663 chr8 782958 783914 1.03028 1.88066 22.8188 ERICH1 111733 upstream -2160 disjoint 0.01665 chr2 234327018 234327830 0.38037 1.95772 22.8117 UGT1A3 24507 inside intron 504 disjoint 0.01665 chrl 6 34067261 34067906 0.35171 1.61377 22.8028 LOC649159 197258 upstream -512 disjoint 0.01666 chr4 100069578 100070639 0.13895 1.00875 22.8024 EIF4E 0 overlaps 5' -3 disjoint 0.01666 chrl7 71642992 71643625 1.22986 -0.099 22.7978 FOXJ1 4535 downstream 1609 disjoint 0.01666 chrl l 90437448 90438404 0.08745 0.98764 22.745 CHORDCl 841595 upstream -841442 disjoint 0.01671 chrl9 54691456 54692651 0.02409 0.82573 22.7253 RPS11 11 covers exon(s) 0 overlap 0.01672 chr4 40013694 40014344 0.58492 1.82755 22.7054 CHRNA9 17881 upstream 120234 disjoint 0.01674 chr9 73250569 73251492 0.91449 -0.0064 22.7029 TMEM2 321735 downstream 0 overlap 0.01674 chr8 25962205 25963282 0.71019 -0.1937 22.7018 EBF2 3897 upstream -446 disjoint 0.01674 chrl5 20042661 20043635 1.01283 2.16855 22.6968 OR4N4 158825 downstream 2947 disjoint 0.01675 chrX 147391004 147391894 0.7511 -0.1508 22.6967 AFF2 1174 inside intron -29 disjoint 0.01675 chrX 24944096 24945079 0.94622 0.10451 22.693 ARX 322 promoter 0 overlap 0.01675 chrll 34333888 34334814 0.99479 0.12951 22.6822 ABTB2 563 inside intron 0 overlap 0.01676 chrl7 70432672 70433700 0.34804 1.16506 22.6778 0T0P2 708 covers exon(s) -58 disjoint 0.01676 chr9 125816441 125817466 1.10187 0.17694 22.6621 LHX2 2732 overlaps exon 0 inside 0.01677 upstream
chrX 9939268 9940550 1.35799 0.2174 22.6607 WWC3 3061 upstream 1963 disjoint 0.01677 chrl8 54683040 54684032 0.40773 1.24646 22.6458 ZNF532 2000 covers exon(s) -772 disjoint 0.01678 chr9 126044511 126045440 0.785 1.84458 22.638 NEK6 14629 upstream 14630 disjoint 0.01679 chr2 115135470 115136151 0.29254 1.65873 22.6326 DPP10 219102 inside intron 47 disjoint 0.01679 chr7 43763958 43764428 1.78764 0.10568 22.6326 BLVRA 368 promoter 0 overlap 0.01679 chrl3 45322884 45324348 0.14484 0.75737 22.6322 LOC283514 0 overlaps 5' -136669 disjoint 0.01679 chrX 39828015 39828833 0.96063 -0.1223 22.6118 BCOR 12766 inside intron 0 overlap 0.01681 chrl7 5613893 5614799 0.02312 1.43018 22.608 NALP1 185341 upstream -268567 disjoint 0.01681 chr20 35472876 35475045 0.85936 1.89224 22.6059 SRC 64906 downstream -4259 disjoint 0.01682 chr6 27172303 27173682 1.29391 0.56843 22.5739 HIST1H2BJ 34871 downstream 0 cover 0.01685 chr4 6249948 6251480 0.91412 1.7051 22.5658 JA MIP1 1702 inside intron 264 disjoint 0.01685 chrl6 3102802 3103758 -0.002 0.95809 22.5404 ZNF205 239 covers exon(s) 5596 disjoint 0.01687 chrl 44218171 44219358 0.72922 1.61573 22.5298 B4GALT2 719 inside intron 0 overlap 0.01688 chrl4 47215525 47216625 0.02396 0.74703 22.5099 MAMDC1 333381 upstream -186 disjoint 0.0169 chrl 9 15527701 15528666 -0.0867 1.08761 22.4978 FLJ39501 47365 downstream -4343 disjoint 0.01691 chrl2 127867722 127868408 0.67551 1.93885 22.4897 SLC15A4 6085 inside intron 5492 disjoint 0.01692 chr3 158288208 158289250 0.15482 0.98903 22.4819 FLJ16641 261419 downstream 129 disjoint 0.01693 chrX 48974558 48975133 2.05366 0.5037 22.4774 CACNA1F 1643 covers exon(s) -94 disjoint 0.01693 chr6 149907573 149908633 0.30029 0.933 22.4745 PPIL4 230 inside intron 91 disjoint 0.01693 chrl 232808420 232809375 0.27305 1.21176 22.4668 IRF2BP2 2518 inside exon 1524 disjoint 0.01694 chr3 2113733 2114998 0.19606 0.8881 22.4291 CNTN4 2248 promoter 31 disjoint 0.01697 chr6 18093331 18093901 0.07311 1.59279 22.419 KIF13A 1790 inside intron 1493 disjoint 0.01698 chrl 40716028 40716633 0.02392 1.38891 22.4177 ZNF642 140 overlaps exon -54 disjoint 0.01698 downstream
chr7 42234456 42235347 1.37892 0.082 22.4075 GLI3 5037 upstream -108 disjoint 0.01699 chr4 108964323 108965033 1.14756 -0.0911 22.4068 MGC26963 68845 upstream 245 disjoint 0.01699 chr4 88076287 88077072 1.07674 0.02261 22.4024 C4orC6 43717 upstream -59 disjoint 0.01699 chrll 16588183 16588929 1.37095 0.34815 22.3837 Cllorf58 127840 upstream 155 disjoint 0.01701 chrl 4 22494938 22495932 0.17357 1.16031 22.374 C14orf94 227 inside intron 0 overlap 0.01702 chrl 7 53437602 53438321 0.14087 1.35404 22.3683 SFRS1 1265 overlaps two exons 428 disjoint 0.01703 chrl 7 35961702 35962241 0.41585 1.88681 22.3534 CCR7 13008 downstream 95229 disjoint 0.01704 chrlS 29945453 29946659 0.39234 1.31404 22.3359 CHRNA7 163358 upstream 162797 disjoint 0.01705 chrl l 119549283 119549966 0.4968 1.77682 22.3183 TRM29 35211 upstream -3788 disjoint 0.01707 chr20 20817901 20818374 0.65032 2.36003 22.3014 C20orf74 176779 upstream 130391 disjoint 0.01709 chrl 158159568 158160878 0.34987 0.94857 22.2893 TAGLN2 1029 inside intron 75 disjoint 0.01709 chrl 90060349 90061065 1.9534 1.07972 22.2841 LRRC8D 249 inside intron -539 disjoint 0.0171 chr2 54535446 54536496 0.95171 0.15618 22.2764 SPTBN1 461 promoter 0 overlap 0.0171 chrl4 81068322 81069501 -0.0815 0.68846 22.2762 SEL1L 384 inside intron 3 disjoint 0.0171 chr2 9689240 9690265 1.1995 0.48349 22.2708 YWHAQ 684 promoter -227 disjoint 0.01711 chr4 76774925 76775602 1.64849 0.5387 22,2648 CDKL2 331 promoter 0 overlap 0.0171 1 chr6 146099423 146100242 0.42825 1.36883 22.2467 EPM2A 740 promoter -749 disjoint 0.01713 chrl 8 74574075 74574920 0.04083 1.1994 22.2113 SALL3 266342 upstream -9409 disjoint 0.01716 chr20 20128127 20128729 0.20745 1.51025 22.205 C20or£26 146932 covers exon(s) -146656 disjoint 0.01717 chr3 151384255 151385141 0.03524 0.94354 22.1966 PFN2 212825 upstream -2263 disjoint 0.01717 chr5 151764850 151765680 0.70877 1.76397 22.1926 N UR2 0 overlaps 5' -479833 disjoint 0.01718 chrl 42157649 42158594 1.29463 0.27216 22.1912 HIVEP3 868 promoter -1059 disjoint 0.01718 chr6 1566585 1568050 1.36016 0.71793 22.1837 G DS 622794 downstream -492 disjoint 0.01718 chr5 159730318 159730788 0.20646 1.78989 22.177 C1QTNF2 93 promoter -43 disjoint 0.01719 chr7 39631072 39631954 -0.1382 0.99516 22.1756 RALA 1386 inside intron -755 disjoint 0.01719 chr3 96138188 96138982 1.22847 2.5243 22.166 NSUN3 873644 downstream 437 disjoint 0.0172 chrl2 3468415 3469441 0.23412 1.25281 22.1518 PRMT8 1244 promoter 786 disjoint 0.01721 chr22 47762262 47763050 0.52034 1.44711 22.1475 FAM19A5 411422 downstream 0 cover 0.01721 chr8 22355669 22356630 0.21092 0.91846 22.135 PPP3CC 1129 inside intron -582 disjoint 0.01722 chrl 3 78081593 78082552 0.76661 -0.0111 22.1342 C13orf7 48762 downstream 0 overlap 0.01722 chr2 227370044 227371285 0.49637 1.42275 22.1289 IRS1 1433 inside exon 0 overlap 0.01723 chrl 119349924 119350433 2.1671 0.56682 22.1073 TBX15 16223 upstream 234 disjoint 0.01725 chrl 5 70234653 70235543 0.27923 1.23843 22.097 GRA D2 41636 downstream 28187 disjoint 0.01726 chrl 6 66827848 66828699 0.93081 -0.0841 22.0961 RBM35B 212 promoter 0 inside 0.01726 chr8 38244256 38245038 0.82329 1.89399 22.0874 PPAPDC1B 833 covers exon(s) 216 disjoint 0.01727 chr6 166405574 166406359 0.98032 1.94866 22.0748 LOC441177 84546 downstream -63343 disjoint 0.01728 chr8 73078887 73079961 1.48168 0.3548 22.0666 TRPA1 70411 downstream 0 overlap 0.01728 chr6 26125295 26126121 0.68788 1.62773 22.0621 HIST1H1A 0 overlaps 5' 2529 disjoint 0.01729 chr8 79879836 79881043 0.1762 0.9005 22.0601 IL7 0 overlaps 5' 0 overlap 0.01729 chrl 8 75638252 75639226 0.81199 1.77112 22.0505 CTDP1 97464 downstream -4671 disjoint 0.0173 chrl l 62067233 62068240 0.36765 1.1541 22.0419 AHNA 2667 inside intron 1618 disjoint 0.01732 chr8 100019629 100020960 0.8441 -0.0232 22.0418 OSR2 4901 upstream 236 disjoint 0.01732 chrlO 22643793 22644671 0.88237 -0.1608 22.041 C0MMD3 633 promoter 242 disjoint 0.01732 chr3 61211906 61213209 0.11174 1.03751 22.0371 FHIT 0 overlaps 5' 0 overlap 0.01732 chr2 128358078 128358950 0.56054 1.74353 22.0345 MGC4268 0 overlaps 5' 307 disjoint 0.01732 chrlO 71885836 71886766 1.2753 0.46745 22.0262 NODAL 14408 upstream 1370 disjoint 0.01733 chrl 113736024 113736776 0.12029 1.26627 22.0219 MAGI3 846 inside intron -431 disjoint 0.01733 chrl 7 7732293 7733297 0.54833 1.43424 22.0195 CHD3 3445 inside intron -2477 disjoint 0.01734 chrl 4093494 4094418 0.66924 1.55556 22.0042 Clorfl74 286786 upstream -391 disjoint 0.01735 chrl l 82548065 82548962 -0.0738 0.88837 21.9963 PCF11 2205 inside intron -1857 disjoint 0.01736 chr2 161987262 161988044 1.27039 0.26029 21.9769 TBR1 6397 inside intron 37 disjoint 0.01737 chrl 9 1834499 1835704 0.54016 1.84189 21.9624 FAM108A1 727 inside intron 64 disjoint 0.01739 chr21 45319928 45321040 0.30479 1.31526 21.9453 AD ARB 1 986 inside intron -28 disjoint 0.0174 chrl l 2601496 2603184 0.30429 0.80832 21.9417 KCNQ1 162237 inside intron -41451 disjoint 0.01741 chr21 32169427 32170241 0.81434 1.82832 21.8872 HUNK 1929 inside intron -947 disjoint 0.01746 chr5 54636925 54638868 0.13807 0,89274 21.8854 DHX29 409 inside intron 98 disjoint 0.01746 chr9 36991137 36991676 0.80571 2.14189 21.8838 PAX5 32799 inside intron 813 disjoint 0.01746 chrX 41219178 41220199 1.19763 0.23456 21.8823 NYX 27548 overlaps 3' -108 disjoint 0.01746 chr20 21319104 21320024 0.87773 0.07944 21.8809 XRN2 87163 downstream 17 disjoint 0.01746 chrl 9 35631401 35632494 0.09209 0.81079 21.8758 ZNF536 76234 inside intron 1199 disjoint 0.01747 chr3 19252137 19252988 0.10192 1.06502 21.8746 KCNH8 87117 inside intron -87033 disjoint 0.01747 chrl 4 93323873 93324487 1.38019 0.08791 21.8741 PRIMA 1 31 inside intron 0 inside 0.01747 chrl l 65003107 65004030 0.34789 1.4536 21.847 SCYL1 45093 upstream 0 overlap 0.0175 chrl l 124241849 124243387 0.24586 0.83526 21.8341 R0B03 1358 inside intron -174 disjoint 0.01751 chr2 30224764 30225861 1.29723 0.61615 21.8224 YPEL5 1433 inside intron -339 disjoint 0.01753 chr7 77264267 77265259 0.09593 1.1701 21.8156 TMEM60 423 inside intron 8 disjoint 0.01753 chrl 16148010 16148582 0.77621 2.14213 21.777 ZBTB17 26518 inside intron -3841 disjoint 0.01756 chrl l 87880443 87881328 1.4178 0.51105 21.7734 GRM5 539509 overlaps 3' 30 disjoint 0.01756 chrl 183970441 183971496 0.04602 0.76241 21.7716 H CN1 136 overlaps exon -156 disjoint 0.01757 downstream
chr4 42095363 42096654 1.0525 0.30382 21.7689 ATP8A1 256992 downstream 0 overlap 0.01757 chr5 95321187 95322119 0.26984 1.23952 21.7663 ELL2 1411 inside intron 5 disjoint 0.01757 chrl 43195016 43196051 1.59114 0.34181 21.759 SLC2A1 1036 inside intron 3 disjoint 0.01758 chrl l 65941391 65942367 0.33192 1.31691 21.7584 PAS4 2683 upstream 2339 disjoint 0.01758 chrl 7 56884781 56885392 1.09842 -0.1816 21.7531 TBX4 3196 upstream 0 overlap 0.01759 chr4 111767049 111767621 1.58192 0.19776 21.7503 ΡΓΓΧ2 10335 inside intron 1707 disjoint 0.01759 chr6 100166667 100167738 0.9635 0.13494 21.7412 PRDM13 5297 overlaps exon 0 overlap 0.0176 upstream
chr22 18220701 18221699 0.37919 1.24116 21.734 C22or£29 639 inside intron 184 disjoint 0.01761 chr7 147131236 147131988 0.33411 1.24491 21.7339 CNTNAP2 1686851 inside intron 535439 disjoint 0.01761 chrl 204873560 204874560 0.30274 1.2543 21.7338 DYRK3 943 promoter 586 disjoint 0.01761 chrl 4 103732260 103733567 0.37512 1.4277 21.7232 TDRD9 225574 downstream -16029 disjoint 0.01762 chr20 5935729 5936586 -0.45 0.35885 21.7042 CRLS1 851 inside intron -432 disjoint 0.01764 chrX 151559858 151561150 1.57419 0.63851 21.6857 GABRQ 2566 inside intron -2255 disjoint 0.01766 chrl9 60690067 60691236 0.2046 0.99727 21.6581 NAT 14 1662 overlaps 3' -36 disjoint 0.01769 chrlO 103528229 103529095 1.25846 0.25915 21.6554 NPM3 4052 downstream 0 overlap 0.01769 chrlO 102986673 102988123 0.86654 0.13717 21.6524 LBX1 7967 upstream -37 disjoint 0.0177 chr5 114906637 114907566 0.13893 1.01576 21.6496 FEM1C 923 overlaps exon 446 disjoint 0.0177 upstream
chr6 52966527 52967252 -0.1327 1.03968 21.648 GSTA4 846 covers exon(s) 272 disjoint 0.0177 chr6 31739482 31740684 0.34771 1.01018 21.6425 BAT4 457 covers exon(s) 110 disjoint 0.01771 chrl l 2659433 2660734 0.32085 0.93189 21.6423 KCNQ1 220174 inside intron 16252 disjoint 0.01771 chr20 48781985 48782595 1.07151 -0.227 21.6239 PARD6B 498 inside intron 0 overlap 0.01773 chr2 65208973 65210139 0.14129 0.92614 21.6072 RAB1A 653 inside intron 100 disjoint 0.01774 chrX 103104235 103105108 0.01231 0.91374 21.6009 MGC39900 375 inside intron 0 overlap 0.01775 chrl 119335829 119336562 1.92316 0.60276 21.5988 TBX15 2128 promoter 627 disjoint 0.01775 chr9 129363274 129364643 0.77769 1.66699 21.5708 C9orf88 6532 inside intron 5718 disjoint 0.01778 chrl4 53756161 53756985 1.1009 0.1319 21.5703 CD N3 176490 upstream 176188 disjoint 0.01778 chr5 112286167 112286949 0.35219 1.43928 21.5352 REEP5 238 promoter -136 disjoint 0.01781 chrl 7 70444424 70446058 0.61189 1.42809 21.5294 OTOP3 933 inside intron -228 disjoint 0.01782 chrl l 31787082 31788016 0.81008 -0.0847 21.5254 PAX6 1417 inside intron 180 disjoint 0.01782 chr5 53851745 53852905 0.08379 1.4063 21.5224 SNAG1 2206 close to 3' -682 disjoint 0.01782 chr3 120702133 120702846 0.28425 1.27808 21.5216 C3orfl 2076 covers exon(s) -1690 disjoint 0.01782 chrX 103695300 103696347 0.45462 1.30307 21.5123 IL1RAPL2 1304 promoter 103 disjoint 0.01783 chrl 2 34208737 34210167 1.10597 1.91199 21.5069 ALG10 142255 downstream 781 disjoint 0.01784 chrl 6 31793543 31794498 -0.2337 0.56934 21.5062 ZNF267 883 inside intron -442 disjoint 0.01784 chr6 99396335 99397127 1.07791 -0.0192 21.4936 POU3F2 7035 downstream 0 overlap 0.01785 chrl5 21445549 21447200 0.37471 1.25631 21.4924 NDN 36342 downstream 35452 disjoint 0.01785 chrl 9 10393069 10394100 0.41529 1.25752 21.4896 CDC37 17799 upstream -65 disjoint 0.01786 chrl 39053719 39054421 0.66777 1.65115 21.4874 RRAGC 43505 downstream 1775 disjoint 0.01786 chrl 7 34261296 34262720 -0.0285 0.83885 21.4812 RPL23 858 covers exon(s) 277 disjoint 0.01786 chr22 36145110 36145832 0.96874 1.98247 21.4593 LRRC62 43586 upstream 0 overlap 0.01788 chr3 37470112 37470861 0.21204 1.20272 21.4428 ITGA9 1296 inside intron -570 disjoint 0.01789 chr4 174684373 174684978 1.23564 -0.0213 21.4334 HAND2 2974 inside exon 0 overlap 0.0179 chrX 153014689 153015369 0.26841 1.42759 21.4211 MECP2 953 inside intron 393 disjoint 0.01791 chr7 96468721 96469347 1.36646 0.05083 21.4204 DLX6 3878 upstream 0 overlap 0.01791 chr9 85782225 85783399 -0.0331 0.72928 21.4181 HNRPK 1502 covers exon(s) 747 disjoint 0.01791 chr5 140719534 140720335 0.91768 2.11722 21.4093 PCDHGB2 0 overlaps 5' 1023 disjoint 0.01792 chr20 591479 592174 0.20606 1.39841 21.4074 SCRT2 12648 inside exon 0 overlap 0.01792 chr3 8458697 8459554 1.05977 2.16268 21.4029 LMGD1 58956 upstream 58647 disjoint 0.01793 chrX 128915143 128916414 0.5271 -0.2348 21.4007 UTP14A 47304 downstream 0 overlap 0.01793 chrl6 71648030 71648827 0.8285 -0.1027 21.3951 ATBF1 8256 upstream 188 disjoint 0.01794 chrl9 15882902 15883702 0.10673 1.14731 21.3925 CYP4F11 22623 downstream 0 overlap 0.01794 chr2 24569499 24570485 0.64038 1.48292 21.3723 NC0A1 90364 upstream -827 disjoint 0.01795 chrl8 43039338 43040579 0.04369 0.70416 21.3597 FUSSEL18 9787 upstream 825 disjoint 0.01796 chr3 53505270 53506157 1.31219 0.58452 21.3533 CACNA1D 1155 inside intron -124 disjoint 0.01797 chrl 26989096 26990346 0.64302 1.56144 21.3505 PIGV 2024 covers exon(s) -1817 disjoint 0.01798 chr4 154933036 154934076 1.3049 0.66041 21.3494 SFRP2 3359 upstream 0 overlap 0.01798 chr2 241859065 241859987 0.35726 0.96242 21.3403 HDLBP 936 inside intron 0 overlap 0.01798 chrl 237617749 237618788 0.49315 1.183 21.3205 CHRM3 240207 upstream 0 overlap 0.018 chrl 3 23633871 23634562 1.89658 0.84489 21.3185 SPATA13 985 inside intron -333 disjoint 0.018 chr22 17797550 17798415 -0.2739 0.90853 21.3138 HULA 803 inside intron 330 disjoint 0.01801 chr7 121738280 121738960 1.08157 -0.1157 21.3067 FEZF1 6446 upstream -117 disjoint 0.01802 chrl 6 158259 159434 0.6736 1.3946 21.3057 HBM 2287 close to 3' -1539 disjoint 0.01802 chr5 27154316 27155320 0.54967 1.4414 21.3038 CDH9 79871 upstream ^ 8655 disjoint 0.01802 chrX 101268226 101269819 0.42566 1.25716 21.3034 TCEAL2 911 overlaps 3' 14142 disjoint 0.01802 chr8 82187100 82188417 2.06378 1.01083 21.2869 PAG1 243 promoter -62 disjoint 0.01803 chr9 124022027 124023303 0.68116 -0.0135 21.2828 LHX6 7501 inside intron 0 overlap 0.01804 chr9 99304726 99305685 1.02259 0.23263 21.2753 TDRD7 90604 downstream 0 overlap 0.01805 chrl 6 52879680 52880487 1.06974 0.08181 21.2744 IRX3 1802 promoter 0 inside 0.01805 chr6 30797531 30799046 0.40389 1.55193 21.2631 TUBB 1396 covers exon(s) -22 disjoint 0.01805 chrl2 47466713 47467898 0.11131 0.8445 21.2624 ADCY6 1188 inside intron 790 disjoint 0.01806 chrX 48341327 48342037 0.73961 1.90151 21.2624 WDR13 483 overlaps exon 0 overlap 0.01806 downstream
chr20 47530179 47531035 0.77612 1.64866 21.2501 KCNB1 1552 inside intron 884 disjoint 0.01807 chrl 9 48786249 48787246 0.5785 1.44713 21.2443 IRGQ 4269 downstream 817 disjoint 0.01807 chr8 142385532 142386248 1.73829 0.71559 21.2376 GPR20 60298 downstream 1287 disjoint 0.01808 chrS 43030487 43031484 0.50559 1.39248 21.2222 LOC389289 44613 downstream 0 cover 0.01809 chrl2 55916961 55918116 1.19707 0.52954 21.194 NDUFA4L2 2625 covers exon(s) 83 disjoint 0.01812 chrl 245749057 245750037 0.56976 1.55791 21.1933 OR2C3 13726 downstream -483 disjoint 0.01812 chr4 122906008 122908186 2.18751 0.59821 21.1856 TMEM155 219 promoter 0 overlap 0.01813
Chr2 208338978 208339822 1.33494 0.24162 21.1753 FZD5 2565 inside exon 0 overlap 0.01814 chrlS 72251806 72252274 0.60954 2.27225 21.1651 ISLR 865 promoter 2392 disjoint 0.01815 chrl 231817221 231817973 1.29689 0.3141 21.1602 CNK1 849 inside intron -284 disjoint 0.01815 chrl 7 8219504 8220660 0.46338 1.56009 21.1565 RPL26 6629 downstream 0 overlap 0.01816 chrl 160798449 160799344 0.13128 0.96012 21.1475 UAP1 503 inside intron 0 overlap 0.01816 chrl 145536206 145537236 0.91041 0.14592 21.1446 BCL9 56401 inside intron 637 disjoint 0.01817 chr2 222893577 222894302 1.25482 0.26181 21.1367 FLJ32447 22468 downstream 0 overlap 0.01817 chrX 68300402 68301402 0.81467 1.59064 21.1336 PJA1 594 inside intron 236 disjoint 0.01817 chr5 158463523 158464897 1.18842 0.52834 21.132 EBF1 4177 upstream 0 cover 0.01817 chr5 180417384 180418337 0.73678 1.61008 21.1269 BTNL9 17528 covers exon(s) 423 disjoint 0.01818 chrl7 21129373 21130541 0.12914 1.08499 21.1248 MAP2K3 813 inside intron -337 disjoint 0.01818 chr21 33315435 33316668 0.19429 0.9454 21.1248 0LIG2 3440 upstream 330 disjoint 0.01818 chr2 60636334 60637481 0.78997 0.08898 21.1231 BCL11A 2198 promoter -51 disjoint 0.01818 chr3 199171748 199172774 0.05213 0.87899 21.1016 LMLN 281 inside intron -20 disjoint 0.0182 chrl l 2806132 2807312 0.39565 1.1019 21.0818 KCNQ1 366873 inside intron 20628 disjoint 0.01822 chr9 126060930 126061727 -0.0954 0.99636 21.0755 NEK6 861 inside intron -368 disjoint 0.01823 chrX 39891183 39892049 1.07401 0.11025 21.0694 BCOR 49584 upstream 0 overlap 0.01823 chrl7 7998825 7999750 0.45539 1.4294 21.0595 PERI 2399 promoter 531 disjoint 0.01824 chr2 86872570 86874631 0.70942 1.32682 21.0504 CD8A 933 promoter -877 disjoint 0.01825 chr3 32837311 32838062 1.02747 -0.0077 21.044 TRIM71 2798 inside intron 116 disjoint 0.01826 chrl9 55918147 55919281 0.10948 0.79398 21.0401 CLEC11A 0 overlaps 5' 192 disjoint 0.01826 chr8 134376299 134377353 0.60333 1.67488 21.038 NDRG1 1326 inside intron 157 disjoint 0.01827 chr7 27111528 27112589 0.92049 0.2178 21.0296 HOXA3 7551 overlaps 3' 5 disjoint 0.01827 chr7 157332062 157334002 1.89179 3.25941 21.0295 PTPRN2 739176 inside intron 6559 disjoint 0.01827 chrl 149296849 149297975 0.13755 1.15696 20.9969 CDC42SE1 773 inside intron 416 disjoint 0.01831 chrl l 2595803 2597528 0.08097 0.74602 20.9852 KCNQ1 156544 inside intron -35758 disjoint 0.01832 chr7 137793949 137794785 1.37053 0.06555 20.9766 TR 24 833 promoter 422 disjoint 0.01833 chrl 23943453 23944370 0.19332 1.35762 20.9732 TCEB3 905 inside intron -251 disjoint 0.01833 chrl 6 1697128 1698070 0.32656 1.29955 20.9676 MAPK8IP3 907 inside intron -28269 disjoint 0.01833 chr4 81336365 81337010 1.43438 0.27797 20.9497 PRDM8 11903 covers exon(s) 151 disjoint 0.01835 chr7 45929178 45930311 0.74772 0.05711 20.9496 IGFBP3 1783 promoter -1306 disjoint 0.01835 chrl2 102849227 102850328 -0.1092 0.63209 20.9213 HSP90B1 909 covers exon(s) -286 disjoint 0.01838 chrl2 129215982 129216897 0.02345 0.90624 20.9054 FZD10 2998 overlaps 3' -1041 disjoint 0.01839 chr9 10604306 10605210 0.21781 1.20993 20.8976 PTPRD 1798 promoter -973 disjoint 0.0184 chrl 6 3448690 3449688 -0.1191 0.87164 20.8939 FLJ14154 612 inside intron -83 disjoint 0.01841 chrl2 48509161 48509772 2.42831 0.90425 20.8908 LOC144233 13369 downstream -285 disjoint 0.01841 chrl2 28017741 28019082 0.95489 0.33285 20.8655 PTHLH 1559 promoter 75 disjoint 0.01844 chrl 8 68360885 68361677 -0.0112 1.03486 20.8648 CBLN2 864 inside intron 0 inside 0.01844 chrl 7 73548721 73549470 -0.0755 1.09848 20.8644 TNRC6C 7118 upstream 0 overlap 0.01844 chr3 71917617 71918662 0.15254 0.96311 20.8637 PROK2 716 promoter -218 disjoint 0.01844 chr20 47988173 47988886 1.01395 2.00782 20.8337 ZNF313 1853 inside intron -1232 disjoint 0.01846 chrl 29378733 29379535 0.12054 1.44709 20.8296 SFRS4 1412 inside intron 1028 disjoint 0.01847 chr8 27403289 27404341 0.18739 1.02807 20.8274 EPHX2 220 promoter 234 disjoint 0.01847 chr2 1800032 1801168 0.81533 1.44183 20.8201 MYT1L 512883 inside intron -18965 disjoint 0.01848 chr3 186782873 186784350 1.33203 0.28838 20.8146 SENP2 2374 promoter 2163 disjoint 0.01848 chrl 2 109998710 109999435 0.21767 1.28034 20.8141 CUTL2 42499 inside intron -39085 disjoint 0.01848 chrl 179720562 179721627 0.33346 1.06749 20.8021 CACNA1E 1224 inside intron 0 overlap 0.01849 chr6 36104745 36105770 0.04474 0.8812 20.7984 MAP 14 1195 inside intron -395 disjoint 0.0185 chr2 231613912 231615143 0.8002 1.53721 20.7969 PSMD1 14709 upstream -2546 disjoint 0.0185 chr6 31742123 31742806 0.22647 1.30905 20.7904 CSNK2B 488 covers exon(s) -51 disjoint 0.01851 chrl 58485193 58486995 0.39534 0.85604 20.7844 DAB1 1803 inside intron 865 disjoint 0.01851 chr7 154976940 154977863 1.28975 0.45729 20.753 EN2 34765 downstream 0 overlap 0.01855 chr3 135853020 135854290 0.65669 1.43138 20.75 KY 467 promoter -91 disjoint 0.01855 chr2 218423333 218423914 0.76353 2.24138 20.7459 TNS1 93091 inside intron -93590 disjoint 0.01855 chr9 111582761 111583859 -0.1111 0.6297 20.7328 PALM2 139869 inside intron -273 disjoint 0.01857 chrl9 47478884 47479633 -0.1169 0.82049 20.7127 CIC 1023 promoter -1502 disjoint 0.0186 chrlO 22651402 22652156 0.88003 -0.1941 20.7103 BMI1 1257 inside intron 2125 disjoint 0.0186 chr6 27385939 27387213 0.25397 0.88476 20.7029 PRSS16 62453 downstream 560 disjoint 0.01861 chrl l 61105727 61106703 0.02276 1.02634 20.6963 SYT7 854 promoter -113 disjoint 0.01861 chr2 176673493 176674326 1.31708 0.41181 20.6957 H0XD12 718 overlaps 3' 0 overlap 0.01861 chr2 115636878 115638082 0.06969 0.71203 20.6792 DPP 10 677 inside intron 0 overlap 0.01863 chrl l 17452524 17453316 0.93589 1.89229 20.6712 ABCC8 1708 covers exon(s) 723 disjoint 0.01863 chr8 30360106 30361089 1.09541 0.04462 20.6701 RBPMS 396 promoter 0 overlap 0.01863 chrl 47681555 47682312 1.24774 0.1019 20.6699 FOXD2 7280 downstream 0 overlap 0.01863 chr6 6488016 6488942 0.86702 1.64954 20.6415 LY86 44990 upstream 2427 disjoint 0.01866 chr6 21775268 21776017 1.3711 0.31646 20.6389 S0X4 73318 downstream -427 disjoint 0.01866 chr2 70987535 70988478 1.31388 036421 20.6307 VAX2 6308 inside intron 0 cover 0.01867 chrlS 74418545 74419338 1.23305 0.01967 20.6274 ISL2 2344 inside intron 0 overlap 0.01868 chrl 7 75423490 75424308 1.10295 0.14135 20.623 CBX4 3499 covers exon(s) 0 overlap 0.01868 chrl2 52807785 52808546 1.50119 0.49535 20.6124 S UG1 60477 downstream -1061 disjoint 0.01869 chr8 22279130 22280264 1.69465 1.07463 20.6057 SLC39A14 472 promoter 200 disjoint 0.01869 chr6 41546535 41547461 1.29312 0.51993 20.6023 F0XP4 74680 upstream 0 overlap 0.01869 chr4 99799441 99800260 1.48294 0.30341 20.5991 TSPAN5 692 promoter -258 disjoint 0.0187 chrl l 18611177 18612196 -0.1383 0.72422 20.5884 SPTY2D1 399 inside intron 191 disjoint 0.01871 chr6 117691769 117692869 0.06706 0.73196 20.5876 VGLL2 544 promoter -260 disjoint 0.01871 chrlO 101285708 101286613 0.92034 0.02896 20.5825 NKX2-3 3009 overlaps 3' 0 inside 0.01872 chr7 72769969 72770923 0.60819 1.45699 20.5744 STX1A 1000 inside intron 401 disjoint 0.01873 chrl 9 53707072 53707575 0.69269 2.49788 20.5718 PSCD2 42649 downstream -320 disjoint 0.01873 chrl 3 111680466 111681309 0.5222 1.6763 20.5542 SOX1 88604 upstream -1669 disjoint 0.01875 chrl4 38804650 38805510 -0.1124 0.68833 20.55 CTAGE5 0 overlaps 5' 43 disjoint 0.01875 chr21 26461734 26462672 0.67762 -0.1975 20.5309 APP 2330 inside intron 1092 disjoint 0.01878 chrl l 64401019 64401774 0.01207 1.01841 20.5284 EHD1 992 inside intron 231 disjoint 0.01878 chrl l 2055080 2056853 0.04907 0.91953 20.5282 IGF2 59926 downstream 53756 disjoint 0.01878 chr9 132958851 132959966 0.91274 1.79584 20.5231 LAMC3 84527 downstream 1525 disjoint 0.01879 chr22 31528711 31529325 -0.0462 1.0417 20.513 TIMP3 1910 inside intron -444 disjoint 0.0188 chr7 814894 819665 0.53868 1.56263 20.5076 UNC84A 3112 upstream 0 overlap 0.01881 chr4 13156941 13158041 0.66826 -0.0563 20.4868 BAPX1 1806 promoter 0 overlap 0.01883 chrl 2 968656 969701 -0.0135 1.06701 20.4688 ERC1 963 promoter 117 disjoint 0.01885 chr2 139252241 139253404 0.7324 -0.028 20.4652 NXPH2 876 inside intron 758 disjoint 0.01885 chr2 236792588 236793373 0.89 1.80027 20.4553 ASB18 21623 inside intron -4277 disjoint 0.01887 chrl 90964401 90965155 1.2131 0.12725 20.4534 BARHL2 9020 upstream 0 inside 0.01887 chr4 1 11755728 111756441 1.20534 0.20704 20.4522 PITX2 7261 downstream 2236 disjoint 0.01887 chr6 106539995 106540967 1.35939 0.50564 20.4373 PRDM1 99920 upstream 0 overlap 0.01888 chr22 30480380 30481547 0.66646 1.39997 20.4323 DEPDC5 312 covers exon(s) -316 disjoint 0.01888 chrl 247085907 247086761 -0.0706 0.87605 20.4301 SH3BP5L 15 overlaps two exons 312 disjoint 0.01889 chrl 5 94703340 94703952 1.30861 0.02862 20.4293 R2F2 28391 downstream 363 disjoint 0.01889 chrl l 10273067 10273715 1.29157 0.06606 20.423 SBF2 756 promoter -22 disjoint 0.01889 chr6 44147320 44147898 0.48028 1.71552 20.4185 MRPL14 55270 downstream 1094 disjoint 0.0189 chr20 540140 541182 0.23584 1.06465 20.4167 TCF15 1231 promoter -918 disjoint 0.0189 chrl 5 87723582 87724160 1.48003 0.21072 20.4062 POLG 44553 upstream 0 Overlap 0.01891 chrl5 64330319 64331390 1.46119 0.45954 20.4032 MEGF11 1738 inside intron 96 disjoint 0.01892 chrlO 131648687 131649650 0.73302 -0.1448 20.3781 EBF3 2430 inside intron 0 overlap 0.01894 chrl7 78634960 78635571 0.79106 2.00167 20.354 METRNL 4105 inside intron 344 disjoint 0.01896 chrl4 63733238 63734008 0.23057 1.16368 20.3472 SYNE2 121153 inside intron 96604 disjoint 0.01897 chr22 49258803 49259646 0.35636 1.74628 20.3288 SBF1 673 inside intron 0 overlap 0.01899 chrl8 51599115 51600116 0.78638 -0.0065 20.3087 TCF4 192675 upstream -275 disjoint 0.01901 chr8 125807309 125808274 0.10805 0.94001 20.3073 MTSS1 1565 inside intron 592 disjoint 0.01902 chrlS 74421774 74422793 0.16005 1.06691 20.3046 SALL3 418469 upstream 870 disjoint 0.01902 chrl2 52646660 52647724 0.79614 0.09357 20.2863 H0XC11 5452 upstream 0 overlap 0.01903 chr2 210383046 210383993 0.11294 1.34709 20.277 C2or£21 38085 downstream -552 disjoint 0.01904 chrl l 66166606 66167286 0.43744 1.5816 20.2742 RBM4 3893 inside intron 215 disjoint 0.01905 chr9 139313724 139314707 1.1654 0.39168 20.2562 MGC61598 1816 close to 3' 615 disjoint 0.01907 chrl l 11597517 11598534 1.03611 0.21769 20.2499 GALNTL4 1593 inside intron 163 disjoint 0.01908 chrl 57861340 57861987 0.09751 1.22655 20.2494 DAB1 626811 inside intron -198115 disjoint 0.01908 chrX 39843665 39844552 0.73416 -0.1216 20.2463 BCOR 2066 promoter 0 inside 0.01908 chr6 107544228 107545411 0.58322 -0.0273 20.2446 PDSS2 342036 downstream -225 disjoint 0.01908 chrlO 129976636 129977401 0.28933 1.36101 20.2438 MKI67 161992 upstream -22368 disjoint 0.01908 chrl 8 70302828 70303379 0.40608 1.70755 20.239 CNDP2 11197 upstream 10536 disjoint 0.01909 chr2 45088210 45088869 1.21937 0.10249 20.2381 SK2 1156 inside intron 146 disjoint 0.01909 chr3 51984311 51985098 0.50651 1.92473 20.2328 ABHD14A 188 inside intron 0 overlap 0.01909 chr5 150439475 150440357 0.41758 1,62254 20.2255 ΤΝΠΗ 832 inside intron 0 overlap 0.0191 chrlO 127573396 127574322 0.05805 0.96681 20.2247 FAN 1 778 promoter 0 overlap 0.0191 chr6 139390108 139391026 1.18344 0.29723 20.2212 REPS1 39018 upstream 622 disjoint 0.01911 chrlO 103593842 103594483 1.66723 0.5909 20.2207 KCNIP2 176 promoter -210 disjoint 0.01911 chrl 165949115 165949825 1.52669 0.37559 20.2116 RCSD1 83162 downstream 276 disjoint 0.01912 chr6 7675570 7676424 0.63425 1.48416 20.2028 BMP6 4267 inside intron -1463 disjoint 0.01913 chr7 55608160 55608828 1.47752 0.16314 20.1965 ECOP 467 promoter -67 disjoint 0.01913 chr4 164471395 164472342 0.60308 1.51036 20.1951 NPY1R 855 inside intron 62 disjoint 0.01913 chrl 9275528 9277565 0.2575 1.51219 20.1801 SPSB1 0 overlaps 5' -27925 disjoint 0.01915 chr3 142268701 142269751 0.32458 1.22822 20.1793 SPSB4 15269 inside intron -533 disjoint 0.01915 chr3 1191 7273 119198199 0.10347 0.96411 20.1777 1GSF11 1038166 downstream 588 disjoint 0.01915 chr4 168392603 168393497 0.20395 1.02731 20.1728 SPOCK3 288 promoter -263 disjoint 0.01915 chrl9 50835964 50836713 1.52632 0.414 20.1431 EML2 1456 promoter 0 overlap 0.01918 chr20 48034576 48035573 0.4585 1.49135 20.136 SNAI1 1643 inside intron -1512 disjoint 0.01919 chrl 4 58171209 58172131 0.61834 -0.1869 20.1318 DACT1 2480 promoter 1921 disjoint 0.01919 chrl3 99437104 99437959 0.86022 0.00876 20.1301 ZIC2 4785 downstream 1376 disjoint 0.0192 chrl 9 47447352 47448046 -0.1783 1.04254 20.115 ERF 3066 inside intron 1289 disjoint 0.01922 chr6 32226447 32227133 1.28353 0.09443 20.101 PRRT1 564 overlaps exon 0 overlap 0.01923 upstream
chrl2 52376282 52377029 0.98423 -0.0826 20.0763 CALCOCOl 30456 downstream -602 disjoint 0.01926 chr4 95898789 95899871 1.29764 0.23835 20.0757 BMPR1B 639 inside intron 0 overlap 0.01926 chr6 51956087 51956911 0.31178 1.22311 20.0708 P HD1 103470 inside intron 300197 disjoint 0.01926 chr3 142265881 142266926 0.83566 1.54569 20.0692 SPSB4 12449 inside intron 570 disjoint 0.01927 chr3 195687095 195687945 0.36648 1.29094 20.0637 GP5 85812 upstream 726 disjoint 0.01927 chr20 61375334 61376026 0.49052 1.51196 20.0625 ARFGAP1 725 inside intron -188 disjoint 0.01927 chrl 2 54994472 54995840 0.14242 0.65278 20.0343 T EM4 546 covers exon(s) 0 overlap 0.01931 chr6 76700825 76701823 0.35164 0.92957 20.0294 IMPG1 137231 inside intron -184838 disjoint 0.01931 chrX 39888485 39889147 1.23462 0.0114 19.9949 BCOR 46886 upstream 102 disjoint 0.01935 chrl5 72252434 72253193 0.43562 1.78399 19.9841 ISLR 0 overlaps 5' 1473 disjoint 0.01936 chrl6 30589988 30597671 1.29604 0.10226 19.9814 FBS1 5861 downstream -11332 disjoint 0.01936 chr5 180006297 180007521 0.72831 1.37399 19.9738 FLT4 1684 inside intron 773 disjoint 0.01937 chr22 29147613 29148491 0.64907 1.70242 19.9729 SEC14L2 24681 overlaps exon 908 disjoint 0.01937 upstream
chrl2 116888048 116889157 0.06714 1.02124 19.9554 RFC5 49735 upstream 1816 disjoint 0.01939 chr2 106823810 106824681 0.60664 1.53195 19.9432 ST6GAL2 45300 inside intron 1274 disjoint 0.0194 chrlO 94816765 94817743 -0.0203 0.75367 19.9292 CYP26C1 5755 inside intron 349 disjoint 0.01942 chr7 97750010 97750618 0.69526 1.78655 19.9286 BRI3 1088 inside intron -456 disjoint 0.01942 chr7 35264692 35265804 1.21274 0.26398 19.924 TBX20 4926 upstream 0 overlap 0.01942 chrl 198276933 198277906 0.97861 0.22008 19.8997 NR5A2 13541 inside intron 117 disjoint 0.01946 chrl7 75393235 75394437 0.45264 -0.227 19.8975 CBX8 7751 upstream -172 disjoint 0.01946 chrl 18678954 18679794 0.61773 1.75516 19.8883 KLHDC7A 216 promoter 1666 disjoint 0.01947 chr2 222865021 222865521 1.42048 0.01467 19.8847 PAX3 6422 inside intron -623 disjoint 0.01948 chrl 204446112 204447047 0.63372 1.28356 19.8837 Clorfl86 8222 inside intron -55461 disjoint 0.01948 chr4 154608177 154609032 0.40902 1.51248 19.8724 KIAA0922 1176 inside intron -112 disjoint 0.01949 chrl4 72430928 72432018 0.42087 -0.236 19.8598 DPF3 335 promoter -241 disjoint 0.01951 chr22 23672705 23677038 0.51537 1.2098 19.8524 bA9Fll.l 7392 upstream 1113 disjoint 0.01952 chr3 62336746 62337634 1.04244 0.17718 19.8335 FEZF2 2686 upstream 13 disjoint 0.01954 chrlO 71871600 71874437 0.98705 0.15767 19.8252 NODAL 172 promoter -226 disjoint 0.01954 chrl 4 100991921 100992740 1.18765 0.25271 19.8203 DI03 104700 upstream 588 disjoint 0.01955 chr4 186171484 186172642 0.95897 1.7266 19.8156 HELT 4434 upstream 1594 disjoint 0.01956 chr7 29199469 29200290 1.27847 0.43977 19.7973 CHN2 355 promoter 0 overlap 0.01958 chr2 73817431 73818006 -0.0277 1.18466 19.7908 TPR B 14 overlaps exon 0 overlap 0.01958 downstream
chr6 35290813 35291874 0.997 0.3251 19.7831 SCUBE3 646 inside intron -288 disjoint 0.01959 chr8 486388 487032 1.30982 0.23023 19.7737 C8orf42 1058 promoter -305 disjoint 0.0196 chrl 9 49022069 49023126 1.08301 1.76967 19.7713 LYPD5 5444 upstream -5220 disjoint 0.01961 chrl 2891582 2892187 0.41763 1.59694 19.7647 ACTRT2 35718 upstream -14799 disjoint 0.01961 chr20 24396196 24397231 1.78501 0.83906 19.7586 C20orO9 603 promoter 613 disjoint 0.01961 chrl 4 96742468 96743239 0.27299 1.37639 19.7582 VR 1 409032 downstream 11573 disjoint 0.01961 chrl 153556078 153557263 0.78212 1.70241 19.7567 FDPS 9878 overlaps 3' 0 overlap 0.01962 chr3 159299933 159300739 0.95282 0.17618 19.746 SH0X2 2780 covers exon(s) -1147 disjoint 0.01963 chrX 24928743 24929284 1.50414 0.15944 19.7432 ARX 14490 downstream 874 disjoint 0.01963 chr2 156893008 156893849 1.3894 0.42526 19.7422 NR4A2 3596 covers exon(s) 0 overlap 0.01963 chrl5 64577286 64578002 -0.0621 1.09116 19.74 SNAPC5 87 promoter 0 overlap 0.01964 chrl2 11694989 11695840 0.10523 0.95729 19.7318 ETV6 935 inside intron -739 disjoint 0.01964 chr20 32046533 32047496 -0.2463 0.73484 19.7202 RALY 1141 inside intron -370 disjoint 0.01966 chr7 63278263 63278997 0.40421 1.39214 19.707 ZNF680 381921 downstream 477 disjoint 0.01967 chr6 2712261 2713113 0.48832 1.52194 19.7001 WRNIP1 1597 inside intron -487 disjoint 0.01968 chrl l 2660825 2661961 0.51978 1.17375 19.6941 KCNQ1 221566 inside intron 15025 disjoint 0.01969 chr2 190845 192127 0.68685 1.48318 19.6887 SH3YL1 54213 downstream -2310 disjoint 0.01969 chr!6 3088137 3089226 0.74712 -0.0505 19.6825 ZNF206 5276 upstream 7024 disjoint 0.0197 chr6 78233255 78234190 1.3329 0.63497 19.6822 HTR1B 3417 upstream -2448 disjoint 0.0197 chr8 49630179 49631153 0.03281 1.02677 19.6819 EFCABl 179190 downstream 83 disjoint 0.0197 chrl 7 7699109 7700071 0.94364 0.20092 19.6819 TMEM88 1 overlaps two exons 0 cover 0.0197 chrl 19407903 19408553 0.09598 1.16457 19.6792 ZUBR1 779 inside intron 185 disjoint 0.01971 chr6 75973109 75974383 0.69635 0.11214 19.6711 COL12A1 767 promoter -2 disjoint 0.01972 chr3 184455373 184456017 1.50008 0.403 19.6657 B3GNT5 1648 inside intron -47 disjoint 0.01973 chrl2 48731130 48731945 1.19755 0.21083 19.6643 ACCN2 5808 upstream 5519 disjoint 0.01973 chrl2 120503326 120504291 0.69401 -0.1427 19.663 FBXL10 55 promoter -486 disjoint 0.01973 chr4 109310022 109310990 0.8402 0.10353 19.6389 LEF1 996 promoter -166 disjoint 0.01976 chrl l 46220781 46221497 0.08203 1.14221 19.6341 CREB3L1 34306 upstream 52 disjoint 0.01977 chrl7 61617469 61618252 -0.2818 0.85884 19.6274 CCDC46 1 2 overlaps exon 0 overlap 0.01978 downstream
chrlO 719351 720013 0.951 2.06373 19.6238 DIP2C 5592 inside intron 4694 disjoint 0.01978 chrl8 55513639 55514432 1.39507 2.45114 19.6033 CCBE1 1137 inside intron 262 disjoint 0.01981 chrl4 72772610 72773969 1.10076 0.17947 19.6004 PAPLN 38 promoter 0 overlap 0.01981 chr7 16760597 16761464 1.58862 0.32006 19.5953 TSPAN13 722 inside intron 0 overlap 0.01982 chrl5 20049184 20050413 0.41315 2.02969 19.5812 OR4N4 165348 downstream -529 disjoint 0.01983 chr5 122454674 122455548 0.94553 0.14231 19.5675 PPIC 54351 upstream 0 overlap 0.01985 chrl5 33159611 33160701 0.5001 1.63378 19.5519 ZNF770 91866 upstream 11662 disjoint 0.01987 chr7 25859617 25860330 1.08563 0.10213 19.5518 NFE2L3 298054 upstream -477 disjoint 0.01987 chrlO 75202908 75203762 0.15708 0.92998 19.543 FUT11 854 covers exon(s) -85 disjoint 0.01988 c rl2 52000502 52001366 0.23036 1.10872 19.5429 AAAS 274 covers exon(s) 34 disjoint 0.01988 chr4 174663276 174664238 0.97448 0.27243 19.5408 HAND2 23714 downstream 228 disjoint 0.01988 chrl2 119247719 119248360 0.20579 1.3298 19.5402 PLA2G1B 1614 covers exon(s) -7664 disjoint 0.01988 chr2 222872701 222873417 0.86931 -0.0635 19.5377 FLJ32447 1592 inside intron -545 disjoint 0.01988 chrl l 64858595 64859613 0.02593 0.72233 19.5369 DPF2 674 inside intron -176 disjoint 0.01988 chrl7 21163207 21164448 0.62783 1.4444 19.5352 MAP2K3 27834 downstream -2202 disjoint 0.01989 chrl7 56890448 56891517 1.24719 0.10126 19.5307 TBX4 1860 inside intron -412 disjoint 0.0199 chr3 32796641 32797481 1.00669 0.11714 19.5251 CNOT10 94940 downstream 0 overlap 0.0199 chrl2 108544138 108544698 0.05251 1.35915 19.5133 MVK 48139 downstream -48156 disjoint 0.01992 chrl4 56346232 56347277 0.5771 -0.1071 19.5127 OTX2 0 overlaps 5' 0 overlap 0.01992 chrl7 44155950 44156642 1.1027 -0.0054 19.5073 HOXB13 4467 downstream 0 overlap 0.01993 chrl 231008306 231009193 2.16162 0.93264 19.4907 Clorf57 143799 upstream 0 overlap 0.01995 chrl3 99441708 99442808 0.80672 0.15406 19.4884 ZIC2 9389 downstream -613 disjoint 0.01995 chrl 6 66825945 66827009 1.01338 0.20623 19.4647 RBM35B 627 inside intron 0 overlap 0.01998 chrl 7 2595144 2597833 1.18923 2.08886 19.464 KIAA0664 33468 upstream 1371 disjoint 0.01998 chr9 96808269 96808982 0.16781 1.09512 19.4594 C9orf3 279455 inside intron -493 disjoint 0.01999 chrl 3 50315830 50316826 1.08915 0.29398 19.4555 DLEU7 0 overlaps 5' 0 overlap 0.01999 chrl 8 28305333 28306211 1.45678 0.27431 19.4524 FAM59A 889 promoter 0 overlap 0.02 chrl 7 53650943 53651554 0.15521 1.45788 19.4518 MKS1 110 covers exon(s) 0 overlap 0.02 chr2 225613857 225614660 0.20721 1.11018 19.4207 DOCK10 206701 upstream 237 disjoint 0.02004 chrX 111213303 111214223 0.53867 -0.2328 19.4164 ZCCHC16 395 inside intron -1345 disjoint 0.02004 chrl5 34956732 34957491 1.24351 0.04958 19.4139 MEIS2 220303 downstream 2274 disjoint 0.02004 chrl l 16581580 16582357 1.46716 0.51579 19.3937 SOX6 127087 upstream 272 disjoint 0.02007 chrl 9 47188555 47189803 0.73258 1.48436 19.3867 ATP1A3 418 inside intron 0 overlap 0.02008 chr6 26302610 26303860 0.19475 0.80249 19.3844 HIST1H3D 3582 downstream 1189 disjoint 0.02008 chr6 15352372 15352875 1.44731 0.05496 19.3726 JARID2 1630 promoter 0 overlap 0.02009 chrl 4 105923371 105924672 0.08421 0.73136 19.3682 TMEM121 859374 downstream 1178 disjoint 0.0201 chrl 2 48962715 48963500 0.35025 1.37461 19.3563 LIMA1 38 overlaps exon -115062 disjoint 0.02012 downstream
chrl9 63766660 63767165 0.36206 1.81866 19.3475 MZF1 9588 overlaps exon -93 disjoint 0.02013 upstream
chr5 180005526 180006275 0.70043 1.6508 19.3449 FLT4 2930 inside intron 2019 disjoint 0.02014 chr7 47984240 47985303 0.24162 1.16518 19.3431 HUS1 467 covers exon(s) 310 disjoint 0.02014 chr2 96563766 96564713 0.5209 1.34955 19.3382 ARJ0D5A 1477 promoter 1327 disjoint 0.02015 chrlO 5774977 5775480 1.92325 0.61483 19.3176 ASB13 26431 upstream -7274 disjoint 0.02017 chr8 49590206 49591301 0.20592 0.93994 19.3113 EFCAB1 219042 downstream -237 disjoint 0.02017 chr2 38455970 38456844 0.32965 1.19632 19.3029 ARL6IP2 1074 inside intron 229 disjoint 0.02019 chrl7 59272149 59272919 -0.0154 0.92606 19.2762 SMARCD2 1163 inside intron 472 disjoint 0.02022 chr6 35293302 35294309 0.35218 1.01969 19.2708 SCUBE3 3135 inside intron -2777 disjoint 0.02023 chrl 6 6474113 6474865 0.28327 1.23045 19.2556 A2BP1 464981 inside intron -129 disjoint 0.02025 chr2 121214264 121215380 0.96779 0.31715 19.2416 GLI2 50946 upstream 318 disjoint 0.02026 chr6 1255485 1256397 1.33581 0.52496 19.2391 F0XQ1 1277 promoter 0 overlap 0.02026 chr3 194116370 194117111 0.99994 0.01653 19.2191 C3orf59 1532 inside intron 0 overlap 0.02029 chrl 32418706 32419500 0.362 1.17654 19.2051 TXLNA 775 overlaps exon -305 disjoint 0.02031 upstream
chr2 238863009 238863692 1.89525 0.84663 19.2023 PER2 1179 promoter -370 disjoint 0.02031 chr7 130890067 130891273 0.75923 0.19851 19.2 PODXL 634 inside intron 0 overlap 0.02031 chr5 180168460 180169309 0.96098 1.8665 19.1971 MGAT1 5807 upstream 289 disjoint 0.02032 chrl 8 66850594 66851589 0.51106 1.34133 19.1943 SOCS6 743352 downstream -601518 disjoint 0.02032 chr5 72562287 72563030 1.64336 0.50733 19.1905 TMEM174 62458 downstream -34 disjoint 0.02032 chr6 27837986 27838651 1.4716 0.4615 19.1862 HIST1H2BL 45036 downstream 44657 disjoint 0.02033 chr5 134851359 134852247 1.13741 0.15209 19.1834 C5orf20 40423 upstream 84 disjoint 0.02033 chr20 39092019 39092757 -0.3142 0.78246 19.1809 TOPI 1144 inside intron -193 disjoint 0.02033 chr3 109424564 109425634 -0.0265 0.57374 19.1701 IFT57 627 promoter -374 disjoint 0.02035 chrX 54403340 54404617 -0.296 0.20985 19.1583 WN 3 2178 promoter -1138 disjoint 0.02036 chrl l 65020387 65021459 -0.0037 0.81623 19.1533 SCYL1 27664 upstream 74 disjoint 0.02037 chr4 42097524 42098165 1.14678 2.20589 19.1521 ATP8A1 255481 downstream -1965 disjoint 0.02037 chr3 73022967 73023470 0.05303 1.4178 19.1506 SHQl 42680 upstream 37216 disjoint 0.02037 chr2 176664628 176665275 1.24113 0.17992 19.142 HOXD13 502 promoter 0 cover 0.02038 chrl5 77509620 77510267 1.73855 0.67714 19.142 IAA1024 1645 promoter 887 disjoint 0.02038 chr2 222143386 222144463 0.25515 1.42245 19.127 EPHA4 790 inside intron 0 overlap 0.0204 chr20 23347938 23349037 0.10299 1.00732 19.1169 NAPB 1043 inside intron 71 disjoint 0.02041 chrl 8 58428995 58429534 0.52508 1.65799 19.111 ZCCHC2 71102 downstream -13767 disjoint 0.02042 chr22 25629641 25630252 1.27424 0.15892 19.1055 CRYBA4 281714 downstream -146491 disjoint 0.02043 chr3 195600216 195601199 1.88084 1.01656 19.0741 GP5 84 overlaps exon 0 overlap 0.02047 upstream
chr22 40804540 40805148 0.89735 2.18156 19.049 FA 109B 4340 inside exon 272 disjoint 0.0205 chrl 9 62040790 62041509 0.81089 1.77436 19.0307 PEG3 2366 inside intron 300 disjoint 0.02053 chr3 49424826 49425483 0.45423 1.80413 18.9969 TCTA 184 overlaps exon 0 overlap 0.02057 downstream
chr5 140481143 140482033 0.62283 1.37773 18.9913 PCDHB4 0 overlaps 5' 1041 disjoint 0.02058 chrl 35792714 35793663 1.02046 0.03214 18.9842 IAA0319L 1927 inside intron 1604 disjoint 0.02059 chr5 75736756 75737508 0.30017 1.34544 18.9825 IQGAP2 1852 inside intron -840 disjoint 0.02059 chrl 9 42099161 42100176 -0.2265 0.58055 18.9795 ZNF568 88 overlaps exon 0 overlap 0.0206 downstream
chrX 40677282 40677815 0.57562 2.05112 18.9773 USP9X 152016 upstream -99892 disjoint 0.0206 chr9 128425188 128426358 0.8716 0.17781 18.9769 LMX1B 8570 inside intron 0 overlap 0.0206 chrl l 41284514 41285451 0.23143 1.21745 18.9759 LRRC4C 1012275 upstream 2004564 disjoint 0.0206 chrl5 87760475 87761685 0.47675 1.04223 18.9665 RHCG 79117 downstream 0 cover 0.02062 chr9 138206723 138207439 0.26093 1.10237 18.9663 LHX3 27385 downstream 2137 disjoint 0.02062 chrl 6 3868590 3869450 0.17902 1.04603 18.9604 CREBBP 1261 inside intron 34 disjoint 0.02063 chrl l 115036030 115036884 1.5011 0.60173 18.9538 IGSF4 155706 upstream -272 disjoint 0.02064 chrl 145014367 145015164 0.54395 1.56259 18.9523 PRKAB2 95588 downstream 1310 disjoint 0.02064 chr3 45183717 45184370 0.14497 1.20682 18.9482 CDCP1 20800 upstream -20767 disjoint 0.02064 chrl l 68273546 68274236 1.67953 0.78227 18.943 MTL5 1327 overlaps exon 7 disjoint 0.02065 downstream
chr!2 12762652 12763512 -0.306 0.51741 18.9374 CDKN1B 1077 covers exon(s) -137 disjoint 0.02066 chr3 150329148 150329864 0.00976 0.91424 18.9358 HPS3 196 promoter 21 disjoint 0.02066 chrl l 31779015 31779938 0.53953 -0.1716 18.9309 PAX6 9495 covers exon(s) -1023 disjoint 0.02067 chrlO 94824973 94825966 0.99593 0.28518 18.9272 CYP26A1 1317 covers exon(s) 0 overlap 0.02067 chrl3 35440501 35441100 0.97925 2.15167 18.9243 DCAMKL1 162342 inside intron 161940 disjoint 0.02068 chrl 219135759 219136637 1.35688 0.62594 18.9241 HLX1 16378 downstream 0 overlap 0.02068 chrl 148472330 148473535 0.19452 1.28793 18.9173 A P32E 1548 inside intron 60 disjoint 0.02068 chrl 8 5184965 5185614 -0.2408 0.8457 18.9044 ZFP161 97698 downstream 629 disjoint 0.0207 chrlO 88152024 88153055 0.17937 0.67602 18.9044 WAPAL 118465 downstream -633 disjoint 0.0207 chr21 43399018 43399773 -0.2029 0.57429 18.8996 U2AF1 983 inside intron 459 disjoint 0.0207 chrl5 65912007 65913046 0.81734 -0.0247 18.8984 LBXC0R1 7013 covers exon(s) 30 disjoint 0.0207 chr8 96214135 96214836 1.41724 0.30334 18.8961 PLEKHF2 377 promoter 100 disjoint 0.02071 chr2 81281094 81281847 0.21082 1.12309 18.8922 CTNNA2 1687461 downstream -5051 disjoint 0.02071 chr7 141341765 141342307 0.84369 2.17491 18.8921 MGAM 0 overlaps 5' -256903 disjoint 0.02071 chr4 55685148 55685826 1.27752 0.29113 18.8829 KDR 692 inside intron 333 disjoint 0.02072 chr9 70979378 70980658 0.07167 0.63083 18.8603 TJP2 470 inside intron -16 disjoint 0.02075 chrl9 13976546 13977292 0.72776 1.75376 18.8569 RFX1 804 inside intron 240 disjoint 0.02075 chrl 7 72246131 72247042 -0.1472 0.89225 18.8439 ET 754 covers exon(s) -314 disjoint 0.02077 chr8 2405348 2406211 0.16473 1.28187 18.8362 YO 2 424694 downstream 131 disjoint 0.02078 chr20 388867 389808 0.69652 1.84194 18.8355 TBC1D20 1378 inside intron 722 disjoint 0.02078 chr2 109113073 109113824 0.52019 1.47663 18.8314 EDAR 140814 upstream 0 overlap 0.02078 chr8 17315551 17316271 1.62397 0.61257 18.82 MTMR7 345 promoter -60 disjoint 0.0208 chrl2 54936033 54936785 0.51759 1.38284 18.7993 COQ10A 10207 upstream 1174 disjoint 0.02082 chrlO 115989697 115990340 1.35173 0.32294 18.7921 VWA2 690 inside intron -104 disjoint 0.02083 chrlO 79354710 79355457 0.3844 1.58031 18.7891 DLG5 896 inside intron 268 disjoint 0.02083 chrl 177811864 177813130 0.17296 0.82965 18.7888 NPHS2 174 promoter 0 overlap 0.02083 chr6 31903659 31910233 0.08266 1.06999 18.7758 C6orf48 438 promoter 0 overlap 0.02085 chrl 7 27615458 27616643 0.61248 0.03891 18.7712 RHBDL3 664 promoter 668 disjoint 0.02086 chrl6 85973253 85974163 0.17001 1.32325 18.7682 FBX031 700 inside intron 0 overlap 0.02087 chr22 44841920 44842585 0.47241 1.52594 18.7654 C22orf26 13233 upstream 2055 disjoint 0.02087 chr2 46380700 46381795 1.66675 0.77831 18.7514 EPAS1 2634 inside intron -56 disjoint 0.02089 chrl 8 4331 1196 43311708 0.02434 1.31587 18.7464 FUSSEL18 281645 upstream 217695 disjoint 0.02089 chrl5 29944784 29945254 0.29245 1.67588 18.7202 CHRNA7 164763 upstream 164202 disjoint 0.02093 chr2 161801236 161802239 1.15306 0.38488 18.7122 TANK 99525 downstream 467 disjoint 0.02095 chrS 172605911 172606465 1.58297 0.24597 18.7081 NKX2-5 11044 upstream -334 disjoint 0.02095 chrl 3 44051295 44052004 1.42626 0.32419 18.6998 TSC22D1 2595 upstream -1007 disjoint 0.02097 chr4 7235970 7238149 1.21427 1.88427 18.699 SORCS2 7223 upstream 7289 disjoint 0.02097 chr9 95632502 95633517 0.46981 1.26473 18.692 BARX1 123905 downstream -3748 disjoint 0.02098 chrl 8 18010086 18010709 0.79688 -0.3037 18.6897 GATA6 6673 inside intron 83 disjoint 0.02098 chrlO 121568812 121569456 1.08187 0.00954 18.681 INPP5F 93214 inside intron -437 disjoint 0.02099 chr9 84865948 84866714 0.72301 1.73042 18.677 RASEF 1148 inside intron 121 disjoint 0.021 chr9 137305541 137306239 1.32456 2.31804 18.6673 OLFM1 198550 downstream -8737 disjoint 0.02101 chrlO 94809396 94809995 1.90381 0.69618 18.6494 EXOC6 211175 downstream 21 disjoint 0.02104 chr5 14493382 14494101 0.3164 1.26074 18.6367 TRIO 296554 inside intron 20029 disjoint 0.02105 chrl 7 40584104 40585176 -0.1512 0.63843 18.635 HEXIM1 3638 inside exon -705 disjoint 0.02105 chr3 37782171 37782743 0.65528 1.72237 18.6338 ITGA9 313355 inside intron 94199 disjoint 0.02106 chrl7 37862282 37863024 0.23351 1.12932 18.6251 ATP6V0A1 1363 promoter 1248 disjoint 0.02106 chr4 113519509 113520402 1.2598 0.49565 18.5865 ALPK1 1209 inside intron 0 cover 0.02112 chr2 32436677 32437252 0.1795 1.12634 18.5864 BIRC6 1444 inside intron 0 overlap 0.02112 chr5 88024656 88025466 0.94642 0.1029 18.5793 MEF2C 189313 downstream -3090 disjoint 0.02113 chrlS 74575392 74575985 0.55172 1.89886 18.5749 SALL3 265277 upstream -10726 disjoint 0.02113 chr9 960276 961489 0.98305 0.30311 18.5726 DMRT1 128587 downstream 0 inside 0.02114 chrl7 24642310 24643100 -0.2857 0.53634 18.5536 NUFIP2 2102 inside intron 517 disjoint 0.02116 chrl 47125858 47126941 0.12656 0.76364 18.5494 ARHGEF1 45573 downstream -1642 disjoint 0.02117 chrl4 23754493 23755818 0.00402 0.5491 18.5486 MDP-1 0 overlaps 5' -1816 disjoint 0.02117 chrl 13836176 13836739 1.09941 2.38876 18.5456 C19orf57 41169 downstream 0 overlap 0.02117 chr4 39043102 39044198 0.04474 0.6109 18.5357 RFCl 191 inside intron 0 overlap 0.02119 chr7 75735667 75736626 0.56067 1.16327 18.5331 FLJ37078 15684 upstream -787 disjoint 0.02119 chrl 9 52921482 52925144 1.60489 0.19021 18.5328 EHD2 12981 inside intron -163 disjoint 0.02119 chr2 119326983 119328025 1.0743 0.27141 18.521 EN1 4755 upstream 0 overlap 0.02121 chrl8 19850663 19851773 1.41785 0.55291 18.5168 C18orfl7 23929 inside intron -1201 disjoint 0.02121 chrl9 63721519 63722392 -0.2093 0.80004 18.5167 ZBTB45 340 inside intron 77 disjoint 0.02121 chrl4 94306491 94307170 1.08815 -0.1615 18.5088 GSC 240 promoter -169 disjoint 0.02122 chr2 176656184 176657317 0.99087 0.38682 18.507 HOXD13 8460 upstream 0 overlap 0.02123 chrl l 1727832 1728500 0.60773 1.69937 18.5041 HCCA2 13576 inside intron -544 disjoint 0.02123 chr2 1463026 1463678 1.0433 2.21457 18.4969 TPO 66785 inside intron -2388 disjoint 0.02124 chrl2 16648886 16649599 0.79261 -0.202 18.4933 LM03 1098 inside intron -693085 disjoint 0.02124 chr6 34468801 34469585 0.6486 1.56794 18.4871 NUDT3 383 promoter -21 disjoint 0.02125 chrl9 50646161 50647015 0.21166 1.00565 18.4861 FOSB 16077 upstream 0 overlap 0.02126 chrl5 94678158 94678946 1.04022 0.12638 18.4742 NR2F2 3209 covers exon(s) 0 overlap 0.02127 chrl7 63963150 63964281 0.13095 0.92204 18.474 WIPI1 928 inside intron 663 disjoint 0.02127 chrl4 34941401 34941941 0.85063 2.05734 18.4684 F BIA 1753 covers exon(s) 857 disjoint 0.02127 chrl9 35556701 35557369 0.74917 -0.4531 18.4682 ZNF536 1534 inside intron 154 disjoint 0.02128 chr2 96568526 96569029 1.61346 0.29364 18.4528 ARBD5A 2336 inside intron -1012 disjoint 0.0213 chr6 167683113 167684193 0.6884 1.69582 18.4505 TTLL2 24550 downstream 319 disjoint 0.0213 chr9 90983474 90984288 1.02554 -0.051 18.4452 SHC3 0 overlaps 5' -43 disjoint 0.02131 chr3 184627355 184628068 1.53917 0.45925 18.4375 MCF2L2 480 inside intron 50 disjoint 0.02132 chrl7 75538918 75539565 1.33014 0.27935 18.4294 TBC1D16 84676 overlaps exon 0 overlap 0.02134 upstream
chrl7 7418174 7418839 0.03852 1.28683 18.4282 EIF4A1 1394 covers exon(s) -120 disjoint 0.02134 chrl6 67779903 67780862 0.17074 0.94074 18.4204 SNTB2 1353 inside intron -295 disjoint 0.02135 chr9 95755626 95756444 1.01266 0.26401 18.4154 BARX1 978 inside intron 0 inside 0.02136 chrl 149212099 149212953 0.17984 0.93111 18.4124 LASS2 1110 inside intron 167 disjoint 0.02136 chrl8 491107 491721 1.51967 0.34696 18.4021 COLEC12 423 promoter -385 disjoint 0.02138 chr9 136676317 136677114 0.39819 1.1694 18.4019 COL5A1 2845 inside intron -2099 disjoint 0.02138 chr5 150059389 150060296 0.31255 0.97198 18.3942 RB 22 520 covers exon(s) 28 disjoint 0.02139 chr9 23809885 23810601 0.91614 -0.0103 18.3915 ELAVL2 5461 inside intron 90 disjoint 0.02139 chr7 139985650 139986322 0.32447 1.32433 18.3875 DEN D2A 722 inside intron 144 disjoint 0.0214 chr4 54659618 54660658 0.63835 -0.0092 18.3783 GSH2 296 promoter 262 disjoint 0.02141 chrl 9 42400914 42401969 -0.0473 0.61014 18.3725 ZNF383 7236 upstream 0 overlap 0.02142 chr4 139230840 139231699 0.31628 1.22304 18.3672 SLG7A11 151253 downstream 469485 disjoint 0.02143 chr3 127489650 127490348 1.57015 0.67122 18.3552 LF15 68578 downstream 0 cover 0.02145 chrl4 100263488 100264504 0.69711 1.4899 18.353 DL .1 483 overlaps exon -236 disjoint 0.02145 upstream chrl2 113656802 113658173 2.18254 1.38194 18.3501 TBX3 50451 upstream 0 overlap 0.02145 chr3 141137862 141138953 0.34353 0.87255 18.3219 CLSTN2 966 inside intron -60 disjoint 0.02149 chr2 69974139 69975281 -0.1897 0.50566 18.3211 RY1 0 overlaps 5' 19582 disjoint 0.02149 chrlO 28070035 28070958 0.95298 0.39262 18.321 MKX 3794 covers exon(s) 0 overlap 0.02149 chrlO 65058323 65059063 -0.2757 0.72382 18.3155 REEP3 107195 downstream 818 disjoint 0.0215 chr7 44889983 44890807 0.69443 1.39265 18.3149 PURB 677 inside exon -35388 disjoint 0.0215 chrX 39755403 39756218 1.05537 0.22425 18.3107 BCOR 85381 downstream 258 disjoint 0.0215 chr8 100974995 100976166 0.08273 0.80184 18.3096 COX6C 0 overlaps 5' 0 overlap 0.02151 chr6 159158101 159158840 1.32816 0.23093 18.3061 VIL2 406 inside intron 229 disjoint 0.02151 chr8 23317799 23318742 1.10867 0.33328 18.3036 LOXL2 133 promoter 0 overlap 0.02151 chrl l 43859115 43860200 0.58515 1.65672 18.2999 ALKBH3 143 overlaps exon -11 disjoint 0.02152 downstream
chrl 4 87857850 87858773 0.42356 1.17755 18.2967 CNK10 326 inside intron 580 disjoint 0.02152 chrl l 31797403 31798203 1.17145 0.12605 18.2949 PAX6 7949 upstream 0 overlap 0.02153 chrl l 17699973 17701391 0.48948 1.14366 18.281 MY0D1 2288 overlaps 3' 0 overlap 0.02154 chrlO 131646378 131646953 1.13956 -0.0492 18.2804 EBF3 5127 inside intron 0 overlap 0.02154 chrl8 68689190 68689873 0.62207 1.57799 18.2774 NETOl 3401 upstream -1339 disjoint 0.02155 chrl l 2577378 2578340 0.2497 1.08285 18.2722 KCNQ1 138119 inside intron -17333 disjoint 0.02156 chr2 1549996 1550466 0.30706 1.64708 18.2567 TPO 153755 downstream 492 disjoint 0.02158 chrlO 126124594 126125383 0.30261 1.37636 18.2536 LHPP 15018 upstream 416 disjoint 0.02158 chr2 241944931 241945812 0.3134 1.38137 18.2504 FARP2 548 inside intron -57 disjoint 0.02159 chr20 2622865 2623858 1.35233 0.41292 18.2338 Π3Η3Β 30023 upstream -167 disjoint 0.02161 chr2 64938434 64939216 0.55484 1.39584 18.1943 SLC1A4 130881 upstream 1109 disjoint 0.02167 chrl4 105310829 105311926 0.59023 1.3452 18.1851 T EM121 246832 downstream -3991 disjoint 0.02168 chrl9 9883401 9883979 0.72579 1.8101 18.185 OLFM2 24090 inside intron 856 disjoint 0.02168 chrl 116184777 116185508 0.49265 1.38655 18.1703 NHLH2 0 overlaps 5' -890 disjoint 0.02171 chrl5 35174773 35175678 0.90996 0.07739 18.1641 MEIS2 2116 covers exon(s) 0 overlap 0.02171 chr6 43153480 43154199 0.47637 1.3845 18.1625 PT 7 1474 inside intron -445 disjoint 0.02172 chrl 3 111810328 111811378 0.57306 1.53316 18.1509 SOX1 40415 downstream -1214 disjoint 0.02173 chr3 132096464 132097406 -0.0314 0.76265 18.1502 ATP2C1 341 inside intron -292 disjoint 0.02173 chrl4 103790820 103791461 0.44537 1.5669 18.1419 TDRD9 284134 downstream -30793 disjoint 0.02175 chrl 7 6496309 6496956 0.39099 1.3973 18.1382 MED31 660 promoter 0 overlap 0.02175 chr7 44111304 44112168 0.17724 1.04097 18.137 AEBP1 820 inside intron 6584 disjoint 0.02176 chrl 2 12309065 12310062 -0.0975 0.54001 18.127 LRP6 950 inside intron 884 disjoint 0.02177 chr5 180160994 180161898 0.10404 1.27965 18.1156 MGAT1 755 inside intron 83 disjoint 0.02178 chr8 52611547 52612247 0.22642 1.24478 18.0998 PXDNL 127014 upstream -126773 disjoint 0.02181 chrl l 101693010 101693830 0.56689 1.5069 18.0896 BIRC3 0 overlaps 5' 0 cover 0.02182 chrl 3 112048713 112049531 0.03093 0.98195 18.0813 C13or£28 29138 upstream -2438 disjoint 0.02183 chrl7 27208950 27209725 1.07943 2.12834 18.0792 C17orf79 643 inside intron 152 disjoint 0.02184 chrl 7 59561809 59562489 0.50595 1.66727 18.0746 ERN1 602 promoter -27 disjoint 0.02184 chrX 24942581 24943519 0.71676 -0.1449 18.0332 ARX 255 inside intron 66 disjoint 0.0219 chr6 101013370 101014045 1.23335 0.12949 18.0309 SIM1 4226 inside intron 0 overlap 0.0219 chrl 9 5575431 5576334 0.49855 1.27554 18.0155 SAFB 1268 inside intron -719 disjoint 0.02193 chrl l 61078528 61079112 0.58911 1.90558 18.0144 SYT7 25761 inside intron 196 disjoint 0.02193 chr6 47551847 47552870 1.17819 0.4323 18.0124 CD2AP 1028 promoter 197 disjoint 0.02194 chrl 7 16887673 16888362 -0.2596 0.71168 17.9882 -RIP 842 inside intron -631 disjoint 0.02198 chrX 106956972 106957655 -0.2626 0.71212 17.9819 MID2 857 inside intron -115 disjoint 0.02198 chrl5 58071912 58072659 0.51647 1.72582 17.9664 FOXBl 11053 upstream 1740 disjoint 0.02201 chr3 51548490 51549533 -0.0645 0.56107 17.9626 VPRBP 39450 upstream -177 disjoint 0.02201 chrl5 61124780 61126393 0.03273 0.51198 17.9603 TPM1 2890 inside intron 916 disjoint 0.02202 chr3 198667022 198667756 1.60738 0.7205 17.9594 BDH1 99498 downstream 42 disjoint 0.02202 chr3 185805152 185806029 1.76249 0.72 17.9539 EPHB3 42872 downstream -184 disjoint 0.02203 chrl l 70638910 70639665 1.52763 0.90518 17.9521 DHC 7 197381 downstream 156 disjoint 0.02203 chr5 149982202 149983089 0.80995 1.49373 17.9515 SYNPO 17343 upstream 1774 disjoint 0.02203 chr3 150644197 150644769 0.50472 1.4608 17.9479 TM4SF4 30354 upstream 212627 disjoint 0.02204 chr7 27105108 27105714 1.22785 0.22408 17.9364 HOXA2 3204 downstream -1847 disjoint 0.02206 chr3 46911012 46912395 0.65244 1.50172 17.9267 PTHR1 16773 covers exon(s) -1715 disjoint 0.02207 chr2 174900162 174901088 0.84023 0.18558 17.9266 FLJ46347 9451 downstream 0 overlap 0.02207 chr7 27157446 27158536 0.1261 0.68988 17.913 HOXA7 4284 downstream 0 overlap 0.02209 chr20 22514456 22515309 0.15633 0.99223 17.8968 FOXA2 355 promoter 0 cover 0.02212 chrl2 56311216 56311965 1.08801 0.18135 17.8878 B4GALNT1 1286 covers exon(s) 0 overlap 0.02213 chrl4 44437428 44438108 -0.0067 0.92007 17.8829 C14orf28 1172 inside intron -570 disjoint 0.02214 chr5 725339 726370 0.5787 1.34498 17.8824 TPPP 20050 inside intron -3750 disjoint 0.02214 chrl5 61128337 61129453 0.01322 0.85102 17.8822 TPM1 649 inside intron 0 overlap 0.02214 chrl8 44735917 44736567 0.00662 1.01071 17.87 S AD7 4839 upstream -2555 disjoint 0.02216 chr2 10181187 10182313 0.45626 1.29622 17.8686 RRM2 1002 covers exon(s) -255 disjoint 0.02216 chr2 98800952 98801875 0.29023 1.03061 17.8557 MGC42367 117240 inside intron 2854 disjoint 0.02218 chrll 1862040 1862726 0.46013 1.50135 17.8506 LSP1 13311 covers exon(s) -2130 disjoint 0.02219 chrl8 55039895 55040611 1.59685 0.77491 17.8482 GRP 1516 inside intron -1250 disjoint 0.02219 chrl 33572276 33572848 0.79921 1.90542 17.8475 PHC2 15237 covers exon(s) 14522 disjoint 0.02219 chrl2 106677497 106678384 -0.1079 0.56417 17.8353 PRDM4 659 inside intron 140 disjoint 0.02221 chr2 227367237 227368169 0.34273 1.08096 17.835 IRSl 4549 overlaps exon 2157 disjoint 0.02221 downstream
chrlO 22648525 22649310 0.83144 -0.0371 17.8335 COMMD3 3221 overlaps 3' -2887 disjoint 0.02221 chrl4 74816685 74817471 1.31322 0.56552 17.8197 FOS 1402 covers exon(s) -134 disjoint 0.02224 chrl 4 89917759 89918660 0.12448 0.86388 17.8175 CALM1 14465 upstream 87 disjoint 0.02224 chr5 140604555 140605784 0.39248 1.00395 17.7993 PCDHB15 0 overlaps 5' 844 disjoint 0.02226 chrl 3 40135524 40136745 0.80408 0.02423 17.7972 FOX01A 1988 inside intron 0 overlap 0.02226 chrl l 10784774 10785665 0.16039 1.11663 17.7947 EIF4G2 1492 covers exon(s) 272 disjoint 0.02226 chrS 139057835 139058741 0.3514 1.22457 17.7944 CXXC5 49706 downstream -472 disjoint 0.02226 chr6 32230156 32231601 0.58261 1.14124 17.784 PPT2 557 covers exon(s) 0 overlap 0.02228 chr4 154931794 154932978 0.91997 0.35698 17.7778 SFRP2 2117 promoter 0 overlap 0.02229 chrl 7 61727856 61728464 1.74558 0.51758 17.771 PRKCA 923 promoter 45 disjoint 0.0223 chrl l 2217375 2219043 0.41703 1.0771 17.7625 ASCL2 29714 downstream 27637 disjoint 0.02231 chr22 33349250 33349816 0.65395 1.80719 17.7621 ISX 442313 upstream 633545 disjoint 0.02231 chrl 224439398 224440099 0.15813 1.19789 17.7619 ACBD3 946 inside intron 559 disjoint 0.02231 chrl2 47648320 47649454 0.86231 0.1601 17.76 WNT10B 2355 overlaps exon 477 disjoint 0.02232 upstream
chr2 119328113 119328879 1.41454 0.36606 17.756 EN1 5885 upstream 0 overlap 0.02232 chr9 109440646 109441388 0.00993 0.95497 17.7512 KLF4 149071 upstream -259 disjoint 0.02233 chrll 124176005 124177056 0.21515 0.96197 17.7488 Cllorf61 497 promoter -276 disjoint 0.02234 chr9 21985898 21986365 1.27529 -0.0889 17.7346 CDKN2A 1409 promoter 0 overlap 0.02236 chrl 2 116111015 116111629 0.52692 1.69814 17.7261 FBX021 1053 covers exon(s) 404 disjoint 0.02237 chrl 6 25505486 25505851 0.29109 2.05017 17.7252 HS3ST4 104996 upstream 104605 disjoint 0.02237 chrl 7 24299171 24299980 -0.0402 0.90306 17.7249 PHF12 2653 inside intron 365 disjoint 0.02237 chr20 11615995 11616852 0.37086 0.97172 17.7175 BTBD3 202624 upstream 0 overlap 0.02238 chrl3 47964δ70 47965140 0.60988 2.07767 17.716 RCBTB2 40176 inside intron 39272 disjoint 0.02238 chr7 54700121 54700798 0.13646 1.15697 17.7082 SEC61G 93634 downstream -148 disjoint 0.02239 chrl 38817336 38819093 0.41335 1.29468 17.6959 RRAGC 278833 downstream -216 disjoint 0.02241 chr6 44077024 44077937 1.29427 0.33044 17.6946 MGC45491 693 covers exon(s) 114 disjoint 0.02241 chr8 41283603 41284319 0.896 0.04025 17.6853 SFRP1 1817 inside intron 690 disjoint 0.02243 chrl l 131446919 131447428 0.42633 1.66837 17.6824 HNT 160998 inside intron -160177 disjoint 0.02243 chrl 6 30287213 30288052 0.06555 1.06637 17.6801 TBC1D10B 349 overlaps exon 526 disjoint 0.02244 downstream
chrl 8 51240890 51241453 -0.1879 1.1935 17.6767 TCF4 164987 inside intron 166563 disjoint 0.02244 chr7 90064451 90065634 -0.1819 0.33597 17.6752 PFTK1 111013 upstream -151 disjoint 0.02244 chr4 557326 558365 0.46557 1.19209 17.6733 PIGG 74317 downstream 148 disjoint 0.02245 chr7 157126899 157127612 1.51355 2.41891 17.6665 PTPRN2 945566 inside intron 5173 disjoint 0.02246 chrl l 2406185 2407852 0.85429 1.4054 17.6633 TRPM5 5335 upstream -7207 disjoint 0.02246 chr3 113764705 113765612 1.32517 0.5942 17.6631 SLC35A5 1121 covers exon(s) -1068 disjoint 0.02246 chrl2 6584885 6585442 -0.13 0.9932 17.6519 CHD4 1369 inside intron 319 disjoint 0.02248 chrl l 77807490 77808239 0.44929 1.46835 17.6387 GAB2 1077 promoter -442 disjoint 0.0225 chrl 3 24643853 24644635 0.08572 1.07871 17.6272 FAM123A 0 overlaps 5' 0 overlap 0.02252 chr2 70221603 70222562 1.19556 0.58463 17.603 C2orf42 49092 downstream 81 disjoint 0.02256 chr20 19138839 19139711 0.22936 0.9533 17.5984 SLC24A3 1578 promoter 748 disjoint 0.02257 chr2 5755247 5756116 1.08926 0.39556 17.5772 S0X11 4998 inside exon -153 disjoint 0.0226 chr8 103204213 103205096 0.37003 1.08689 17.5772 NCALD 641 inside intron 0 overlap 0.0226 chr3 50201486 50202562 1.14156 1.83719 17.57 SEMA3F 33635 overlaps 3' 2872 disjoint 0.02261 chr6 30759332 30760362 0.30968 0.9963 17.568 NRM 6385 downstream 2009 disjoint 0.02262 chr5 140559290 140560072 0.81796 1.67185 17.5606 PCDHB11 0 overlaps 5' 835 disjoint 0.02263 chrl 7 14142006 14142612 0.82324 -0.1623 17.5524 HS3ST3B1 2618 upstream 0 overlap 0.02264 chrl 75363852 75365048 0.48549 1.38955 17.5407 LHX8 1658 promoter 0 overlap 0.02266 chr7 12695285 12695997 1.00571 0.1272 17.54 ARL4A 1800 inside exon -1512 disjoint 0.02266 chr9 1039790 1040329 1.6091 0.4391 17.532 DMRT2 1284 promoter 0 overlap 0.02268 chr3 154036624 154037268 2.1041 1.11931 17.5279 P2RY1 1199 inside exon -225 disjoint 0.02268 chrl 8 46444919 46445666 0.41052 1.53053 17.5259 MAP 4 104438 inside intron -252 disjoint 0.02268 chr2 198087702 198088714 0.10053 0.80995 17.5232 PREI3 0 overlaps 5' 0 overlap 0.02269 chrl l 124213389 124214069 1,55379 0.39931 17.5197 ROB03 26422 upstream 363 disjoint 0.0227 chr3 148557194 148558051 0.79699 -0.0458 17.5184 ZIC4 49045 downstream 1751 disjoint 0.0227 chrl 2 55899740 55900389 1.28838 0.11959 17.5105 XPH4 2896 inside intron -2305 disjoint 0.02271 chr6 166190210 166191067 0.02832 0.7401 17.5087 LOC441177 129961 upstream -1759 disjoint 0.02272 chrl 7 62673082 62673897 1.09541 0.34103 17.5053 HELZ 1309 promoter -122 disjoint 0.02272 chr8 57148494 57149184 0.1466 1.13676 17.4835 RPS20 438 covers exon(s) 0 overlap 0.02276 chrl l 2415536 2418185 0.4324 1.07996 17.4694 CNQ1 4611 upstream 3562 disjoint 0.02278
Chr6 74461558 74462565 0.24285 0.93789 17.4625 CD 109 0 overlaps 5' 0 overlap 0.0228 chr7 157086267 157087100 0.29213 1.22595 17.4523 PTPRN2 986078 inside intron -6184 disjoint 0.02281 chr6 1561288 1562046 1.13985 0.34932 17.4189 FOXC1 5609 downstream -423 disjoint 0.02286 chr6 89848794 89849408 0.09612 1.32062 17.4155 PNRC1 1579 inside intron -294 disjoint 0.02287 chrlO 21829495 21830316 1.09396 0.28742 17.4053 ClOorflH 3299 upstream 0 overlap 0.02288 chr4 36923851 36924606 0.21683 1.06849 17.4026 C4orfl9 337643 upstream -477 disjoint 0.02289 chrl l 107497934 107498656 0.8671 1.81117 17.3982 AC ATI 467 inside intron 0 overlap 0.0229 chrX 24080642 24081498 0.15712 0.97934 17.39 ZFX 914 covers exon(s) -1936 disjoint 0.02291 chrl l 31781251 31782078 0.64127 -0.1414 17.3742 PAX6 7355 inside intron 241 disjoint 0.02294 chrl 7 33864086 33864664 0.02721 1.10622 17.3618 SOCS7 102556 downstream -240 disjoint 0.02296 chrl9 1811835 1812650 1.33202 0.57973 17.3603 KLF16 1913 inside intron 61 disjoint 0.02296 chr20 29913269 29913985 1.08971 0.22462 17.3589 DUSP15 7476 inside intron -15 disjoint 0.02296 chrl7 2445232 2446206 -0.3313 0.26475 17.3496 PAFAH1B1 1547 inside intron -459 disjoint 0.02298 chr2 86868329 86869345 0.5798 1.37661 17.3473 CD8A 2292 covers exon(s) 140 disjoint 0.02298 chrl5 43794102 43794815 0.60038 1.46881 17.3447 SQRDL 79555 downstream -9934 disjoint 0.02299 chrl8 13817249 13817821 0.509 1.92857 17.3254 MC5 1485 close to 3' -726 disjoint 0.02302 chrl9 750120 751356 0.17257 0.93449 17.3036 PTBP1 1710 covers exon(s) -184 disjoint 0.02305 chr2 170392950 170394137 0.11748 0.7911 17.2995 METTL5 3352 upstream -75 disjoint 0.02306 chrl6 8963004 8963750 1.69655 0.70367 17.2903 USP7 1091 inside intron 123 disjoint 0.02307 chr9 90794820 90795852 0.97374 0.20856 17.2778 C9orf47 0 overlaps 5' 0 overlap 0.02309 chr8 3257254 3257862 0.6572 1.61338 17.2656 CSMD1 1581873 inside intron -389899 disjoint 0.0231 1 chrl3 11 1811502 1 11812718 0.16616 1.02817 17.2651 S0X1 41589 downstream -2388 disjoint 0.02311 chrl 43003628 43004277 -0.1751 1.07588 17.2575 LEPRE1 992 inside intron 524 disjoint 0.02313 chr5 126654790 126655682 0.6795 -0.0072 17.2572 MEGF10 277 inside intron 0 overlap 0.02313 chrl 9 56261110 56261862 0.05887 0.8667 17.2454 KL 13 932 promoter -886 disjoint 0.02314 chrl 7 71579129 71579635 -0.2358 1.00024 17.2381 SRP68 566 inside intron 134 disjoint 0.02316 chr4 183303493 183304275 0.83874 0.0628 17.2326 DCTD 771348 downstream -129 disjoint 0.02317 chrl 112336813 112337804 1.07819 2.04575 17.2279 CND3 3514 upstream -1517 disjoint 0.02318 chrl l 93772648 93773901 0.60046 1.38431 17.2241 GPR83 164 overlaps exon 0 overlap 0.02318 downstream
chrl 212427057 212427737 0.39984 1.26591 17.223 SMYD2 93461 upstream 0 cover 0.02318 chr6 41451502 41452116 1.13563 0.18651 17.22 NCR2 39998 downstream -981 disjoint 0.02319 chr2 68330652 68331398 0.25211 1.32994 17.2119 PPP3R1 1756 inside intron 1167 disjoint 0.0232 chr6 44342597 44343241 1.01337 1.92331 17.2036 NFKBIE 1095 promoter -1172 disjoint 0.02321 chrlO 6170285 6170752 0.29322 1.55026 17.1957 RB 17 260 promoter 40 disjoint 0.02322 chrl 2 1 12557312 112558383 0.88445 1.68844 17.1893 LHX5 163053 upstream -43177 disjoint 0.02323 chrl 4 75914376 75915165 0.65725 1.46021 17.1831 ESRRB 6898 inside intron -777 disjoint 0.02324 chrlO 21837934 21838506 1.25116 0.16479 17.172 FLJ45187 16110 downstream 0 inside 0.02326 ehr3 15445015 15445662 0.7162 1.743 17.162 EAF1 948 inside intron -579 disjoint 0.02328 chr8 94782561 94783400 0.47554 1.36878 17.1548 RB 12B 38963 downstream -40 disjoint 0.02329 chr22 48267352 48268069 0.4505 1.24686 17.1521 FLJ44385 60263 upstream 1003 disjoint 0.02329 chrl 3 49605851 49606705 1.26687 0.63855 17.1519 CNRG 118461 downstream 0 overlap 0.02329 chrlO 97039000 97040027 0.90924 0.38983 17.1491 PDL 1 743 inside intron 148 disjoint 0.02329 chrlO 75301508 75302119 0.9459 1.99667 17.1445 CAMK2G 2224 inside intron 1487 disjoint 0.0233 chrl 3 99408985 99409905 0.67219 -0.0178 17.1426 ZIC5 12273 downstream 0 overlap 0.0233 chrl5 61459961 61460699 0.69884 1.70222 17.1365 CA12 428 inside intron 242 disjoint 0.02331 chrl 4 70442988 70443498 0.62855 1.81357 17.1324 PCNX 376 promoter 219 disjoint 0.02332 chrl 2 119451528 119452403 0.01263 0.98702 17.1287 COQ5 182 promoter -107 disjoint 0.02332 chr5 89888959 89889777 0.98386 0.02185 17.1263 GPR98 595 promoter 269 disjoint 0.02333 chr6 166037267 166037878 0.79614 1.72515 17.1209 PDE10A 41693 upstream 22113 disjoint 0.02334 chrlO 102016917 102017744 0.66254 1.49648 17.1199 CWF19L1 0 overlaps 5' 0 cover 0.02334 chr2 42572847 42573245 1.68239 0.18558 17.1118 CNG3 1495 inside intron 43 disjoint 0.02335 chr5 76960357 76961344 0.67117 0.06564 17.1079 OTP 8933 inside exon 0 overlap 0.02336 chr8 8783354 8784900 0.14298 0.82714 17.1063 MFHAS1 3640 inside intron 1162 disjoint 0.02336 chrl 4 73248421 73249071 0.32687 1.42786 17.0996 P MA1 1809 inside exon 1200 disjoint 0.02337 chrl 4 88951191 88951936 0.49825 1.64799 17.0928 CHES1 1190 inside intron 238 disjoint 0.02338 chr6 5938645 5939671 1.15058 0.34079 17.0823 RNl 12960 downstream 237 disjoint 0.0234 chr6 1332823 1333224 1.64327 0.04132 17.0811 FOXF2 1843 promoter 914 disjoint 0.0234 chrl6 87376705 87377724 0.3703 1.10931 17.0695 CDT1 19962 upstream 0 overlap 0.02342 chrlO 90631297 90632155 0.91921 1.71092 17.0545 STAMBPL1 1292 inside intron -694 disjoint 0.02345 chr3 1 10613361 110613900 0.05412 1.22091 17.052 DPPA4 74279 upstream -293585 disjoint 0.02345 chrl l 19755949 19756387 1.17892 -0.2417 17.0472 NAV2 64462 inside intron -424 disjoint 0.02346 chr5 41960469 41961005 0.49195 1.56338 17.047 FBX04 107 promoter 41 disjoint 0.02346 chr3 173011251 173011852 0.04224 1.3922 17.0391 PLD1 72686 upstream -102 disjoint 0.02347 chrl7 44431640 44432230 0.85474 -0.2102 17.039 IGF2BP1 1868 inside intron -599 disjoint 0.02347 chr7 6112030 6112709 0.09573 0.98479 17.038 USP42 929 inside intron -185 disjoint 0.02348 chrl5 83162258 83162939 1.32973 0.49624 17.0372 ALP 3 1344 inside intron -680 disjoint 0.02348 chrl6 84566219 84567195 0.58351 1.48119 17.0364 IRF8 75945 downstream -1031 disjoint 0.02348 chr7 37964501 37965047 0.55794 1.70319 17.0342 EPDR1 37814 downstream -36930 disjoint 0.02348 chr8 41467751 41468763 -0.1613 0.55396 17.0329 GOLGA7 422 inside intron -13 disjoint 0.02348 chrlO 71682313 71683415 0.07607 0.76469 17.0309 PFFR1 12738 downstream 1368 disjoint 0.02349 chr2 64098322 64099046 0.30493 1.18338 17.0301 VPS54 671 inside intron 392 disjoint 0.02349 chrH 24587503 24588014 0.16134 1.47008 17.0136 STXBP6 920 inside intron 250 disjoint 0.02352 chr7 65308679 65309462 0.45488 1.29625 16.9984 TPST1 931 inside intron -299 disjoint 0.02355 chrl l 120828566 120829482 1.36763 0.56822 16.9891 S0RL1 437 inside intron -54 disjoint 0.02357 chrl5 82110477 82112371 0.49147 1.49826 16.9823 ADAMTSL3 1470 promoter 955 disjoint 0.02358 chr2 11019941 11021925 1.09508 1.9697 16.9757 KCNFJ 50428 downstream -1002 disjoint 0.0236 chr8 139579116 139579742 0.03981 0.98169 16.9739 C80RFK32 870 promoter -160 disjoint 0.0236 chrl8 12278141 12278998 0.40469 -0.3072 16.9673 CEDEA 33354 downstream -579 disjoint 0.02361 chrl 87573890 87574698 0.32476 1.17046 16.966 LM04 7152 inside intron -50 disjoint 0.02361 chr2 74611226 7461 1735 0.33893 1.51481 16.9546 HTRA2 1187 covers exon(s) 0 overlap 0.02364 chr6 34833041 34833889 0.08494 0.85586 16.9412 SNRPC 0 overlaps 5' 0 cover 0.02366 chr6 42824064 42824852 0.91021 1.68705 16.9349 TBCC 2253 promoter -1044 disjoint 0.02367 chr6 166152464 166153086 0.73451 1.78309 16.9281 PDE10A 156890 upstream 7414 disjoint 0.02368 chrl 7 56887322 56888176 1.0305 0.20958 16.9247 TBX4 412 promoter 0 inside 0.02368 chr2 238859948 238860684 0.76436 1.77154 16.9191 PER2 1146 inside intron 978 disjoint 0.02369 chrlO 99071092 99071859 1.63789 0.8338 16.918 FRAT1 2081 overlaps 3' -54 disjoint 0.02369 chr6 119442147 119442948 0.08091 0.84266 16.9178 C6orf60 637 promoter -225 disjoint 0.02369 chrl 7 28279579 28280730 -0.2253 0.64388 16.9083 T EM98 539 inside intron -74 disjoint 0.02371 chr9 115901027 115901533 1.45489 0.29582 16.9006 KIF12 0 overlaps 5' 0 overlap 0.02373 chrl 5 74422659 74423255 1.41731 0.2469 16.8978 ISL2 6458 downstream -89 disjoint 0.02373 chr5 87477000 87477930 0.87701 0.19592 16.8918 TMEM161B 122490 downstream -3739 disjoint 0.02374 chrl 9 60589653 60590531 0.14366 0.92387 16.8871 RPL28 542 covers exon(s) 0 overlap 0.02375 chrl l 59081984 59082736 1.19083 0.29808 16.8862 OSBP 57456 downstream 1977 disjoint 0.02375 chrl 7 45219508 45220365 1.133 0.33944 16.8697 MYST2 704 promoter 608 disjoint 0.02378 chr6 91063791 91064543 2.21811 1.21615 16.8392 BACH2 610 promoter -126 disjoint 0.02383 chrl 7 55510037 55510756 -0.0886 0.69836 16.8384 ABCl 317 inside intron 36 disjoint 0.02383 chrl 4 105019205 105019900 0.38414 1.22621 16.8232 CRIP2 7030 downstream -2460 disjoint 0.02385 chr6 107915679 107916679 1.03931 0.30137 16.8205 FLJ10159 1330 promoter 80 disjoint 0.02385 chr8 2062262 2062837 -0.1083 0.94505 16.8118 MYO 2 81608 inside intron 22 disjoint 0.02387 chrl 8 72369835 72370305 0.56203 1.82901 16.8107 FLJ44881 160668 upstream -32209 disjoint 0.02387 chr2 19422490 19423308 1.00855 0.31649 16.8086 OSR1 638 promoter -606 disjoint 0.02388 chrl l 62482486 62483019 0.79456 1.869 16.7894 SLC22A6 26025 downstream -31138 disjoint 0.02391 chr7 148743369 148743910 1.51859 0.40006 16.778 ZNF777 39395 downstream 0 overlap 0.02394 chrlO 118018016 118018865 -0.0332 0.72007 16.772 GFRA1 2918 inside intron 1857 disjoint 0.02395 chrl l 62449438 62449944 1.70674 0.40836 16.7681 CHRM1 3851 upstream 5 disjoint 0.02396 chr9 97824229 97825075 0.99232 0.13503 16.7674 C9orfl02 49260 downstream -44 disjoint 0.02396 chr2 151826574 151827312 0.34872 1.20336 16.7563 C2orB8 0 overlaps 5' 0 overlap 0.02398 chr6 167410614 167411123 0.91743 2.12657 16.7459 FGFR10P 77809 downstream 16301 disjoint 0.024 chr5 453127 454013 0.39045 1.13404 16.7423 AHRR 95837 inside intron 20211 disjoint 0.02401 chrlO 60607083 60607742 0.66744 1.63223 16.7325 PHYFflPL 731 inside intron -28 disjoint 0.02403 chrl3 38162880 38163419 0.75104 2.07923 16.7289 FREM2 3399 inside exon -2581 disjoint 0.02404 chr3 14829969 14831013 0.37088 1.13511 16.7269 FGD5 4796 upstream -1871 disjoint 0.02404 chr9 37023001 37023889 0.75944 1.46408 16.7215 PAX5 586 inside intron 246 disjoint 0.02405 chr22 27610672 27611352 1.50311 0.56262 16.7179 XBP1 84113 upstream -385 disjoint 0.02405 chrl l 44285814 44286621 1.91114 0.90144 16.7159 ALX4 1670 inside intron 497 disjoint 0.02406 chrl 224365720 224366608 1.12176 0.42649 16.7081 ACBD3 74437 downstream -511 disjoint 0.02407 chr4 140419505 140420580 1.31013 0.62605 16.7021 OSAP 361 inside intron 0 overlap 0.02408 chr7 27144976 27145486 1.32019 -0.0429 16.6972 HOXA5 4325 downstream 101 disjoint 0.02409 chr6 169168007 169168620 0.53671 1.48461 16.6913 THBS2 227441 downstream -561 disjoint 0.0241 chr4 17390905 17391682 0.83851 1.85864 16.6687 C4orf30 29796 downstream 58 disjoint 0.02414 chrlO 25277822 25280837 1.38114 0.08991 16.6664 PRTFDC1 701 inside intron 279 disjoint 0.02415 chrl 2 129217057 129217776 0.21174 1.0904 16.6468 FZD10 4073 downstream -2116 disjoint 0.02418 chr6 7055609 7056348 1.74926 0.82449 16.6459 RREB1 2347 inside intron -756 disjoint 0.02418 chr2 119306760 119307509 1.08318 0.3505 16.6352 E 1 14719 downstream 1563 disjoint 0.0242 chrlO 102484267 102485092 0.70476 -0.0489 16.6328 PAX2 10229 upstream 14 disjoint 0.02421 chrl 5 68931614 68932504 0.5054 1.30538 16.6296 LARP6 1047 inside intron 545 disjoint 0.02421 chrl 51967085 51967519 1.48715 -0.0469 16.6286 OSBPL9 111734 inside intron 97 disjoint 0.02422 chrl 4 60174434 60174971 1.17047 -0.0126 16.6262 SKI 10961 downstream -18 disjoint 0.02422 chr4 75184086 75185125 0.26055 1.1158 16.6234 CXCL2 311 promoter 0 overlap 0.02423 chr5 137905485 137906063 0.12655 1.1332 16.6224 ETF1 738 inside intron 100 disjoint 0.02423 chrl2 51355642 51356394 1.20387 2.08145 16.6114 KRT1 4051 covers exon(s) 37785 disjoint 0.02425 chrX 118712584 118713123 1.5853 0.47088 16.6114 1224 promoter -299 disjoint 0.02425 chrl 9 4782004 4782405 0.07349 1.50882 16.608 M6PRBP1 36270 downstream 28 disjoint 0.02426 chr5 92948839 92949616 1.15646 0.30157 16.608 NR2F1 4041 overlaps exon 0 overlap 0.02426 upstream
chrl 6 19990882 19991549 0.10793 1.21043 16.6051 GPR139 1051 inside intron 659 disjoint 0.02426 chr5 43075175 43075957 1.22444 0.33899 16.6023 LOC389289 140 inside exon 145 disjoint 0.02427 chrl 9 3818141 3818853 0.48896 1.29706 16.6002 ATCAY 12785 upstream 733 disjoint 0.02427 chr22 38131289 38131864 0.43663 1.43176 16.6001 MAP3K7IP1 5585 inside intron -5172 disjoint 0.02427 chr7 27152662 27153252 1.77577 0.72083 16.5978 HOXA6 640 inside intron 200 disjoint 0.02428 chr7 1234101 1235129 0.60419 -0.0183 16.5944 ZFAND2A 67778 upstream 562 disjoint 0.02428 chr2 241107683 241108328 0.60575 1.45749 16.5843 ANKMY1 37749 inside intron 0 overlap 0.0243 chrl 7 44037719 44038556 0.96394 0.22196 16.5812 HOXB6 387 promoter 1687 disjoint 0.0243 chrl 150428544 150429321 0.16331 1.16044 16.5791 HRNR 33971 downstream 0 overlap 0.02431 chrl 40891032 40891889 1.0574 1.68732 16.5777 RJMS3 12021 inside intron 550 disjoint 0.02431 chr9 34581800 34582600 1.12942 0.33637 16.5767 CNTFR 2079 promoter 0 overlap 0.02431 chr4 42092929 42093871 1.20823 0.45907 16.5756 ATP8A1 259775 downstream 38 disjoint 0.02431 chr4 147776235 147777335 0.17233 0.67805 16.5726 POU4F2 2159 promoter 346 disjoint 0.02432 chrl 7 70519198 70520157 0.09839 1.04042 16.5706 ICT1 217 promoter 0 overlap 0.02432 chrl3 98027944 98028693 1.34603 0.47612 16.5536 STK24 548 promoter -367 disjoint 0.02435 chrl 7 74346672 74347556 0.25014 1.07783 16.5498 USP36 900 inside intron 99 disjoint 0.02436 chr6 42955466 42956209 0.31633 1.125 16.5362 RPL7L1 0 overlaps 5' 9938 disjoint 0.02438 chrl 204009733 204010446 1.48632 0.8322 16.5358 RAB7L1 300 inside intron 77 disjoint 0.02438 chrl 154517786 154518794 0.45926 1.31141 16.5321 SMG5 445 inside intron 9029 disjoint 0.02439 chr5 139262376 139263316 0.92164 0.31032 16.5186 NRG2 139746 inside intron 218 disjoint 0.02441 chr22 18132148 18132933 1.2055 0.50234 16.5181 TBX1 7923 covers exon(s) -239 disjoint 0.02441 chrl 3 47566161 47567199 0.15459 0.79556 16.5106 MED4 41 overlaps exon 0 overlap 0.02443 downstream
chr6 143424084 143424766 0.93737 0.11568 16.5061 AIG1 369 inside intron -473 disjoint 0.02444 chrX 118622731 118623446 0.16365 1.16298 16.5058 N RF 394 inside intron 291 disjoint 0.02444 chr5 92939321 92940190 1.10409 0.38493 16.4925 NR2F1 4608 upstream 336 disjoint 0.02446 chrl 3 47776661 47777564 0.04563 0.79172 16.4914 RBI 778 inside intron -159 disjoint 0.02446 chr8 4837866 4838608 -0.0762 0.88671 16.4785 CSMD1 1127 inside intron 0 inside 0.02449 chrl 2 56299065 56299673 1.69033 0.64337 16.4741 SLC26A10 286 promoter 0 overlap 0.0245 chrl 16567259 16568139 0.19589 0.99298 16.4673 Clorfl44 953 inside intron -402 disjoint 0.02452 chrl9 19035990 19036879 0.26306 0.86704 16.4659 SLC25A42 183 inside intron 0 overlap 0.02452 chrl l 67794646 67795503 0.23722 0.77339 16.4559 Cllorr24 493 inside intron 373 disjoint 0.02454 chrl l 115721419 115722143 0.38538 1.52079 16.4556 BUD13 426770 downstream 154249 disjoint 0.02454 chrl9 41396541 41397313 0.81125 1.43015 16.4474 ZNF565 92 inside intron 0 overlap 0.02455 chrl l 122435593 122436765 0.23588 1.00914 16.4451 HSPA8 1288 covers exon(s) 618 disjoint 0.02456 chrl 7 47589463 47590305 -0.1136 0.69612 16.4399 CA10 780 overlaps exon 0 overlap 0.02457 downstream
chrl5 39003709 39005073 1.25397 0.39013 16.4237 DLL4 3765 upstream 8 disjoint 0.0246 chrl 9 62044119 62044730 0.35621 1.62749 16.4217 ZIM2 233 promoter -23 disjoint 0.0246 chr3 149898704 149899246 0.91973 2.15085 16.4209 AGTR1 350 inside intron -85 disjoint 0.0246 chr6 125517483 125518524 1.35615 0.48682 16.4107 TPD52L1 365 inside intron -62 disjoint 0.02462 chr5 122448195 122449267 1.42275 0.78818 16.3885 PPIC 47872 upstream 2969 disjoint 0.02466 chrl 149244804 149245524 0.09364 0.83106 16.3785 FAM63A 432 overlaps exon 1835 disjoint 0.02468 downstream
chr6 146389265 146390147 0.24242 0.93251 16.3551 GRM1 1964 promoter 2068 disjoint 0.02472 chr8 48811127 48811705 -0.0435 0.93449 16.3538 CEBPD 1617 close to 3' 614 disjoint 0.02472 chrl l 58099384 58099854 0.37259 1.63745 16.3537 LPXN 55 overlaps exon 2395 disjoint 0.02472 downstream
chrl2 56294113 56294691 2.79263 1.74026 16.353 GEFT 2151 covers exon(s) -2495 disjoint 0.02472 chrl 6 19993114 19994020 0.04981 0.92352 16.3503 GPR139 514 promoter -308 disjoint 0.02473 chrl 33667959 33668537 1.082 -0.0701 16.3492 ZNF31 42308 upstream 52 disjoint 0.02473 chrl 8 42169270 42170295 0.52437 -0.0768 16.3444 RNF165 1086 inside intron -795 disjoint 0.02474 chr22 44850960 44851727 0.4529 1.23622 16.3394 FLJ27365 8819 upstream -3768 disjoint 0.02474 chrlO 22655295 22655951 1.13875 0.15556 16.3371 BMI1 5150 covers exon(s) -355 disjoint 0.02475 chr2 239360257 239360800 0.70814 1.79741 16.333 FLJ43879 152101 downstream 59045 disjoint 0.02476 chrlO 119299715 119300629 0.84898 -0.0078 16.3212 E X2 7770 downstream 565 disjoint 0.02478 chrl 7 8019634 8020484 0.37191 1.13106 16.3165 T EM107 0 overlaps 5' 0 overlap 0.02479 chr21 42934605 42935777 0.6624 1.53782 16.3135 PDE9A 11153 upstream 10493 disjoint 0.0248 chrl4 54105318 54106136 0.29668 0.98624 16.2978 SAMD4A 932 inside intron -538 disjoint 0.02483 chrl 31489215 31490061 1.24435 1.77806 16.2824 WDR57 52169 downstream -3816 disjoint 0.02486 chr3 185764726 185765717 1.02106 0.39222 16.2753 EPHB3 2446 inside intron -1314 disjoint 0.02487 chr22 41370172 41371296 0.67156 1.62811 16.2748 CYB5R3 1665 inside intron 3657 disjoint 0.02487 chrX 21869993 21870814 0.89851 -0.0234 16.2734 SMS 1231 inside intron -371 disjoint 0.02488 chr5 71051944 71052828 0.59186 1.24927 16.2732 CARTPT 1195 overlaps 3' -473 disjoint 0.02488 chrl 7 11083286 11083867 1.24E-05 1.04455 16.272 FLJ45455 1903 promoter 345 disjoint 0.02488 chr9 78980317 78981323 0.06454 0.79119 16.2698 VPS13A 857 promoter 567 disjoint 0.02488 chr6 42966431 42967006 0.02622 1.00208 16.2649 LOC441150 0 overlaps 5' 0 overlap 0.02489 chrl 4090337 4091103 0.92874 2.02137 16.2649 Clorfl74 283629 upstream 1390 disjoint 0.02489 chr6 168988758 168990492 0.48774 1.36507 16.2617 SM0C2 403879 downstream -3662 disjoint 0.0249 chrl l 124047515 124048229 2.05491 1.19855 16.2601 S1AE 697 inside intron 365 disjoint 0.0249 chr6 17388388 17388825 1.66652 0.23493 16.2589 RBM24 2085 promoter 0 overlap 0.0249 chr9 135231330 135231999 0.2636 1.20588 16.2533 SURF4 791 inside intron 128 disjoint 0.02491 chr9 14301857 14302654 0.47493 -0.2442 16.2515 NFIB 1290 inside intron 298 disjoint 0.02491 chr20 1113011 1113525 0.36349 1.66298 16.2498 C20orf46 0 overlaps 5' 0 overlap 0.02492 chr7 157209210 157209782 1.6305 2.88494 16.2497 PTPRN2 863396 inside intron 7136 disjoint 0.02492 chrlO 99200020 99200856 0.75931 1.56225 16.2457 ZDHHC16 4084 covers exon(s) -3756 disjoint 0.02493 chrll 117520068 117S21046 0.99582 1.75627 16.2358 SCN4B 7698 overlaps exon 401 disjoint 0.02495 downstream
chr6 41545353 41546028 1.40808 0.40966 16.2308 F0XP4 76113 upstream 12 disjoint 0.02496 chr8 37762735 37763274 0.8009 1.86552 16.2233 PROSC 23903 downstream 9932 disjoint 0.02497 chrl5 38590110 38590685 0.87175 1.97285 16.2158 D4ST1 39606 downstream 187 disjoint 0.02498 chr6 39301657 39302625 1.06449 1.83058 16.214 KCN 5 2603 inside intron 2170 disjoint 0.02499 chr3 197000904 197001446 1.36835 2.44927 16.2138 MUC4 22098 inside intron -25293 disjoint 0.02499 chr2 1192902 1193687 1.11291 1.81315 16.2088 SNTG2 256348 inside intron -39082 disjoint 0.025 chrl 3 44782576 44783223 0.74621 1.77663 16.2068 TPT1 30073 downstream 531 disjoint 0.025 chr7 91408751 91409750 -0.0154 0.64081 16.2059 A AP9 624 inside intron -467 disjoint 0.02501 chrl5 72214146 72214751 1.24446 0.33453 16.2041 ISLR2 4149 inside exon 0 inside 0.02501 chr3 180650127 180650909 -0.0287 0.70355 16.2028 GNB4 1155 inside intron 517 disjoint 0.02501 chrl 8 44188147 44188581 1.72758 0.37591 16.2 IAA0427 130843 upstream 0 overlap 0.02502 chr6 36752797 36753977 0.28867 0.91197 16.1924 CDK 1A 487 promoter 245 disjoint 0.02503 chr8 142078891 142079458 -0.0874 1.11212 16.1911 PT 2 1055 inside intron 164 disjoint 0.02503 chr6 75968873 75969478 1.11425 0.14924 16.1894 COL12A1 2864 covers exon(s) -20 disjoint 0.02503 chrlO 104050163 104050672 0.31834 1.47127 16.1716 GBF1 54865 inside intron -54581 disjoint 0.02507 chr2 1 4916944 174917624 1.12857 0.19779 16.1664 CIR 51064 downstream 0 overlap 0.02508 chr2 232958587 232959417 0.70315 1.43543 16.1604 ALPP 6996 downstream 188 disjoint 0.02509 chr7 157883191 157883862 0.83347 1.74273 16.1536 PTPRN2 189316 inside intron 7444 disjoint 0.0251 1 chrl 7 43982298 43982876 0.93317 -0.0806 16.1446 HOXB3 23932 inside exon 0 overlap 0.02512 chr9 103538706 103539560 0.13349 1.04169 16.1323 GRIN3A 1122 overlaps exon 110 disjoint 0.02514 downstream
chrl 9 60838061 60839128 0.07448 0.56366 16.1214 ZNF580 5075 upstream 4200 disjoint 0.02517 chr20 21320460 21321039 0.97801 -0.0483 16.1132 XRN2 88519 downstream 0 overlap 0.02518 chr5 50295795 50296517 1.27811 0.29459 16.1102 PARP8 297226 downstream 4325 disjoint 0.02518 chr2 71358949 71359598 1.18824 0.2614 16.1043 ZNF638 52798 upstream -1208 disjoint 0.0252 chr4 81104306 81104941 1.51951 0.50483 16.1038 ANTXR2 108335 inside intron 0 overlap 0.0252 chr6 41483828 41484646 1.07438 0.34236 16.0982 NCR2 72324 downstream 0 overlap 0.02521 chrl 212219253 212219828 1.51148 0.52994 16.0924 PROX1 8654 upstream 9 disjoint 0.02522 chrl 53693507 53694549 0,49163 1.29902 16.0919 DMRTB1 3110 upstream 3230 disjoint 0.02522 chrl7 43977471 43978326 0.4975 -0.2144 16.0873 HOXB2 80 promoter -1099 disjoint 0.02523 chr2 176685943 176686662 1.17905 0.3509 16.0849 HOXD10 3075 upstream -157 disjoint 0.02524 chr2 222996496 222997108 1.07066 0.19322 16.0801 SGPP2 457 promoter 58 disjoint 0.02524 chr2 160361641 160362537 0.07931 0.68216 16.0781 CD302 461 inside intron 0 overlap 0.02525 chr7 157917658 157918167 0.61398 1.76944 16.0778 PTPRN2 155011 inside intron -4188 disjoint 0.02525 chrl 62432789 62433259 1.27977 0.16541 16.0761 L1TD1 0 overlaps 5' 0 overlap 0.02525 chr9 133238224 133238865 0.33443 1.21431 16.0745 PPAPDC3 83280 downstream 0 overlap 0.02526 chr5 140060142 140061040 0.29727 1.14339 16.0661 ZMAT2 0 overlaps 5' -8630 disjoint 0.02528 chr7 72795258 72796024 1.70951 0.55511 16.0657 ABHD11 4139 upstream -3606 disjoint 0.02528 chr3 157753847 157754613 0.32626 1.14089 16.0647 SSR3 1015 Covers exon(s) 714 disjoint 0.02528 chrlO 1 19794759 119795631 0.06684 0.73873 16.0613 RAB11FIP2 472 overlaps exon 184 disjoint 0.02529 downstream
chrX 107863234 107864052 0.32095 1.134 16.0496 IRS4 2242 inside exon -356 disjoint 0.02532 chr4 174657366 174657881 1.67117 0.50849 16.046 HAND2 30071 downstream 41 disjoint 0.02532 chrl7 37327053 37327739 0.31743 1.28129 16.0415 ACLY 1058 inside intron 78 disjoint 0.02533 chr7 1296319 1297265 0.59018 1.38592 16.0384 ZFAND2A 129996 upstream -120 disjoint 0.02533 chrlO 81828970 81829965 0.09938 0.87903 16.0352 C10orf57 565 inside intron 0 overlap 0.02534 chr8 61998980 61999729 1.27531 0.68745 16.0338 CHD7 245088 downstream -555 disjoint 0.02534 chr6 10517489 10518172 0.87903 0.09431 16.0258 TFAP2A 2420 overlaps exon 0 overlap 0.02536 downstream
chrl6 2743904 2744922 0.20702 1.21823 16.0247 SRRM2 1250 inside intron -494 disjoint 0.02536 chrlO 15800429 15800968 0.5422 1.612 16.0179 ITGA8 807 covers exon(s) 461 disjoint 0.02537 chr5 88025769 88027101 0.92995 0.40167 16.0164 MEF2C 187678 downstream -4203 disjoint 0.02537 chrl7 44062279 44063061 0.56436 1.25346 16.0068 H0XB9 3446 upstream 2750 disjoint 0.02539 chrl9 626554 627215 0.57035 1.59744 15.9974 FSTL3 173 promoter 0 cover 0.02541 chrl3 52315555 52316235 0.13947 0.93922 15.9927 PCDH8 4539 overlaps 3' 1663 disjoint 0.02542 chrl4 102314529 102315164 0.48167 1.57032 15.99 TRAF3 961 inside intron 128426 disjoint 0.02543 chr6 106546199 106546948 0.85862 0.09188 15.9822 PRDM1 93939 upstream 1731 disjoint 0.02544 chrl2 112144206 112145716 0.45841 1.41152 15.9661 TPCN1 555 inside intron -166 disjoint 0.02548 chrl7 32924879 32925816 -0.1241 1.04262 15.9618 DUSP14 760 inside intron -283 disjoint 0.02549 chrl7 44047783 44048609 1.02136 0.21758 15.9585 H0XB8 484 promoter -687 disjoint 0.02549 chr22 41090539 41091263 -0.0331 0.80655 15.9525 NFAMl 67076 downstream 3070 disjoint 0.0255 chrl4 87863066 87863734 0.3868 1.25426 15.9486 KCNK10 63 promoter 0 overlap 0.02551 chrl2 52432229 52433099 1.42633 0.67204 15.9418 CALCOCOl 24744 upstream -492 disjoint 0.02553 chr6 101022005 101022721 1.059 0.33272 15.94 SMI 3734 upstream 0 cover 0.02553 chrl 201586761 201587330 0.31462 1.54823 15.933 FMOD 0 overlaps 5' -23209 disjoint 0.02555 chr4 174490521 174491222 0.21114 1.05262 15.9279 HMGB2 944 covers exon(s) 36 disjoint 0.02556 chrl 9 63757466 63758287 0.0641 0.83601 15.9148 CH P2A 0 overlaps 5' 0 overlap 0.02559 chr2 30102737 30103594 0.71246 1.4381 15.9078 ALK 104802 upstream -104609 disjoint 0.0256 chr2 46374183 46375070 0.14134 0.8222 15.9004 EPAS1 2996 upstream 2223 disjoint 0.02561 chr7 27129116 27129655 1.79849 0.58302 15.8991 HOXA3 3508 inside intron -165 disjoint 0.02562 chr8 126515753 126516474 1.08871 1.85092 15.8937 TRIB1 4009 inside intron -2131 disjoint 0.02563 chr5 72566193 72566818 1.60018 0.57653 15.8932 TME 174 66364 downstream -461 disjoint 0.02563 chrl 8 46337626 46338283 0.47754 1.61283 15.8917 MAPK4 2198 promoter 1553 disjoint 0.02563 chrl 8 32663397 32664218 0.14324 0.80279 15.882 KIAA1328 320 inside intron -110 disjoint 0.02565 chr5 102117146 102117934 1.55563 0.69028 15.8759 PA 111491 upstream 404 disjoint 0.02566 chr7 100673791 100674330 1.00366 2.04463 15.8721 FIS1 755 covers exon(s) 459 disjoint 0.02567 chr4 7096902 7097621 0.87185 1.80753 15.8657 CCDC96 1274 promoter -269 disjoint 0.02568 chrl 8 73988809 73989606 1.1305 1.78683 15.8629 SALL3 851656 upstream -1020 disjoint 0.02569 chrl l 11 460915 1 18461730 -0.0862 0.72978 15.8604 HMBS 119 overlaps exon 0 overlap 0.02569 downstream
chrl 2 70520135 70521095 -0.0674 0.51194 15.8593 TBC1D1S 330 inside intron -233 disjoint 0.0257 chrl 20569337 20570697 0.20441 1.17627 15.8511 FLJ32784 79321 downstream -3216 disjoint 0.02572 chr2 54538925 54539476 0.37357 1.49153 15.8365 SPTBN1 1968 inside intron -1047 disjoint 0.02575 chrlO 723973 724625 1.10753 2,01151 15.8261 DIP2C 980 inside intron 82 disjoint 0.02577 chr3 148605238 148606098 1.23801 0.34567 15.8229 ZIC4 998 inside intron 3577 disjoint 0.02578 chrl4 53482427 53483002 1.29335 0.36376 15.8191 BMP4 8017 downstream 52 disjoint 0.02579 chrl 154659622 154660758 0.16447 0.58797 15.8168 Clorf61 5049 inside intron -1417 disjoint 0.02579 chr5 16986168 16987251 0.30977 1.18955 15.8162 MYO10 1887 inside intron 1304 disjoint 0.02579 chr8 20203762 20204841 1.31996 0.72589 15.8144 LZTS1 46680 upstream 250 disjoint 0.0258 chr7 49781357 49782840 0.76583 1.57118 15.8126 VWC2 962 promoter 714 disjoint 0.0258 chr2 175058732 175059222 0.31625 1.41581 15.7914 GPR155 834 inside intron 388 disjoint 0.02584 chrl2 116984579 116985795 0.89987 -0.0166 15.7854 WSB2 1246 promoter -723 disjoint 0.02585 chrl 149370394 149371160 1.13782 0.43128 15.771 SE A6C 14567 overlaps 3' 0 inside 0.02588 chrl 3 98535076 98535933 1.54379 0.85425 15.7661 D0CK9 727 inside intron 399 disjoint 0.0259 chr7 4222963 4223829 1.34759 2.66118 15.7631 SDK1 915358 inside intron 45776 disjoint 0.0259 chr6 42126489 42127322 0.59756 1.43406 15.7595 TBN 261 covers exon(s) 0 overlap 0.02591 chrl 11463220 11464178 0.59197 1.34471 15.7568 FBX02 173147 downstream -291 disjoint 0.02591 chrl 6 65760508 65761425 0.64452 0.01786 15.7533 HSF4 5651 overlaps 3' 284 disjoint 0.02592 chrl 2 48963826 48964440 0.53309 1.5954 15.7523 LIMA1 288 promoter -116173 disjoint 0.02592 chr5 10407790 10409230 0.24327 0.94094 15.7519 963 inside intron -278 disjoint 0.02592 chrl 9 7175267 7175839 0.66544 1.6553 15.751 INSR 69171 inside intron -25706 disjoint 0.02593 chrl 5 91414958 91415941 0.99499 0.37949 15.7508 RGMA 17495 inside intron 685 disjoint 0.02593 chr7 50437087 50437835 0.41972 1.65609 15.7495 KZFl 122164 inside exon -1193 disjoint 0.02593 chrl 26103045 26104276 0.00197 0.79653 15.7438 STMN1 954 covers exon(s) 261 disjoint 0.02594 chrl 143751580 143752368 1.22615 0.4684 15.7437 PDE4DIP 35011 inside intron -43 disjoint 0.02594 chr7 56139709 56141762 0.36305 1.34094 15.7397 CHCHD2 0 overlaps 5' 0 overlap 0.02594 chr5 148908686 148909783 0.00695 0.59533 15.7329 CSNK1A1 1416 inside intron 659 disjoint 0.02596 chrl l 15054838 15055539 0.70923 1.5262 15.7326 CALCB 3117 overlaps exon -2390 disjoint 0.02596 upstream
chrlO 133729373 133730086 1.05163 1.88505 15.7235 C10orf39 75335 upstream -128 disjoint 0.02598 chr5 74198292 74198969 0.88699 0.08069 15.7228 TINP1 99434 downstream 0 overlap 0.02598 chr7 155614046 155614516 1.17227 2.36241 15.7159 SHH 316319 upstream -5572 disjoint 0.02599 chr21 44581843 44582593 0.32699 1.00042 15.7093 C21or£2 980 covers exon(s) 810 disjoint 0.026 chr4 13153530 13154108 1.68149 0.6539 15.7026 BAPX1 1027 inside intron 0 inside 0.02602 chr5 54555011 54555872 1.09187 0.35859 15.7002 UNG2 9392 downstream 0 overlap 0.02602 chrS 76972113 76972967 0.95352 0.3064 15.6981 OTP 1836 promoter 0 overlap 0.02603 chr3 73916801 73917271 0.71351 1.87786 15.6957 PDZRN3 160040 upstream -159739 disjoint 0.02603 chrl l 118373114 118373842 0.06085 1.4531 15.6945 CCDC84 219 promoter 9 disjoint 0.02604 chr8 104222902 104223524 1.0392 0.14951 15.6896 BAALC 806 inside intron -336 disjoint 0.02604 chr8 73613899 73614570 0.68454 1.57185 15.6808 KCNB2 1720 inside intron -1620 disjoint 0.02606 chrl 4 105159824 105166300 0.80107 1.34225 15.6738 TMEM121 95827 downstream -21577 disjoint 0.02608 chrl 7 70688553 70689540 0.00834 0.70826 15.6628 SUM02 1152 covers exon(s) 117 disjoint 0.02609 chrl3 112142200 112143003 0.92699 1.70985 15.6547 C13orf28 63531 downstream 11335 disjoint 0.02611 chrl 114499439 114500463 1.07691 1.76723 15.6521 SYT6 1445 promoter -731 disjoint 0.0261 1 chrl 8 59138953 59139492 1.7647 0.6793 15.6463 BCL2 1361 promoter 0 overlap 0.02612 chr8 42867637 42868344 1.10557 2.08021 15.644 RNF170 2594 inside intron 2025 disjoint 0.02613 chrlO 31650264 31650945 -0.0137 0.82267 15.6396 TCF8 2117 inside intron -164 disjoint 0.02614 chrl 163592931 163593654 1.30089 0.30506 15.6364 LMX1A 1291 promoter 0 overlap 0.02614 chr2 222146931 222147863 0.21671 0.84661 15.6115 EPHA4 1678 promoter 0 overlap 0.02619 chr6 138468321 138469115 1.18901 0.58558 15.6007 PERP 1164 inside intron 766 disjoint 0.02621 chrll 2731084 2732064 0.37873 1.07764 15.5997 CNQ1 291825 inside intron 36927 disjoint 0.02622 chr8 23594555 23595340 1.22592 0.51161 15.596 NKX3-1 1054 overlaps exon 412 disjoint 0.02622 upstream
chr2 176723900 176724580 1.17517 0.3365 15.585 HOXD4 0 overlaps 5' 82 disjoint 0.02624 chr9 138810115 138812923 0.52237 1.23234 15.5828 KIAA1984 0 overlaps 5' 881 disjoint 0.02625 chr3 197107717 197108427 0.28981 1.13194 15.582 TN 2 11849 inside intron -290 disjoint 0.02625 chrX 136479176 136479820 0.64895 -0.2463 15.58 ZIC3 3165 overlaps exon 0 overlap 0.02625 upstream
chrlO 102984005 102986302 0.48978 0.06423 15.5694 LBX1 5299 upstream 0 overlap 0.02628 chrlO 119483799 119484377 1.06679 0.01316 15.5589 EMX2 191854 downstream 106 disjoint 0.0263 chr5 272477 273379 0.76041 1.48431 15.5586 SDHA 1031 inside intron -349 disjoint 0.0263 chrl6 67037420 67038045 0.99793 1.92852 15.5508 SMPD3 1859 inside intron 320 disjoint 0.02632 chrl7 260730 261485 0.15581 1.1527 15.5492 LOC400566 297 overlaps exon -108 disjoint 0.02632 downstream
chrl7 25468769 25469534 -0.1972 0.73541 15.5395 CCDC55 810 covers exon(s) -632 disjoint 0.02633 chrl l 2233400 2234180 0.8216 1.63515 15.5367 ASCL2 14577 downstream 12500 disjoint 0.02634 chr9 132701631 132702763 0.14232 0.83722 15.5352 ABL1 980 inside intron -525 disjoint 0.02635 chr4 171205682 171206224 0.15767 1.21789 15.5327 AADAT 41533 downstream -20199 disjoint 0.02635 chrI9 47121534 47122274 0.08171 0.84473 15.5182 ARHGEF1 41249 downstream 1482 disjoint 0.02639 chrl4 52326302 52327205 1.20365 0.30153 15.5168 GNPNAT1 927 inside intron 209 disjoint 0.02639 chrlO 38187070 38187744 0.31847 1.37687 15.5138 ZNF248 579 promoter 0 overlap 0.0264 chrlO 1437849 1438244 1.61183 3.02187 15.5105 ADARB2 331425 inside intron -7835 disjoint 0.02641 chrl l 112257294 112258088 0.58572 1.33657 15.5042 NCAM1 79116 upstream 79646 disjoint 0.02642 chrl l 64786554 64787264 0.11292 0.98828 15.5037 POLA2 547 inside intron -52 disjoint 0.02642 chr7 1409956 1410722 0.45241 1.22819 15.5033 MICAL-L2 54889 downstream 0 cover 0.02642 chr2 31660479 31661114 0.69811 1.56988 15.5016 SRD5A2 936 promoter -193 disjoint 0.02643 chr2 81279773 81280420 0.97524 1.81965 15.5001 CTN A2 1686140 downstream -3730 disjoint 0.02643 chrl5 87708267 87709190 0.05364 0.66243 15.4999 POLG 29238 upstream -1213 disjoint 0.02643 chrl 1325244 1325855 0.6302 1.59438 15.494 CCNL2 692 promoter 0 overlap 0.02645 chrl6 66558661 66559131 0.14286 1.4012 15.4926 SLC12A4 894 inside intron 286 disjoint 0.02645 chr4 83185609 83186253 0.25629 1.10416 15.4924 HNRPD 327919 downstream -689 disjoint 0.02645 chrY 14323724 14324332 1.32721 0.34492 15.4864 T SB4Y 508 promoter 550 disjoint 0.02647 chr8 59486870 59487586 1.10546 0.27552 15.4837 LOC137886 494 inside intron -136 disjoint 0.02647 chrl5 49174889 49176059 1.34992 0.47059 15.4767 TNFAIP8L3 8705 inside intron 0 overlap 0.02649 chrS 4892601 4893156 0.36097 1.36642 15.4754 CSMD1 52866 upstream -52558 disjoint 0.02649 chr3 53355225 53356115 -0.1088 0.53389 15.4747 DCP1A 537 inside intron 270 disjoint 0.02649 chr8 1486921 1487915 1.12993 2.25627 15.4717 DLGAP2 49946 inside intron 899 disjoint 0.0265 chrl 35815799 35816790 1.38259 0.32547 15.4614 TFAP2E 4242 inside intron 0 overlap 0.02652 chr8 145896851 145897426 1.23268 2.27676 15.4613 ZNF34 79042 downstream 0 overlap 0.02652 chr6 84992701 84993453 0.37595 1,23432 15.4492 IAA1009 579 inside intron 382 disjoint 0.02655 chr2 172682353 172683223 1.76476 0.92015 15.4315 DLX2 6630 upstream -865 disjoint 0.02659 chr3 128832791 128833399 0.92423 1.92431 15.4292 PODXL2 2042 inside intron -1245 disjoint 0.02659 chrl 151618150 151618825 0.76593 1.63656 15.4271 S100A12 3452 upstream 156223 disjoint 0.0266 chr22 19106483 19107080 1.05505 2.388 15.4188 SCARF2 15065 downstream 2306 disjoint 0.02662 chr4 54795356 54796081 -0.0526 0.85712 15.4182 PDGFRA 5153 inside intron -268 disjoint 0.02662 chr7 130002701 130003357 0.71913 1.68624 15.417 COPG2 780 covers exon(s) 253 disjoint 0.02662 chrlO 112392344 112393466 0.72726 0.1414 15.4144 SMC3 74906 downstream 0 overlap 0.02663 chr3 157052936 157054036 -0.0365 0.46347 15.4133 SLC33A1 824 overlaps exon 1013 disjoint 0.02663 downstream
chr5 3586182 3587073 0.42079 1.77282 15.4069 mxi 62094 upstream 1557 disjoint 0.02664 chr5 72781504 72782325 0.73358 0.07979 15.406 FOXD1 1397 promoter 420 disjoint 0.02664 chrl 9 323482 324300 0.47949 1.15514 15.4001 THEG 2708 covers exon(s) 2530 disjoint 0.02666 chr8 103889499 103890537 0.33606 1.04961 15.3908 FLJ45248 1274 overlaps two exons -828 disjoint 0.02668 chrl9 55631804 55632172 0.78706 2.21173 15.3839 YBPC2 3801 inside intron -4315 disjoint 0.02669 chrl9 6696187 6696735 0.99877 2.15359 15.3826 TRIPIO 5481 inside intron 288 disjoint 0.0267 chr5 74386170 74386944 1.97676 0.92732 15.3779 GCNT4 23691 upstream -175 disjoint 0.02671 chr3 49288985 49289455 0.18855 1.33875 15.3779 C3orf62 0 inside exon 0 overlap 0.02671 chr3 135609994 135610556 1.7487 0.67496 15.3755 AM0TL2 33899 upstream -1436 disjoint 0.02671 chrl l 124122358 124123111 1.04323 -0.0154 15.3648 VSIG2 4207 overlaps 3' -142 disjoint 0.02674 chr6 31478010 31479068 0.26794 0.93529 15.3636 HLA-B 45097 upstream 0 overlap 0.02674 chr5 134909298 134909942 1.29946 0.44101 15.3576 NEUR0G1 9761 upstream -1580 disjoint 0.02676 chrS 140551701 140553038 0.15559 0.72525 15.3526 PCDHB10 0 overlaps 5' 569 disjoint 0.02677 chr22 44832107 44832952 0.31519 1.02964 15.3423 C22orf26 3420 upstream 2807 disjoint 0.02679 chr9 128923507 128924325 0.23331 0.96152 15.3372 ANGPTL2 539 inside intron 102060 disjoint 0.0268 chrl 226257863 226258330 0.42682 1.5571 15.3236 WNT3A 3044 upstream 2389 disjoint 0.02683 chr2 30225919 30226318 1.69492 0.3331 15.309 YPEL5 2588 inside intron -1494 disjoint 0.02687 chr6 137153442 137154342 0.27777 0.98213 15.3035 MAP3K5 1006 inside intron 27 disjoint 0.02688 chr3 48318639 48319271 2.08476 1.10688 15.2924 NME6 788 promoter -377 disjoint 0.02691 chrl3 49467747 49468284 1.77428 0.80156 15.2919 TR1M13 859 promoter 92 disjoint 0.02691 chrl2 55905583 55906370 1.16032 0.4279 15.2911 NXPH4 8739 inside exon 0 overlap 0.02691 chr8 15137662 15138483 1.31826 0.5035 15.2906 SGCZ 1679 inside intron 125 disjoint 0.02691 chrX 48930018 48930419 1.2056 -0.1773 15.2906 LM06 299 promoter -15 disjoint 0.02691 chr4 146758835 146759622 0.21354 0.91685 15.2905 MMAA 20054 upstream 0 overlap 0.02691 chr4 190898206 190898952 0.87047 2.02887 15.2901 FRG1 200015 upstream 69688 disjoint 0.02691 chrl l 22644161 22644841 0.01611 0.71635 15.2863 GAS2 1388 promoter 20 disjoint 0.02693 chrl l 20583088 20583802 0.25006 1.03898 15.2813 SLC6A5 5567 inside intron -3113 disjoint 0.02694 chrl 27190479 27191261 0.5858 1.45827 15.2758 LOC388610 1523 promoter 1453 disjoint 0.02695 chrl l 14337480 14338084 0.49409 1.58624 15.2691 RRAS2 192 promoter -167 disjoint 0.02696 chr6 19262997 19263500 0.5834 1.63792 15.2677 ID4 682095 upstream 536389 disjoint 0.02696 chrl 33585813 33587233 0.14676 0.72567 15.2617 PHC2 852 inside intron 137 disjoint 0.02697 chr8 97343844 97344674 -0.0844 0.62614 15.2556 PTDSS1 502 inside intron 0 overlap 0.02698 chr2 176676298 176676864 1.19493 0.10226 15.2501 HOXD12 3523 downstream 599 disjoint 0.02699 chrl 3 113847249 113847724 0.33186 1.48917 15.2415 RASA3 68472 inside intron 6444 disjoint 0.02702 chr2 63137696 63138644 0.76846 0.02332 15.2352 0TX1 6228 overlaps 3' -45 disjoint 0.02703 chrlO 102972917 102973669 1.04858 0.40719 15.2289 LBX1 5037 downstream 0 overlap 0.02704 chr3 114899050 114899760 0.43344 1.33532 15.2206 KIAA2018 868 promoter -627 disjoint 0.02705 chr8 21922845 21923702 2.01194 1.12602 15.2178 XP07 89718 downstream 0 overlap 0.02706 chr22 44851821 44852418 0.46084 1.38448 15.2154 FLJ27365 8128 upstream -4629 disjoint 0.02706 chrl 5 41573127 41573941 0.20707 1.05128 15.2111 TP53BP1 16086 inside intron -345 disjoint 0.02707 chrX 39561125 39561768 1.0984 0.07683 15.2075 BCOR 279831 downstream 3316 disjoint 0.02708 chrll 132734187 132734820 0.663 1.93001 15.2042 OPCML 172792 inside intron 1174 disjoint 0.02708 chr8 41677777 41678529 0.77165 1.49127 15.1997 ANK1 95767 covers exon(s) 0 overlap 0.0271 chr8 143520005 143520703 0.43648 1.37926 15.1962 BAI1 21675 upstream 6944 disjoint 0.0271 chr2 16071365 16071974 1.10592 1.99944 15.1924 MYC 73232 downstream 0 cover 0.02711 chrlO 127576346 127582137 0.33558 1.11967 15.1861 FANK1 1246 inside intron -818 disjoint 0.02713 chr5 122449361 122449936 1.16058 0.1885 15.1822 PPIC 49038 upstream 2300 disjoint 0.02714 chrl 35164579 35165834 0.83139 1.40041 15.1746 ZMYM6 104321 downstream 1500 disjoint 0.02715 chr2 44881611 44882401 1.08309 0.32633 15.1524 C2orf34 439005 downstream 58 disjoint 0.0272 chrl 1 12328329 112329138 1.48482 2.16214 15.1522 KCND3 4161 inside intron -1421 disjoint 0.0272 chr21 45831566 45834165 0.25255 1.07988 15.1504 SLC19A1 44788 upstream 259 disjoint 0.0272 chr21 25932552 25933367 -0.1119 0.62399 15.1501 JANG 92 promoter 128 disjoint 0.0272 chrl3 975947S0 97595538 0.01719 0.91905 15.1483 FARP1 1316 inside intron -508 disjoint 0.0272 chr2 45081099 45081920 1.0882 0.4251 15.1396 SK2 8105 downstream 0 overlap 0.02722 chrl l 61080219 61081410 0.87123 1.61375 15.1369 SYT7 23463 overlaps exon -358 disjoint 0.02722 upstream
chrl9 44584613 44585047 0.48835 1.78111 15.1313 D L 10811 downstream 0 overlap 0.02723 chrl l 122637261 122637974 0.50981 1.1627 15.1306 ASA 66045 upstream 39690 disjoint 0.02723 chr] 5 46722606 46723742 -0.2372 0.27437 15.1291 FBN1 1467 inside intron 360 disjoint 0.02724 chrl2 55167104 55167856 1.58417 0.49943 15.1173 GLS2 591 inside intron 0 overlap 0.02726 chr6 80769881 80770735 0.22946 0.83552 15.1065 TTK 342 promoter 133 disjoint 0.02728 chr8 13032835 13033449 -0.0721 0.79584 15.1064 DLC1 1730 inside intron 302 disjoint 0.02728 chr7 69699330 69699728 1.61336 0.17148 15.1012 AUTS2 997076 inside intron 0 overlap 0.02729 chr9 139171521 139172093 0.5235 1.4741 15.0987 GRIN1 18092 inside intron 0 overlap 0.02729 chr4 56948879 56949726 -0.0659 0.68606 15.0954 AASDH 485 promoter -377 disjoint 0.0273 chr!8 65221152 65221622 2.19837 1.00601 15.0928 DO 6 1882 inside intron -1 disjoint 0.02731 chr8 25955347 25955854 1.11128 0.02147 15.0886 EBF2 2454 covers exon(s) 0 overlap 0.02731 chrlO 131653893 131654612 0.83669 0.08574 15.0858 EBF3 1813 promoter 0 inside 0.02732 chr3 72978988 72979952 -0.0012 0.65466 15.0849 SHQ1 335 inside intron 0 overlap 0.02732 chr6 5940422 5941253 1.25161 0.63604 15.0834 NRN1 11378 downstream 0 overlap 0.02732 chr4 122904262 122904903 2.57904 1.65171 15.0801 TMEM155 886 covers exon(s) 407 disjoint 0.02733 chrl4 44141209 44141919 0.43938 1.28939 15.0738 C14orfl55 95002 upstream 284503 disjoint 0.02734 chr2 161977993 161979013 1.19104 0.45992 15.0716 PSMD14 104808 downstream 121 disjoint 0.02735 chrlO 116152400 116153218 0.94622 0.11313 15.069 K.IAA1914 1286 inside intron 163 disjoint 0.02735 chr3 87221047 87221691 0.38495 1.30742 15.0642 VGLL3 98101 upstream 0 overlap 0.02736 chrl4 50067445 50068098 -0.1121 0.76803 15.0638 MAP4 5 1027 inside intron 229 disjoint 0.02736 chrl l 124127304 124128078 0.98984 0.23231 15.0635 VSIG2 0 overlaps 5' -5088 disjoint 0.02736 chrl2 55685014 55685869 0.64843 1.32498 15.0631 ZBTB39 627 inside intron 266 disjoint 0.02737 chr20 36708568 36709077 0.09019 1.36954 15.0587 SMAF1 65317 downstream -20 disjoint 0.02737 chrl7 37561192 37561869 1.60689 0.81695 15.0569 KCNH4 24952 downstream -403 disjoint 0.02738 chrl7 69937619 69938474 1.03946 0.24177 15.054 GPRC5C 787 promoter 0 overlap 0.02739 chrl2 103222055 103222492 0.67489 1.98578 15.0535 EED3 377 inside exon 0 overlap 0.02739 chr21 42058814 42059460 1.45931 0.19321 15.0482 RIPK4 857 inside intron 0 overlap 0.0274 chrl6 87301006 87301650 0.67333 1.51719 15.047 LOC348180 615 covers exon(s) -310 disjoint 0.02741 chrl4 37123952 37124678 0.86669 -0.0521 15.0414 FOXA1 9561 downstream -35 disjoint 0.02742 chrl 19682705 19683385 0.51831 1.34957 15.0335 CAPZB 1193 inside intron 905 disjoint 0.02743 chr5 77176600 77177336 1.15505 0.32576 15.0304 TBCA 68660 upstream 0 overlap 0.02744 chr8 77753622 77754089 1.2959 0.09087 15.0304 ZFHX4 24745 upstream -694 disjoint 0.02744 chrl6 52872839 52873899 1.02558 0.33892 15.0286 IRX3 3979 downstream 0 overlap 0.02744 chr9 128607581 128608455 -0.0735 0.80029 15.0274 ZBTB43 400 inside intron 0 overlap 0.02744 chrl 3 112615733 112616098 0.79776 2.30145 15.0263 ATP11A 223090 downstream -14959 disjoint 0.02745 chr5 124015630 124016414 0.18642 0.87722 15.0262 ZNF608 92289 inside intron 0 overlap 0.02745 chrl6 49741273 49741917 0.7214 -0.1234 15.0257 SALL1 735 inside intron 0 inside 0.02745 chr8 134654780 134655742 0.1456 0.98679 15.0159 ST3GAL1 1437 promoter -723 disjoint 0.02746 chr4 122942025 122942740 -0.0963 0.92863 15.0095 EXOSC9 104 covers exon(s) 0 overlap 0.02748 chr2 5783637 5784279 0.90548 0.07169 15.0084 SOX11 33388 downstream -18625 disjoint 0.02748 chrl 9 57181221 57181826 0.62624 1.49654 14.9823 ZNF350 64 inside intron 21214 disjoint 0.02754 chrlO 69318121 69318888 0.10052 0.84712 14.9799 SIRT1 3689 covers exon(s) -2937 disjoint 0.02754 chrl6 815603 816020 0.75091 2.1257 14.9795 LOC388199 20160 downstream -13 disjoint 0.02755 chrl9 9469617 9470258 0.75928 1.62166 14.9748 ZNF560 20 covers exon(s) 0 overlap 0.02756 chr7 27171724 27172368 0.38059 1.25006 14.9747 H0XA9 51 promoter 0 inside 0.02756 chrl3 27964629 27965244 1.13327 0.0761 14.9695 FLT1 1987 inside intron 544 disjoint 0.02757 chr7 137997915 137998457 0.84423 1.69826 14.9604 LOC136306 1051 covers exon(s) 1045 disjoint 0.02759 chrl l 35117910 35118551 0.0955 1.02643 14.9592 CD44 918 inside intron -334 disjoint 0.02759 chr22 48211830 48212645 0.99611 1.64645 14.9577 FLJ44385 115687 upstream -13358 disjoint 0.02759 chrl2 14819211 14819924 -0.2623 0.45004 14.9544 H2AFJ 650 overlaps exon 0 overlap 0.0276 upstream
chr6 67714981 67715526 0.68763 1.7221 14.9531 EGFL11 1368564 upstream -853429 disjoint 0.02761 chr9 138413143 138413683 0.75992 1.84653 14.9507 SNAPC4 434 promoter 224 disjoint 0.02762 chr4 104337583 104338191 0.23928 1.16334 14.9503 CENPE 823 inside intron 577 disjoint 0.02762 chrl 47682470 47683045 0.99741 0.06444 14.9488 F0XD2 8195 downstream 0 inside 0.02762 chr7 157871895 157872587 1.25244 1.96991 14.9464 PTPRN2 200591 inside intron 18719 disjoint 0.02763 chr2 113753158 113753700 1.81956 0.70989 14.9431 PAX8 191 promoter -647 disjoint 0.02763 chrl 9 60319154 60319939 0.37314 1.07696 14.9392 PPP1R12C 799 inside intron 361 disjoint 0.02764 chrlO 103034262 103034909 0.89459 0.11748 14.9372 LBX1 55556 upstream 0 overlap 0.02765 chrlO 103039940 103040725 2.13074 1.34066 14.935 LBX1 61234 upstream 393 disjoint 0.02765 chr2 28826837 28827718 0.46995 1.34783 14.9238 PPP1CB 399 promoter 0 overlap 0.02767 chrl l 2628780 2629706 0.67155 1.22845 14.9212 KCNQ1 189521 inside intron 47280 disjoint 0.02768 chr2 70979465 70980354 0.96165 0.18925 14.9184 VAX2 873 promoter 0 overlap 0.02769 chr7 129204531 129205391 1.13886 0.51468 14.9136 NRF1 147377 downstream 131 disjoint 0.0277 chr8 145094527 145095312 0.64483 1.30916 14.9117 PLEC1 1719 inside intron 1125 disjoint 0.0277 chr8 97224948 97225884 1.18418 0.44345 14.9094 GDF6 16311 inside exon 55 disjoint 0.02771 chr8 4840313 4840927 0.45365 1.2884 14.9021 CSMD1 578 promoter -270 disjoint 0.02773 chrl 8 21182225 21182803 1.04587 0.08458 14.9018 ZNF521 3310 inside intron 1213 disjoint 0.02773 chr21 37365778 37366675 0.45034 1.96067 14.9005 PIGP 297 overlaps exon 55 disjoint 0.02773 downstream
chrl2 52655851 52656411 1.04174 0.10251 14.8987 HOXC11 2675 inside exon -481 disjoint 0.02773 chrl2 64408533 64409240 0.69746 -0.0957 14.8985 HMGA2 95266 upstream 0 overlap 0.02773 chrl 5 61676146 61676576 0.95407 2.29942 14.8978 FBXL22 72 promoter 3266 disjoint 0.02773 chr5 140515504 140516220 0.85473 1.54515 14.8895 PCDHB6 5482 downstream 860 disjoint 0.02776 chr5 115176846 115177646 0.69011 1.50302 14.8794 CDOl 2657 overlaps exon 1601 disjoint 0.02778 upstream
chr6 26702542 26704015 0.47877 -0.0359 14.8771 ABT1 1143 promoter 10 disjoint 0.02778 chr7 92076072 92076398 1.52496 -0.1266 14.8638 CD 6 224749 inside exon -18263 disjoint 0.02782 chr6 168458758 168459333 1.13393 2.03218 14.861 DACT2 3917 inside intron 3197 disjoint 0.02782 chrlO 53745022 53745597 0.00583 0.9237 14.8597 DK 1 976 inside intron -189 disjoint 0.02783 chr5 15554417 15555494 -0.131 0.47651 14.8561 FBXL7 1113 inside intron -494 disjoint 0.02783 chr4 79692391 79693008 1.15588 0.22636 14.8517 ANXA3 626 inside intron -190 disjoint 0.02785 chr3 129684801 129685448 1.1407 0.25178 14.8511 GATA2 9269 overlaps exon 2734 disjoint 0.02785 downstream
chr3 6881686 6882528 0.34756 1.07099 14.8427 GRM7 3760 inside intron -2045 disjoint 0.02787 chr20 5981431 5982045 1.64903 0.62494 14.8424 C20orf75 630 overlaps exon 0 overlap 0.02787 upstream
chr7 99355191 99355658 0.06145 1.17564 14.8378 TRIM4 102 promoter 0 overlap 0.02787 chr9 116413976 116414707 0.20804 1.26166 14.8344 C9orf91 516 inside intron -79 disjoint 0.02788 chrl 4 91855146 91856054 1.33905 2.17356 14.8249 SLC24A4 2623 upstream 2612 disjoint 0.0279 chrl 89761810 89762505 0.97365 0.15916 14.824 LRRC8B 34354 upstream 0 overlap 0.0279 chr5 1718728 1720081 2.00236 2.67384 14.8214 MRPL36 132864 downstream 106 disjoint 0.02791 chrl 7 20000598 20001427 0.77859 -0.0595 14.8184 SPECC1 605 inside intron 0 overlap 0.02791 chrl2 123568993 123569872 0.19398 1.06819 14.8132 NC0R2 16229 inside intron 0 cover 0.02792 chr6 37775205 37775780 1.36052 0.43482 14.8112 MDGA1 1462 promoter -125 disjoint 0.02793
Chr7 70233160 70234014 0.13093 0.86539 14.8086 WBSCR17 1710 promoter 150 disjoint 0.02794 chrl2 45758756 45759364 0.47417 1.45091 14.8023 AMIG02 550 overlaps exon 80 disjoint 0.02796 upstream
chrl2 33480308 33480958 0.39012 1.01483 14.7925 SYT10 3062 inside intron 2072 disjoint 0.02798 chrl2 120945629 120946201 0.0954 1.08481 14.7919 BCL7A 1386 inside intron 54375 disjoint 0.02798 chrl l 17520680 17521327 0.7592 1.54436 14.786 USH1C 1211 inside intron 1015 disjoint 0.02799 chr9 27517613 27518254 1.12714 0.41538 14.785 M0BKL2B 1595 inside intron 103 disjoint 0.02799 chrl2 125773867 125775943 0.67107 1.60608 14.7834 TMEM132B 1396753 downstream 788 disjoint 0.02799 chrX 82652649 82653356 0.04008 1.09268 14.7784 POU3F4 2709 downstream -217 disjoint 0.028 chrl2 52732715 52733362 0.9963 0.0965 14.7733 H0XC4 35807 covers exon(s) -335 disjoint 0.02802 chrl3 45683296 45683802 0.1735 1.23053 14.771 LOC220416 281 promoter -158276 disjoint 0.02802 chr5 121673027 121673778 0.0923 0.80196 14.7636 SNCAIP 1940 promoter 1571 disjoint 0.02804 chr3 46039842 46041044 0.94552 1.76904 14.7627 XCR1 2938 inside intron -27365 disjoint 0.02804 chr5 175016513 175016914 0.72486 2.07805 14.7588 HRH2 25403 upstream 696 disjoint 0.02805 chr22 27167396 27168083 0.20774 1.16334 14.7534 CHE 2 299738 downstream 237017 disjoint 0.02806 chrl3 29938842 29939450 0.20069 1.12804 14.7524 HMGB1 830 promoter -20705 disjoint 0.02806 chrl2 83831066 83831606 1.10746 0.15345 14.7483 SLC6A15 362 promoter -106 disjoint 0.02808 chr8 1774350 1776320 0.97045 1.77562 14.7483 ARHGEF10 14795 inside intron -7122 disjoint 0.02808 chrl9 11333279 11333864 1.17865 0.39112 14.74 LPPR2 6173 inside intron 0 overlap 0.02809 chrl2 93063350 93063949 0.49366 1.47632 14.7398 PLXNC1 2680 upstream 1909 disjoint 0.0281 chr7 37457213 37458114 -0.0071 0.65514 14.7395 ELM01 2178 promoter -2016 disjoint 0.0281 chrl l 2797136 2798071 -0.3035 0.37292 14.7387 KCNQ1 357877 inside intron -11676 disjoint 0.0281 chr3 12982883 12983533 0.81866 1.58539 14.7179 IQSEC1 426 inside intron 115 disjoint 0.02815 chrl8 21922461 21923560 -0.2872 0.57815 14.7149 SS18 1048 inside intron 409 disjoint 0.02816 chrl7 4940626 4941133 0.3968 1.52758 14.7138 ZFP3 18149 downstream 0 overlap 0.02816 chr20 57229636 57230389 0.74252 1.32368 14.7134 EDN3 78504 upstream 229 disjoint 0.02816 chr7 157064591 157065025 0.66085 1.85994 14.7048 PTPRN2 1008153 inside intron -2436 disjoint 0.02818 chrl 27564181 27564826 0.67915 1.70187 14.7026 MAP3K6 1097 inside intron 173 disjoint 0.02818 chr9 72405541 72406455 0.27625 1.10396 14.6959 TRPM3 267338 inside intron -180273 disjoint 0.0282 chrlO 118913577 118914071 1.25856 0.01406 14.6957 VAX1 25776 upstream -67 disjoint 0.0282 chrl l 107968060 107968776 0.97941 0.18283 14.6937 EXPH5 793 inside intron 32 disjoint 0.0282 chr8 54953591 54954518 0.79777 -0.0399 14.692 RGS20 26671 overlaps exon 0 overlap 0.02821 upstream
chr9 76304756 76305675 0.42496 -0.1508 14.6899 RORB 2685 inside intron -1009 disjoint 0.02821 chr20 9766334 9767024 0.02926 0.84804 14.6884 PAK7 497 inside intron 247 disjoint 0.02822 chr2 219732620 219733293 -0.03 0.65336 14.6874 NHEJ1 473 inside intron 0 overlap 0.02822 chrl4 75917536 75918081 0.84274 1.80301 14.6829 ESRRB 10058 inside intron -3937 disjoint 0.02823 chr20 5538249 5538928 -0.0694 0.68474 14.6773 KIAA1434 743 inside intron 562 disjoint 0.02825 chr3 129685515 129686274 1.14676 0.29821 14.6754 GATA2 8443 overlaps exon 1908 disjoint 0.02825 upstream
chr3 172658401 172659321 0.85723 0.24119 14.669 TND 1224 inside intron 1199 disjoint 0.02826 chrl l 2803338 2803877 0.29838 1.34476 14.6575 CNQ1 364079 inside intron -17878 disjoint 0.02829 chrl 9 38953567 3895421 1 0.8159 1.5948 14.6537 CHST8 86294 covers exon(s) 572 disjoint 0.0283 chrl 39342477 39343015 1.67011 0.6933 14.6522 MACF1 22773 inside intron 237 disjoint 0.0283 chr4 84269307 84269918 1.10966 1.98492 14.6511 PLAC8 14395 upstream -18974 disjoint 0.0283 chrl 5 74414641 74415462 1.4732 0.69628 14.6459 ISL2 739 promoter 0 overlap 0.02832 chrl l 70635083 70636615 0.99158 0.47502 14.639 DHCR7 200431 downstream 3206 disjoint 0.02833 chr6 45495641 45496180 1.15465 0.2247 14.6378 RUNX2 91610 inside intron 0 overlap 0.02833 chrlO 59941366 59942257 0.47223 1.36801 14.6366 TFA 126185 downstream 216 disjoint 0.02834 chrl l 2572538 2573596 -0.122 0.41317 14.6283 KCNQ1 133279 inside intron -12493 disjoint 0.02836 chrl3 111802787 111803867 0.60062 1.27924 14.6195 soxi 32874 downstream 2732 disjoint 0.02838 chr2 60629048 60629833 0.74416 0.04839 14.6134 BCL11A 4303 inside intron 267 disjoint 0.0284 chrl l 8239829 8240484 1.93067 1.06324 14.613 LMOl 1497 inside intron 194 disjoint 0.0284 chrl5 94710291 94710827 1.07514 0.1039 14.6125 NR2F2 35342 downstream 0 overlap 0.0284 chrl4 34252257 34252982 -0.0114 0.77187 14.5965 CFL2 0 overlaps 5' 154 disjoint 0.02844 chr2 10868117 10868797 0.63735 1.51443 14.5935 PDIA6 1613 inside intron 1056 disjoint 0.02845 chr20 36866660 36867292 0.6846 -0.3288 14.5846 PPP1R16B 469 promoter 328 disjoint 0.02847 chr7 145445198 145445968 0.01041 0.86477 14.573 CNTNAP2 813 inside intron -181 disjoint 0.02849 chrl l 59191281 59192386 0.00293 0.63087 14.5628 FLJ36874 8288 upstream 391 disjoint 0.02852 chrl7 44023605 44023970 1.53634 0.08195 14.5591 HOXB5 2131 overlaps 3' 463 disjoint 0.02853 chrl3 88812380 88813132 0.82136 1.72015 14.551 SLITRK5 1689510 downstream 281 disjoint 0.02855 chrlO 118356655 118357265 0.25553 1.06493 14.5493 PNLIPRPl 16176 inside intron 1304 disjoint 0.02855 chrl 110327544 110328434 0.60866 1.29682 14.5488 AHCYL1 396 promoter 337 disjoint 0.02855 chr20 21439773 21440417 1.08747 0.04443 14.5446 N X2-2 2246 inside exon 0 inside 0.02856 chr6 28673036 28674034 0.60061 -0.016 14.5342 ZNF452 9946 upstream -9933 disjoint 0.02858 chr8 122719849 122720614 0.17921 0.75703 14.5212 HAS2 2196 inside intron 232 disjoint 0.02862 chr2 15995890 15996540 1.0211 0.23733 14.5197 YCN 1593 promoter 712 disjoint 0.02862 chrl 223909324 223910007 0.57003 1.17635 14.5187 EN AH 1857 promoter -906 disjoint 0.02862 chr6 168583475 168584083 0.52076 1.35907 14.5117 SMOC2 796 promoter 204 disjoint 0.02864 chr5 55324268 55325058 0.14684 0.84541 14.5106 IL6ST 1461 inside intron 1034 disjoint 0.02864 chrl 233334638 233335289 0.78311 1.70935 14.509 TOMM20 23464 downstream -186 disjoint 0.02865 chrl 9 63653791 63654547 0.10384 0.99964 14.5023 ZNF324B 235 promoter 5 disjoint 0.02866 chrS 172689736 172690314 1.42507 0.51799 14.4951 STC2 625 promoter -32 disjoint 0.02868 chrl2 63957815 63958453 1.06287 0.23648 14.4921 MSRB3 301 promoter 205 disjoint 0.02869 chrlO 85592012 85592587 0.66098 1.55285 14.4909 GHITM 296577 upstream -277030 disjoint 0.02869 chrl2 73886407 73886910 0.76191 1.71253 14.4897 KCNC2 2867 inside intron 438 disjoint 0.0287 chrlO 26266717 26267158 -0.0928 1.05697 14.487 MY03A 3516 inside intron -2689 disjoint 0.0287 chrl5 36330318 36330880 0.94885 -0.025 14.4807 SPREDl 927 promoter 414 disjoint 0.02871 chrl6 71654154 71654483 1.42143 -0.2275 14.4737 ATBF1 14380 upstream 0 overlap 0.02873 chrl 8010643 8011113 -0.0484 1.07026 14.4698 ERRFI1 1701 promoter -1202 disjoint 0.02874 chr20 29772726 29773547 1.41077 0.80888 14.469 BCL2L1 769 overlaps exon 617 disjoint 0.02874 downstream
chrl l 2022535 2024485 -0.0999 0.30021 14.4431 IGF2 92294 downstream -31968 disjoint 0.02881 chrl2 32444502 32445250 0.55579 -0.1683 14.4379 BICDl 293051 downstream -197 disjoint 0.02882 chr2 131385135 131385575 0.49728 1.79374 14.4331 ARHGEF4 5118 upstream 4581 disjoint 0.02883 chr8 120937894 120938809 1.46666 0.57299 14.4323 DCC1 565 promoter -273 disjoint 0.02884 chrl 6 85164209 85164607 2.0044 0.69095 14.4308 FOXC2 5767 downstream 2282 disjoint 0.02884 chr8 35214687 35215491 0.06153 0.638 14.4295 UNC5D 305960 upstream -1034 disjoint 0.02884 chrl 4 76559099 76559608 0.76909 1.87475 14.4216 C14orf4 5178 downstream 2083 disjoint 0.02886 chrl 8 73809395 73809862 0.55018 1.59328 14.4206 GALR1 718675 downstream 9620 disjoint 0.02887 chrl 67922539 67923115 0.12914 1.07043 14.4147 GADD45A 355 promoter 386 disjoint 0.02888 chr9 114861193 114861934 0.86795 1.86073 14.4126 ZFP37 2377 promoter 0 overlap 0.02888 chr3 39166983 39167738 0.26262 1.0138 14.4092 AXUD1 2366 inside intron 1507 disjoint 0.02889 chrl2 26157097 26157825 0.86503 -0.0347 14.4063 BHLHB3 11287 downstream 500 disjoint 0.028? chrl 9 54613139 54613951 0.56541 1.30014 14.4049 FLJ32658 29822 downstream 3487 disjoint 0.02891 chr7 113509772 113510569 0.64416 -0.0823 14.4023 PPP1R3A 163473 upstream 1591 disjoint 0.02891 chrlO 134721239 134722567 1.17434 1.97533 14.3985 GPR123 11855 upstream 3753 disjoint 0.02892 chr6 10497193 10498056 0.65563 -0.0105 14.3978 TFAP2A 22536 downstream 0 overlap 0.02893 chr2 176762539 176763081 1.30097 0.2353 14.3847 HOXD1 987 overlaps exon 0 overlap 0.02896 upstream
chrlO 94446168 94447057 1.25391 0.5014 14.3814 HHEX 6489 downstream -292 disjoint 0.02897 chr20 49818737 49819207 1.01732 2.1733 14.3782 ATP9A 423 promoter -426 disjoint 0.02898 chrl 1 4882586 154883216 0.30175 1.21897 14.3777 BCAN 4223 overlaps exon 0 overlap 0.02898 upstream
chr8 16903999 16904728 0.72951 -0.135 14.3765 FGF20 0 overlaps 5' -176 disjoint 0.02898 chr4 128923722 128924369 0.26092 1.17907 14.3736 HSPA4L 820 inside intron -57 disjoint 0.02899 chrl 16640066 16640925 0.36274 0.89919 14.3699 NECAP2 247 inside intron 0 overlap 0.029 chr7 157927670 157928212 0.67801 1.59302 14.3674 PTPRN2 144966 inside intron 12437 disjoint 0.029 chr9 37475959 37476776 0.07864 0.84764 14.3539 P0LR1E 15 overlaps two exons 0 overlap 0.02904 chrH 36737068 36737872 0.2637 0.98663 14.3357 MIPOL1 162 inside intron 0 overlap 0.02909 chrl 9 59591246 59592116 0.39691 1.30003 14.3324 LAIRl 22714 upstream 27598 disjoint 0.0291 chrl 159437743 159438309 0.33962 1.38371 14.3304 DUFS2 2015 inside intron 124 disjoint 0.0291 chr4 186173087 186173881 0.70024 1.39488 14.3252 HELT 3195 upstream 355 disjoint 0.02912 chr2 219534065 219534783 0.04108 0.92645 14.3091 CD 5R2 1424 inside exon 0 overlap 0.02915 chrl 9 43035884 43036357 1.24997 2.22558 14.2943 SIPA1L3 53350 upstream 1291 disjoint 0.02919 chrl 2211572 2212231 0.45767 1.23754 14.294 SKI 61579 inside intron 0 overlap 0.02919 chr6 106541092 106541454 1.81525 0.32873 14.2916 PRDM1 99433 upstream 0 overlap 0.0292 chr3 55482564 55483478 1.48443 0.67177 14.2909 WNT5A 12892 overlaps exon 0 overlap 0.0292 downstream
chrl l 101721795 101722585 -0.2495 0.53527 14.2861 BIRC2 590 promoter 199 disjoint 0.02921 chrl6 2844064 2845046 0.29089 0.93781 14.2837 PRSS22 3125 inside intron -701 disjoint 0.02922 chr3 42281673 42282210 0.38883 1.32106 14.2828 CCK 275 promoter 0 inside 0.02922 chrl 8 43913981 43914807 0.25731 0.96321 14.2814 ZBTB7C 92490 upstream 1505 disjoint 0.02922 chrl 9 52436356 52437145 1.15005 1.96113 14.2782 BBC3 10066 upstream 1032 disjoint 0.02923 chr6 166890241 166890813 0.75831 1.74922 14.2748 RPS6KA2 69902 inside intron 61507 disjoint 0.02924 chr7 79600875 79601729 1.29316 0.37297 14.2735 GNAI1 346 promoter 0 overlap 0.02925 chr2 128001635 128002489 1.5401 0.93363 14.2707 IWS1 1122 promoter -641 disjoint 0.02925 chrl 9 13067620 13068252 0.92041 0.04504 14.2659 NFK 100037 inside exon 123 disjoint 0.02927 chrl 7 12508737 12509243 0.62292 1.75807 14.2597 MYOCD 987 promoter 149 disjoint 0.02928 chr8 97073095 97073811 0.61306 1.30022 14.2547 GDF6 168384 downstream 152128 disjoint 0.02929 chrl l 2182944 2184035 0.87028 1.59804 14.2532 TH 33334 upstream -38123 disjoint 0.0293 chr9 38417376 38418059 0.13839 0.98189 14.2504 IGFBPL1 2933 upstream -2792 disjoint 0.0293 chrl 163590054 163590812 1.02785 0.26917 14.2437 LMX1A 828 inside intron 0 cover 0.02932 chr7 71440831 71441572 0.35961 1.19668 14.2363 CALN1 73666 inside intron -127 disjoint 0.02934 chrl 7 37679743 37680569 2.02299 1.30598 14.2259 STAT5B 1380 inside intron 908 disjoint 0.02937 chr8 25955870 25956760 0.62878 0.02794 14.2231 EBF2 1548 inside intron 0 overlap 0.02937 chrl 9 54621574 54622428 -0.3571 0.23638 14.2221 SLC17A7 14167 downstream 587 disjoint 0.02937 chrl 2 116018956 116019997 1.01592 1.74409 14.2195 TESC 1636 inside intron 676 disjoint 0.02938 chrl l 2328284 2329471 0.68672 1.2826 14.2189 CD81 25651 upstream 25328 disjoint 0.02938 chr5 79588902 79589441 1.72898 0.80363 14.2183 SERINC5 1277 promoter -852 disjoint 0.02938 chr3 130642132 130644404 0.24886 0.99674 14.2096 IFT122 475 inside intron 0 overlap 0.02941 chr4 2212082 2212798 0.44579 1.17886 14.2086 C4orfl5 859 overlaps exon 251 disjoint 0.02941 upstream
chr3 45322334 45322765 1.11337 2.24125 14.2005 TMEM158 79517 upstream -79291 disjoint 0.02943 chr2 45086025 45086724 1.21111 0.29691 14.1962 SK2 3301 inside exon 0 overlap 0.02944 chr6 26267353 26268787 -0.1623 0.2745 14.1958 HIST1H2BD 1026 inside intron -2228 disjoint 0.02944 chrlO 131649738 131650563 0.59145 -0.0258 14.1951 EBF3 1517 covers exon(s) 596 disjoint 0.02944 chr6 108991923 108992432 0.15512 1.16837 14.1901 F0X03A 3162 inside intron -1826 disjoint 0.02945 chr2 242634002 242634502 1.47305 2.55365 14.1893 FLJ33590 173449 downstream 1812 disjoint 0.02945 chrlO 79139797 79140915 1.24655 0.58234 14.1888 CNMA1 72215 upstream 53 disjoint 0.02945 chr9 140191725 140192942 0.51195 1.62044 14.187 CACNA1B 299664 downstream -1713 disjoint 0.02946 chrl6 3180802 3181694 0.81022 0.16651 14.1868 OR1F1 12553 upstream 929 disjoint 0.02946 chr4 563285 564031 0.8805 1.6249 14.1843 P1GG 80276 downstream -1517 disjoint 0.02947 chr6 34770929 34771504 0.77154 1.61343 14.1625 C6orfl06 1098 inside intron 546 disjoint 0.02952 chr7 1232211 1232786 1.25742 0.32273 14.1552 ZFAND2A 65888 upstream -306 disjoint 0.02953 chr2 242472922 242473395 0.49592 1.63386 14.1544 FLJ33590 12369 downstream -279 disjoint 0.02953 chrl5 87740890 87741711 0.69907 0.03234 14.1482 POLG 61861 upstream 1885 disjoint 0.02955 chrl2 113360936 113361722 0.64405 -0.1664 14.147 TBX5 30307 upstream 804 disjoint 0.02956 chrl 38002227 38003186 0.72788 1.20629 14.1463 EPHA10 189 inside intron 0 overlap 0.02956 chrl7 819525 820097 0.6268 1.64045 14.1451 XN 9662 inside intron 8386 disjoint 0.02956 chrl5 32289759 32291074 0.67243 1.35503 14.1444 C15orf29 245 promoter 0 overlap 0.02956 chr7 30292473 30293166 1.80918 0.79464 14.1439 ZNRF2 2026 inside intron -307 disjoint 0.02956 chrI3 23983538 23984447 0.18601 0.74083 14.1304 PARP4 500 inside intron 75 disjoint 0.0296 chrl 9 63320491 63321102 0.7248 1.72617 14.1103 ZNF329 32857 downstream 19 disjoint 0.02965 chr22 28040180 28040966 0.68384 1.7015 14.1095 RRP22 781 inside intron 0 inside 0.02966 chrl 5 27346354 27347145 2.21677 1.43801 14.1073 NDNL2 2163 close to 3' 1641 disjoint 0.02966 chr9 134396446 134397033 0.66453 1.62779 14.099 FLJ46082 121015 inside intron -44144 disjoint 0.02969 chrl l 74633900 74635228 0.37563 1.17405 14.0948 ARRB1 105292 downstream -2761 disjoint 0.02969 chrl 40612639 40613484 0.19758 0.95732 14.0924 SMAP1L 325 inside intron -30 disjoint 0.0297 chr3 24538878 24539381 1.6204 0.62431 14.0892 THRB 27562 upstream -298 disjoint 0.02971 chrl 202728323 202729500 0.11731 0.55798 14.0848 PI 3C2B 2227 promoter 416 disjoint 0.02971 chr22 19666979 19668016 0.00763 0.63817 14.0781 LZTRl 324 covers exon(s) -40 disjoint 0.02973 chrl 4 32479101 32479745 0.87394 0.09967 14.0694 NPAS3 828 inside intron -5271 disjoint 0.02975 chr2 207735727 207736597 0.16382 0.85789 14.0676 LF7 2261 inside intron 2500 disjoint 0.02976 chrlO 129592625 129593200 0.78914 1.67555 14.0664 PTPRE 2114 promoter 2007 disjoint 0.02976 chrl 9 57144503 57145042 1.35153 2.35396 14.0655 ZNF613 21963 downstream -148 disjoint 0.02977 chrl 9 18820710 18821321 0.77664 1.73631 14.0639 UPF1 16967 inside intron 5314 disjoint 0.02977 chrl 160307373 160308089 1.29962 0.50442 14.0583 NOS1AP 1169 inside intron -697 disjoint 0.02979 chrl 28031272 28031811 0.48819 1.56418 14.0556 PPP1R8 1393 inside intron -897 disjoint 0.02979 chrl5 21484286 21484840 0.64723 1.53961 14.0496 NDN 744 promoter -646 disjoint 0.02981 chrl 5 91225241 91226311 0.16675 0.74954 14.0478 CHD2 18111 upstream 844 disjoint 0.02981 chr7 6486332 6486763 1.53878 2.71268 14.041 DELR2 3461 inside intron 2826 disjoint 0.02983 chrl4 58172183 58173243 0.59081 -0.0128 14.0368 DACT1 1368 promoter 809 disjoint 0.02984 chrl 9 322301 323358 0.78978 1.7143 14.0364 THEG 3650 overlaps exon 3472 disjoint 0.02984 upstream
chr6 49537734 49538834 0.48272 14.0266 MUT 0 overlaps 5' 59 disjoint 0.02986 chrl 2 69844263 69844962 0.34885 1.2942 14.0244 TSPAN8 6218 upstream 274497 disjoint 0.02987 chr4 189154018 189154425 1.72463 0.47677 14.0232 ZFP42 100 inside intron -148 disjoint 0.02987 chr4 78295937 78296443 0.98857 -0.0312 14.0141 CCNG2 1107 promoter 576 disjoint 0.02989 chrl5 19345877 19346287 0.24569 1.50113 14.009 POTE15 9211 upstream 1379 disjoint 0.0299
Chr22 24897633 24898601 0.60234 1.05806 14.0074 SEZ6L 2154 inside intron -1647 disjoint 0.02991 chrl 47949325 47950318 0.67038 1.49579 13.9986 FOXD2 275050 downstream -219 disjoint 0.02993 chr9 126069425 126070108 0.73422 1.48435 13.9971 NEK6 9356 inside intron -8863 disjoint 0.02993 chrl4 36204852 36205497 0.93101 0.13496 13.9929 PAX9 4197 overlaps exon 0 overlap 0.02995 upstream
chr5 140546831 140547958 0.32353 1.1153 13.9898 PCDHB9 0 overlaps 5' 442 disjoint 0.02995 chrl6 55260075 55260759 1.33357 0.23298 13.9889 MT1H 515 promoter 129 disjoint 0.02995 chrl l 125731945 125732605 0.49741 1.54577 13.9889 ST3GAL4 640 inside intron -662 disjoint 0.02995 chrl4 51802869 51803511 0.40976 1.63161 13.9826 PTGDR 669 promoter 446 disjoint 0.02997 chrl6 6815S258 68155905 1.29829 0.54623 13.9802 NFAT5 592 promoter 1033 disjoint 0.02998 chrl2 56310235 56311023 1.23394 0.56637 13.9786 B4GALNT1 2228 covers exon(s) 905 disjoint 0.02998 chrl7 21500500 21501480 0.40227 1.42914 13.9782 KCNJ12 241299 downstream -63577 disjoint 0.02999 chrl5 38117400 38118119 -0.1177 0.74533 13.9744 SRP14 561 covers exon(s) 164 disjoint 0.03 chr2 206259590 206260309 1.6169 0.79069 13.9735 NRP2 4122 inside intron -29 disjoint 0.03 chr8 38974919 38976062 -0.2885 0.44185 13.9689 ADAM9 1258 inside intron -646 disjoint 0.03001 chr3 129850776 129851419 0.16946 0.94543 13.9674 RPN1 989 inside intron 197 disjoint 0.03001 chr5 154113266 154114394 0.68941 1.67304 13.9654 LARP1 40612 inside intron 0 overlap 0.03002 chrl 114495584 114496339 1.31026 0.46282 13.9606 SYT6 1655 inside intron 320 disjoint 0.03003 chr8 58066926 58067826 0.01432 0.78068 13.9577 IMPAD1 1130 inside intron 428 disjoint 0.03004 chrl 112324558 112325109 0.90503 1.91518 13.9575 KCND3 8190 inside intron 882 disjoint 0.03004 chrl2 95315571 95316358 -0.1339 0.47232 13.9567 PCTK2 1995 inside intron 964 disjoint 0.03004 chr3 142251808 142252344 2.03648 0.99927 13.955 SPSB4 1088 promoter 229 disjoint 0.03005 chrl 94778820 94779461 1.44786 0.6795 13.9542 F3 441 inside intron 0 overlap 0.03005 chr5 10383598 10384137 0.62265 1.55282 13.9525 CMBL 22431 upstream 2085 disjoint 0.03005 chrl 4 60052472 60053177 0.91683 -0.0328 13.949 SK6 6698 downstream -83 disjoint 0.03006 chrl l 95762951 95763667 0.14134 0.83155 13.9479 JR L 0 overlaps 5' 0 overlap 0.03006 chrl 7 62262910 62263518 0.50126 1.3283 13.9457 PR CA 533523 downstream -874 disjoint 0.03007 chr6 99401961 99402464 1.78606 0.6937 13.9434 POU3F2 12661 downstream 0 overlap 0.03007 chr2 176734095 176734646 1.33288 0.47158 13.9294 HOXD3 2404 promoter -157 disjoint 0.03012 chrX 48652915 48653741 -0.3061 0.32703 13.9291 SLC35A2 135 inside intron 0 overlap 0.03012 chr3 99024703 99025207 0.37634 1.39381 13.923 ARL6 58419 downstream -383 disjoint 0.03014 chrl6 49746189 49746857 0.84635 -0.0094 13.9167 SALL1 3537 upstream 0 overlap 0.03015 chr2 42129826 42130545 0.61554 1.33155 13.9152 LOC91461 570 inside intron 51259 disjoint 0.03016 chr4 83936981 83937601 1.02343 0.2398 13.9113 SCD5 1347 inside intron 432 disjoint 0.03017 chrl 109742562 109743134 1.37051 0.4435 13.8983 SORT1 477 promoter -145 disjoint 0.0302 chrl2 6908615 6909187 -0.1228 0.72089 13.8775 ATN1 875 inside intron -430 disjoint 0.03026 chr22 36387007 36387817 0.88383 1.74034 13.8659 PDXP 2325 inside intron -1611 disjoint 0.03028 chrl 148560625 148561272 0.2097 0.8877 13.8657 PRPF3 0 overlaps 5' 0 overlap 0.03028 chrlO 32385805 32386284 0.76405 1.83051 13.8641 KIF5B 585 promoter -229 disjoint 0.03029 chrS 134855624 134856058 1.49632 0.34095 13.847 NEUROG1 43479 downstream -81 disjoint 0.03033 chr7 157472901 157473803 0.93376 1.43821 13.8424 PTPRN2 599375 inside intron -76855 disjoint 0.03035 chrl 26017828 26018775 0.43108 1.19995 13.8396 FAM54B 495 promoter 0 overlap 0.03035 chrX 52020356 52021277 0.08673 0.71891 13.8364 LOC401589 60654 downstream 378 disjoint 0.03036 chrl 38958307 38958882 0.68942 1.74603 13.8355 RRAGC 139044 downstream -10780 disjoint 0.03036 chr20 52224686 52225081 1.26479 0.05963 13.8251 CYP24A1 756 promoter -293 disjoint 0.03039 chr6 33500728 33501376 -0.095 0.74885 13.8206 SYNGAP1 4904 inside intron 194 disjoint 0.0304 chrl 86395433 86395865 1.78596 0.57993 13.802 COL24A1 725 promoter 0 overlap 0.03045 chr8 95072357 95072965 0.26231 1.06746 13.7981 PPM2C 74020 downstream -73057 disjoint 0.03046 chr3 135688312 135689212 0.38993 0.96478 13.7975 CEP63 576 inside intron -186 disjoint 0.03047 chrl4 76073951 76074801 0.14259 0.94707 13.7964 ESRRB 166473 downstream -46124 disjoint 0.03047 chr7 128573216 128574146 0.89441 1.56745 13.7947 TSPAN33 1269 inside intron -884 disjoint 0.03048 chr7 157565073 157565675 1.15622 2.01067 13.7876 PTPRN2 507503 inside intron 17742 disjoint 0.0305 chr3 189354995 189355759 0.13068 0.89579 13.7859 LPP 57655 upstream 0 overlap 0.0305 chrl5 27210438 27210941 0.94385 1.97776 13.7843 APBA2 209294 downstream -14917 disjoint 0.0305 chrl 209497084 209497728 1.57969 0.63221 13.7821 RC0R3 2220 promoter 1000 disjoint 0.03051 chr8 145097365 145097868 0.25379 1.27375 13.779 PLEC1 2207 inside intron -198 disjoint 0.03052 chrl 7 18029235 18029992 0.15693 0.94486 13.774 ALKBH5 1222 inside intron -150 disjoint 0.03053 chr8 100028318 100028903 0.82274 -0.093 13.7672 OSR2 2457 inside intron 770 disjoint 0.03056 chr7 97940011 97940481 0.68407 1.83273 13.7663 BAIAP2L1 71696 upstream -1786 disjoint 0.03056 chrl 176960092 176960598 2.09392 1.04702 13.7603 RALGPS2 324 promoter 0 overlap 0.03058 chrl4 59165574 59166329 0.96448 1.72061 13.7545 RTN1 943 inside intron 632 disjoint 0.03059 chrl 8 72300743 72301180 1.45093 2.60088 13.7541 FLJ44881 229793 upstream -964 disjoint 0.03059 chrl 2 120499874 120500451 1.0112 0.15331 13.7516 FBXL10 2295 inside intron 102 disjoint 0.0306 chr3 46992643 46993251 0.70682 1.46032 13.7479 CCDC12 0 overlaps 5' 0 overlap 0.03061 chr9 99920320 99921033 1.46498 0.70908 13.7448 TRIM14 267 inside intron 0 overlap 0.03062 chrl7 7057511 7058230 2.21871 1.22184 13.7423 DLG4 5514 inside intron 90 disjoint 0.03062 chr8 37670554 37671309 0.6275 0.0179 13.7406 ZNF703 1149 promoter 0 overlap 0.03063 chrl 7 40404915 40405454 1.66174 0.70775 13.7388 C1QL1 3746 upstream -1435 disjoint 0.03064 chr5 77175550 77176263 0.8958 0.26639 13.7386 TBCA 67610 upstream 35 disjoint 0.03064 chrl 9 37529125 37529874 -0.3482 0.31914 13.736 ZNF507 733 inside intron -445 disjoint 0.03064 chr9 124023547 124024272 1.24847 0.15881 13.7328 LHX6 6532 inside intron -891 disjoint 0.03065 chr2 409359 409793 0.91968 2.08287 13.7326 LOC285016 131523 upstream 258 disjoint 0.03065 chr4 155881098 155881781 1.46204 0.89757 13.7317 LRAT 2831 upstream 0 cover 0.03066 chr20 25012642 25013466 0.32085 0.91834 13.7275 VSX1 1876 promoter 0 inside 0.03067 chr2 9262997 9263873 1.0457 0.25016 13.727 DDEF2 471 promoter 0 overlap 0.03067 chr5 128822823 128823467 1.0116 0.26636 13.7178 ADAMTS19 534 promoter 0 overlap 0,0307 chr7 154721763 154722696 0.34968 1.12186 13.7159 INSIG1 1288 inside intron -618 disjoint 0.0307 chr5 76964080 76965036 0.54102 0.02787 13.7151 OTP 5241 inside intron -1449 disjoint 0.03071 chr3 55492088 55492594 1.0862 0.07837 13.7032 WNT5A 3776 inside intron 104 disjoint 0.03074 chr5 1033378 1033917 0.66777 1.66526 13.6932 NKD2 28250 upstream -21206 disjoint 0.03076 chrl4 52488658 52489458 0.25094 0.90994 13.6912 PLE HC1 1199 promoter -569 disjoint 0.03077 chrl 7 43958767 43959305 0.93282 0.01598 13.6882 HOXBl 3965 downstream 56 disjoint 0.03078 chrl l 68612545 68613401 1.00953 1.89531 13.6778 TPCN2 39605 overlaps 3' -5418 disjoint 0.03081 chr2 112530397 112531290 0.24889 0.88609 13.6702 TMEM87B 1113 inside intron -312 disjoint 0.03083 chrl 6 65777591 65778199 0.70151 1.50206 13.6684 EXOC3L 3408 covers exon(s) -871 disjoint 0.03084 chr2 139255208 139255850 1.30257 0.30644 13.6681 NXPH2 928 promoter -88 disjoint 0.03084 chrl 233561277 233561945 1.15379 1.9013 13.6657 GGPSl 2786 inside intron -2494 disjoint 0.03084 chr9 35593297 35594010 0.79266 1.78514 13.6645 TES 1 1270 promoter 0 overlap 0.03085 chr4 111765040 111765336 1.63068 -0.0633 13.6592 PITX2 12620 inside intron -1127 disjoint 0.03087 chr6 150108944 150109798 0.4256 0.96136 13.659 NUP43 0 overlaps 5' 0 cover 0.03087 chrl 32981670 32982248 0.38076 1.21573 13.6588 KIAA1522 1572 inside intron -1209 disjoint 0.03087 chrX 150615151 150615600 0.25203 1.48851 13.6558 PRRG3 1834 promoter -417 disjoint 0.03088 chr6 31615649 31616483 0.64611 1.61781 13.6531 BAT1 1720 covers exon(s) 1164 disjoint 0.03089 chrl 2 55899122 55899544 1.83844 0.57692 13.6491 NXPH4 2278 inside intron -1687 disjoint 0.0309 chr6 139136651 139137574 0.03416 0.76651 13.6487 CCDC28A 302 overlaps exon 0 overlap 0.0309 downstream
chrX 18149511 18150664 0.36686 1.31004 13.6476 CXor£20 588 promoter -520 disjoint 0.0309 chrl l 109470082 109470657 0.08198 0.88652 13.6424 RDX 201989 downstream -195 disjoint 0.03091 chr6 40466835 40467370 0.53668 1.56931 13.6407 LRFN2 195733 overlaps 3' 378 disjoint 0.03092 chrl4 60173157 60173854 1.28192 0.28465 13.6299 SKI 12078 downstream 0 overlap 0.03095 chr 138055571 138056572 1.13729 1.95076 13.6286 BTBD14A 70379 inside intron -11829 disjoint 0.03095 chrl 60054857 60055291 0.88678 2.02139 13.6154 H00K1 1737 inside intron -1221 disjoint 0.03099 chrlO 51235760 51237026 -0.1915 0.40002 13.6138 MSMB 16202 downstream -106 disjoint 0.03099 chr3 87121479 87122054 -0.0299 0.84012 13.6091 VGLL3 892 inside intron 243 disjoint 0.03101 chr2 127860261 127860839 0.17462 1.02966 13.6088 PROC 31647 upstream 748 disjoint 0.03101 chr3 135573050 135573786 0.7014 1.63693 13.606 AMOTL2 2309 inside intron 1158 disjoint 0.03102 chrX 128892094 128892735 0.14751 0.95546 13.6019 UTP14A 24255 downstream 565 disjoint 0.03103 chr5 177984487 177985459 0.09664 0.85125 13.6019 CL 4 1200 inside intron 579 disjoint 0.03103 chr8 81802016 81802642 -0.1863 0.7254 13.5881 ZNF704 146928 inside intron 145338 disjoint 0.03108 chrl 9 55563577 55564396 0.81883 1.60542 13.588 NAPSA 2835 upstream 7022 disjoint 0.03108 chrl6 81220536 81221147 -0.2464 0.55265 13.5836 CDH13 2458 inside intron -1222 disjoint 0.03109 chrl4 22360591 22361196 1.33774 0.28047 13.5799 SLC7A7 5740 upstream 0 cover 0.0311 chr5 67519569 67520334 1.19261 0.42601 13.5786 PIK3R1 37883 upstream 26294 disjoint 0.0311 chrl3 112047594 112048169 0.64524 1.47878 13.5786 C13orf28 30500 upstream -1319 disjoint 0.0311 chrl 55454384 55455296 1.84901 1.15068 13.5768 PCS 9 176577 downstream -88 disjoint 0.03111 chrlO 2805760 2806365 0.53401 1.41131 13.5693 PF P 293386 upstream -291 disjoint 0.03113 chrlO 65938073 65938510 0.22926 1.27615 13.5568 REEP3 986945 downstream -337177 disjoint 0.03117 chr7 5533602 5534430 0.87859 1.88318 13.556 ACTB 2316 covers exon(s) 1158 disjoint 0.03117 chrl 9 12641873 12642417 0.30071 1.3054 13.5522 MORG1 290 covers exon(s) 0 overlap 0.03118 chrl 1 15060068 115060883 -0.1317 0.46884 13.5466 NRAS 154 covers exon(s) -45560 disjoint 0.03119 chrlO 23504094 23504946 0.21186 0.79803 13.5461 PTF1A 16519 upstream -199 disjoint 0.0312 chrX 46502130 46502741 1.38726 0.66199 13.5458 SLC9A7 674 inside intron 216 disjoint 0.0312 chr3 49177316 49178173 -0.1319 0.41287 13.5453 CCDC71 584 inside intron 116 disjoint 0.0312 chr6 29707063 29707671 1.05843 0.262 13.541 GABBR1 1167 covers exon(s) 500 disjoint 0.03121 chr2 88705063 88705604 2.3663 1.4731 1 13.5385 EIF2AK3 2469 inside intron 1748 disjoint 0.03122 chr6 160032326 160032905 0.22812 1.11996 13.5376 SOD2 1437 inside intron 642 disjoint 0.03122 chr3 13893586 13894445 0.93041 2.13151 13.5247 WNT7A 2173 inside intron 495 disjoint 0.03125 chrl6 55267336 55267809 1.16267 0.12255 13.5215 MTE 0 overlaps 5' 0 overlap 0.03126 chr7 107172365 107174036 0.27797 0.8973 13.52 CBLL1 544 inside intron -108 disjoint 0.03126 chr4 41058664 41059275 0.94341 0.1073 13.5183 DKFZP686A 1104 inside intron -268 disjoint 0.03127
01247
chrl 7 67627246 67627823 0.87225 -0.0345 13.5129 SOX9 932 promoter 46 disjoint 0.03128 chr3 198765211 198765911 1.10219 2.32903 13.5087 BDH1 1343 inside intron 88 disjoint 0.03129 chrlO 73516432 73516936 1.1502 0.23712 13.5076 SPOC 2 1836 inside intron 0 overlap 0.0313 chr5 112852249 112852824 0.14272 0.9623 13.5055 YTHDC2 24484 upstream -46 disjoint 0.0313 chrl 6 34300504 34301220 0.74294 1.81953 13.5028 LOC649159 430501 upstream -629 disjoint 0.03131 chrl l 786379 786993 0.39239 1.1603 13.4876 SLC25A22 159 promoter 647 disjoint 0.03135 chrl 110412630 110413063 1.20482 0.04304 13.486 ALX3 1781 inside intron 0 inside 0.03136 chrl 9 54251991 54252896 0.05774 0.98596 13.4591 CGB7 1183 promoter 0 overlap 0.03143 chr3 20055205 20055709 0.94383 1.95176 13.4572 PCAF 818 promoter 753 disjoint 0.03144 chrl 9 50150861 50151951 0.14801 0.72611 13.4526 CLPTM1 384 inside intron 0 overlap 0.03145 chrl9 18606694 18607170 0.96978 2.03623 13.4505 KLHL26 1667 promoter 15102 disjoint 0.03146 chr2 61259904 61261137 1.16023 2.16491 13.441 AHSA2 1580 inside intron -1039 disjoint 0.03148 chr6 41502065 41503056 1.10973 0.35074 13.4282 NCR2 90561 downstream 151 disjoint 0.03152 chrl9 18276558 18277236 0.20492 0.99615 13.4276 LSM4 17721 downstream 4253 disjoint 0.03152 chrl 2 6511412 6512494 0.45396 0.99379 13.4224 NCAPD2 37855 downstream 1028 disjoint 0.03154 chrl7 24192923 24193809 0.30637 1.07902 13.4207 C17orf63 157 inside intron 0 overlap 0.03155 chr2 37403714 37404551 -0.1067 0.54293 13.4198 PR D3 5989 upstream 303 disjoint 0.03155 chrl9 59595Ό52 59595754 0.03016 1.00316 13.4175 TTYH1 22692 upstream 23960 disjoint 0.03156 chr9 138157472 138158054 1.03647 1.85214 13.4111 BTBD14A 30521 upstream -2803 disjoint 0.03157 chr8 1104568 1105242 0.7262 1.51093 13.4091 DLGAP2 331733 upstream -3088 disjoint 0.03158 chrX 24939494 24940358 0.55298 -0.0817 13.4079 ARX 3416 inside intron 24 disjoint 0.03159 chr9 137108699 137109490 0.74218 1.40357 13.3978 OLFM1 1708 inside intron -1151 disjoint 0.03161 chr5 32744621 32745110 1.60754 0.41642 13.3891 NPR3 2311 promoter 557 disjoint 0.03164 chr5 177946913 177947626 1.06554 1.76609 13.3886 COL23A1 2535 inside intron 1538 disjoint 0.03164 chr22 39072915 39074068 -0.124 0.83854 13.3871 ADSL 407 inside intron -25 disjoint 0.03164 chr4 184956851 184957393 1.27489 0.43923 13.386 FLJ12716 139412 downstream -103 disjoint 0.03164 chr6 133602937 133603547 1.74246 0.53499 13.3851 EYA4 640 promoter 232 disjoint 0.03165 chr8 109214083 109214556 0.77844 1.7513 13.3844 RSP02 49342 upstream -49058 disjoint 0.03165 chrX 38551027 38551650 0.8936 0.0791 13.3842 MIDlffl 3011 downstream -1319 disjoint 0.03165 chrl8 74249274 74249948 0.54872 1.71386 13.3782 SALL3 591314 upstream 1438 disjoint 0.03167 chr5 139465638 139466543 1.11599 0.43985 13.3743 PURA 7348 upstream 572 disjoint 0.03168 chrll 122439373 122440436 0.44703 1.42919 13.3702 HSPA8 1320 promoter -360 disjoint 0.0317 chrl7 38149309 38150205 0.25195 1.13924 13.3694 EZH1 368 inside intron 0 overlap 0.0317 chrl 182271560 182272105 1.6736 0.77364 13.3611 GLT25D2 1380 inside intron 0 overlap 0.03172 chr2 1041072 1041713 1.6451 0.75729 13.358 SNTG2 104518 inside intron 602 disjoint 0.03173 chr3 140150238 140150900 1.18624 0.40808 13.3569 FOXL2 1748 promoter 422 disjoint 0.03173 chr5 126436555 126437002 0.55874 1.77143 13.354 42411 upstream 0 overlap 0.03174 chrX 102489173 102489641 1.13497 0.18821 13.3523 WBP5 8394 upstream 28336 disjoint 0.03175 chr7 63000158 63000754 0.62243 1.54482 13.3509 ZNF680 660164 downstream -1230 disjoint 0.03175 chr2 176729388 176729963 1.14169 0.31509 13.3499 HOXD4 5030 downstream 2784 disjoint 0.03175 chr22 48392638 48393144 0.56477 1.4803 13.3485 C22orf34 44045 downstream 1818 disjoint 0.03176 chr8 77755277 77755839 1.03636 -0.0123 13.3482 ZFHX4 22995 upstream 971 disjoint 0.03176 chrl 177810876 177811349 1.17031 2.23209 13.3477 NPHS2 341 overlaps exon 0 overlap 0.03176 downstream
chrlO 93383136 93383606 0.0834 1.18754 13.3462 PPP1R3C 299 promoter -9 disjoint 0.03176 chrl4 20218303 20219278 1.54571 0.57997 13.3369 R ASE4 2933 upstream 1480 disjoint 0.03179 chr9 79453577 79454293 1.16385 0.54795 13.3366 GNA14 535 promoter -56 disjoint 0.03179 chrl 8 71054077 71054780 -0.0741 0.7705 13.3364 TSHZ1 2359 inside intron -907 disjoint 0.03179 chr6 1562326 1562799 1.41676 0.43299 13.3318 FOXC1 6647 downstream 1293 disjoint 0.0318 chr6 2915419 2915889 0.67476 1.85105 13.33 SERPI B6 1199 inside intron 196 disjoint 0.03181 chrl2 14027138 14027885 0.29905 1.01322 13.3248 GRIN2B 2820 upstream -629 disjoint 0.03183 chr7 127457740 127458222 1.57194 0.57349 13.3234 LRRC4 15 overlaps two exons 172 disjoint 0.03183 chrX 132374533 132375171 1.08147 0.10848 13.323 GPC4 1699 inside intron 62 disjoint 0.03183 chr6 26721224 26722009 1.1033 0.40017 13.3153 ABTl 16066 downstream 0 overlap 0.03185 chrlO 42712788 42713471 1.2731 2.20125 13.313 BMS1L 114524 downstream 11 disjoint 0.03186 chrl2 125772042 125772615 0.20049 1.2087 13.3104 TMEM132B 1394928 downstream 4116 disjoint 0.03187 chrl2 120504792 120505543 0.75885 -0.0414 13.3086 FBXL10 1521 promoter -1952 disjoint 0.03187 chrl l 62316149 62316757 0.98329 1.99385 13.3061 NXF1 12771 overlaps 3' -18 disjoint 0.03188 chrl 5 53820685 53821191 1.12861 0.14638 13.3022 PRTG 1277 inside intron 663 disjoint 0.03189 chr6 18388245 18388721 0.30484 1.26986 13.3001 DEK 15468 upstream -2204 disjoint 0.0319 chrl l 2600389 2601300 0.00832 1.02775 13.2971 KCNQ1 161130 inside intron -40344 disjoint 0.03191 chrl 8 75346786 75347371 0.54025 1.43043 13.2937 NFATC1 85473 overlaps exon 0 overlap 0.03192 upstream
chrll 6298776 6299273 0.32974 1.33347 13.2923 PRKCDBP 461 promoter -291 disjoint 0.03192 chrlO 99149988 99150811 0.74151 1.52878 13.2902 RRP12 243 covers exon(s) 0 overlap 0.03193 chrlO 102813552 102814114 1.87847 0.94657 13.2895 KAZALD1 1965 overlaps exon -688 disjoint 0.03193 upstream
chr3 46908328 46908834 0.46798 1.39311 13.289 PTHR1 14089 inside intron 0 overlap 0.03194 chr3 9749252 9749899 0.91924 1.66407 13.2858 BRPF1 819 inside intron -341 disjoint 0.03195 chr2 73370758 73371778 0.14827 0.95156 13.272 EGR4 2339 overlaps 3' 94 disjoint 0.03199 chr6 78228778 78229530 1.02728 0.37411 13.2696 HTR1B 308 inside exon 0 overlap 0.032 chr4 84175616 84176520 -0.0607 0.65273 13.266 C0PS4 354 inside intron -22222 disjoint 0.03201 chrl9 49952598 49953101 1.06064 0.2138 13.2595 BCL3 8728 covers exon(s) 0 inside 0.03202 chr2 96236596 96237209 0.42074 1.17077 13.2594 STARD7 1080 inside intron 369 disjoint 0.03203 chrl5 38518602 38519349 0.94079 0.37739 13.2485 BAHD1 1353 promoter 872 disjoint 0.03206 chrl4 67078114 67078797 1.12701 0.49888 13.2423 PLEKHH1 8354 covers exon(s) -7921 disjoint 0.03207 chrl l 62249550 62250239 -0.1766 0.53973 13.2399 TTC9C 2288 promoter 331 disjoint 0.03208 chrl5 75900148 75901065 0.428 1.3387 13.2323 TBC1D2B 255846 downstream -240 disjoint 0.0321 chrl6 414259 414726 0.29156 1.25228 13.2309 RAB11FIP3 942 promoter 197 disjoint 0.03211 chrl9 41037573 41038577 0.80979 1.30882 13.2219 KIRREL2 1086 promoter 307 disjoint 0.03214 chrl7 29990099 29990842 0.74202 1.50166 13.2155 T EM132E 58219 overlaps 3' -553 disjoint 0.03216 ehrl6 30579239 30579781 0.76999 1.96379 13.2134 PRR14 9498 downstream -583 disjoint 0.03216 chrl7 34282127 34282633 0.75129 1.59531 13.2102 LASP1 2234 inside intron -1497 disjoint 0.03217 chrl5 87701231 87702583 0.45058 1.11221 13.2098 POLG 22202 upstream 335 disjoint 0.03217 chr5 151285637 151286708 0.39024 1.07711 13.2051 GLRA1 1042 promoter -620 disjoint 0.03219 chrl3 44050324 44050956 0.72289 -0.083 13.203 TSC22D1 1624 promoter -36 disjoint 0.03219 chrl 32027763 32028426 0.92564 1.67017 13.2019 SPOCD1 25740 downstream -823 disjoint 0.0322 chr2 176655484 176656090 0.97374 0.16545 13.1994 HOXD13 9687 upstream 0 inside 0.0322 chr9 34984864 34985520 0.4357 1.16544 13.1967 DNAJB5 5080 inside intron -4989 disjoint 0.03221 chrl 7 45403386 45403961 1.05288 0.2183 13.1955 DLX4 1824 inside intron 0 overlap 0.03222 chr3 31998257 31998980 0.95724 0.22695 13.1947 OSBPLIO 16 promoter 0 overlap 0.03222 chr5 56281656 56282375 0.0275 0.74134 13.1944 MIER3 1335 covers exon(s) 0 overlap 0.03222 chr7 128616966 128617913 0.11497 0.63087 13.1846 SMO 1018 inside intron -364 disjoint 0.03225 chrl 7 75421439 75422045 0.74621 -0.1257 13.1727 CBX4 5762 overlaps 3' 0 inside 0.03229 chr4 114903448 114904026 0.10898 0.92248 13.1707 CAM 2D 1272 promoter -1113 disjoint 0.03229 chrl 23753032 23753466 1.80285 0.69946 13.1648 ID3 5405 downstream 138 disjoint 0.03231 chrl 9 54723072 54723575 0.4868 1.46455 13.1627 RCN3 386 overlaps two exons 0 overlap 0.03232 chrl3 99417825 99418541 1.06222 0.41448 13.1594 ZIC5 3637 inside intron 0 overlap 0.03233 chrl6 18707595 18708416 0.07466 0.73913 13.1552 RPS15A 740 covers exon(s) 336 disjoint 0.03233 chr9 128421650 128422015 1.20917 -0.0806 13.1538 LMX1B 5032 inside intron -3723 disjoint 0.03234 chr8 72632208 72632963 0.83281 -0.0864 13.1538 EYA1 195188 upstream -93 disjoint 0.03234 chrll 47497000 47497785 0.78313 0.1474 13.1526 CACNB3 993 promoter 578 disjoint 0.03234 chrlO 131650727 131651214 0.84745 -0.1429 13.1454 EBF3 866 overlaps exon 0 overlap 0.03236 downstream
chrl 7 76127473 76128225 0.59199 1.27972 13.1421 KIAA1303 4994 upstream 5120 disjoint 0.03238 chr9 125069075 125069689 1.23691 0.27441 13.1415 STRBP 974 inside intron 1023 disjoint 0.03238 chrl 77519085 77519660 2.55476 1.66369 13.1401 A 5 669 promoter 242 disjoint 0.03238 chr2 47257632 47258332 0.16646 1.36654 13.1378 CALM2 479 promoter -23 disjoint 0.03239 chr8 140780155 140780722 1.06628 1.95454 13.1298 KCNK9 3758 inside intron 3045 disjoint 0.03241 chr4 81346701 81347240 2.1242 1.24909 13.1266 PRDM8 22239 downstream 13 disjoint 0.03242 chrlO 42289640 42290353 0.49355 1.22589 13.1204 ZNF33B 163644 downstream 848 disjoint 0.03244 chr4 40327604 40328306 1.04857 0.01418 13.1202 FLJ20273 114880 upstream -260 disjoint 0.03244 chr7 1233084 1233695 1.30441 0.51799 13.1181 ZFAND2A 66761 upstream -1179 disjoint 0.03245 chrlO S0641197 50642250 0.10051 0.74878 13.1123 OGDHL 823 promoter -586 disjoint 0.03247 chrl7 67630553 67631359 0.84688 0.13156 13.1117 S0X9 1798 overlaps two exons 0 inside 0.03247 chrl6 56619405 56620001 1.2164 0.51893 13.1078 MMP15 2623 inside intron -427 disjoint 0.03248 chr6 40468611 40469712 0.41402 1.19455 13.1054 LRFN2 193391 overlaps exon -195 disjoint 0.03249 upstream
chrl2 55910336 55911013 -0.0054 0.73007 13.1009 SHMT2 518 overlaps exon -166 disjoint 0.0325 upstream
chr8 38209198 38209719 0.18536 1.19299 13.0992 DDHD2 935 overlaps exon -85 disjoint 0.03251 upstream
chr4 29887470 29888201 0.4859 1.11617 13.0855 PCDH7 442933 upstream 439750 disjoint 0.03255 chrl l 65100691 65101194 0.44196 1.37655 13.0846 FAM89B 4296 downstream -266 disjoint 0.03256 chrS 134908442 134908985 1.23384 0.34171 13.0817 NEU 0G1 8905 upstream -724 disjoint 0.03256 chrl l 66949693 66952275 0.89292 1.64402 13.0782 RPS6KB2 235 promoter 101 disjoint 0.03258 chrl4 105183625 105185082 0.63219 1.24964 13.0631 T EM121 119628 downstream 24617 disjoint 0.03262 chrl9 4324969 4325616 0.38535 1.10158 13.0618 SH3GL1 25854 inside intron -2017 disjoint 0.03262 chr3 11733200 11734165 0.43897 1.15125 13.0569 VGLL4 2871 inside intron 1473 disjoint 0.03264 chr9 129992781 129993452 0.20263 1.10313 13.0553 CIZ1 13030 covers exon(s) 0 overlap 0.03264 chr4 46075619 46076155 0.89365 1.82083 13.0493 GABRA2 10546 inside intron 10505 disjoint 0.03266 chr4 78038516 78039022 1.00387 0.01518 13.0487 A RD56 491 promoter 0 overlap 0.03266 chrX 50227403 50228083 -0.1736 0.53808 13.048 DGKK 2393 inside intron 1086 disjoint 0.03266 chr2 94907230 94908354 0.75542 1.42796 13.0418 TEKT4 6272 downstream . -2788 disjoint 0.03269 chr22 29807727 29808577 0.00915 0.58423 13.0349 SMTN 423 inside intron -222 disjoint 0.03271 chrl 110553479 110553916 1.8325 0.71097 13.0327 KCNC4 1671 promoter 0 overlap 0.03272 chr4 134602078 134602407 0.82599 2.32148 13.0326 PCDH10 312159 downstream -309000 disjoint 0.03272 chr3 55500390 55501109 0.53143 1.18165 13.0325 WNT5A 4020 upstream -2514 disjoint 0.03272 chrl l 73034623 73035126 1.38417 0.47417 13.0309 PLE HB1 0 overlaps 5' 14322 disjoint 0.03273 chrl l 2028875 2029906 0.06949 0.54119 13.0289 IGF2 86873 downstream -38308 disjoint 0.03273 chr7 96484928 96485401 1.09354 0.13174 13.0258 DLX5 6677 downstream -393 disjoint 0.03274 chrl 154170172 154170923 0.41492 0.9961 13.0244 KIAA0907 0 overlaps 5' 0 overlap 0.03275 chr4 141436969 141437538 1.18336 2.04992 13.0225 SCOC 39080 inside intron -42952 disjoint 0.03276 chr7 103418081 103418686 0.10494 0.84768 13.0187 RELN 884 promoter -193 disjoint 0.03277 chr4 124646457 124647155 1.38659 0.67908 13.0171 SPRY1 106325 downstream 0 overlap 0.03277 chr3 51720261 51721126 0.90996 1.62081 13.0152 GRM2 2258 inside intron 3668 disjoint 0.03278 chr6 99398597 99399037 1.11281 0.05832 13.0139 POU3F2 9297 downstream -139 disjoint 0.03278 chr7 148823997 148825112 0.84399 2.09426 13.0127 Z F746 614 inside intron 0 overlap 0.03279 chrl 35814593 35815063 1.61398 0.62489 13.0105 TFAP2E 3036 inside intron 0 overlap 0.03279 chr8 81245325 81245900 1.87586 0.99146 13.0069 TPD52 490 inside intron 0 overlap 0.0328 chr3 124227184 124227795 1.38642 0.59568 13.0031 SEMA5B 1470 inside intron 75 disjoint 0.03282 chrl l 127896362 127896835 -0.1594 0.74941 13.0013 ETS1 535 inside intron 87 disjoint 0.03282 chr9 131429107 131430024 -0.0243 0.74739 12.9936 C9crf32 852 inside intron -538 disjoint 0.03285 chrX 18355864 18356344 1.15282 -0.1651 12.989 CD L5 2219 inside intron -1517 disjoint 0.03286 chrl 7 75417942 75418805 1.60692 0.78611 12.9864 CBX4 9002 downstream 1656 disjoint 0.03287 chr6 108598989 108599835 0.87575 0.21441 12.9859 R2E1 5035 covers exon(s) -886 disjoint 0.03287 chr6 88936925 88937539 0.5968 1.30674 12.9851 CNR1 25151 upstream -2757 disjoint 0.03287 chrl l 62123907 62124600 0.28191 1.05221 12.9829 TA2 1278 covers exon(s) 430 disjoint 0.03288 chrl l 132319405 132320016 1.0013 0.18947 12.9787 OPCML 587596 inside intron 0 overlap 0.0329 chr6 27304933 27305472 1.47091 0.6817 12.973 PRSS16 18014 upstream 21299 disjoint 0.03292 chrl9 62395171 62395851 0.42341 1.31074 12.9725 ZNF264 491 inside intron 0 overlap 0.03292 chr4 4300981 4301622 0.2485 0.98063 12.9708 TMEM128 147 promoter 0 overlap 0.03293 chr9 94989396 94990358 1.3427 1.99451 12.9611 WN 2 2364 inside intron -1740 disjoint 0.03296 chrl 168895331 168895837 1.25799 0.31589 12.958 PRRX1 4099 upstream 1243 disjoint 0.03297 chr3 129254683 129255460 0.4327 1.18411 12.9575 SEC61A1 782 inside intron -372 disjoint 0.03297 chrl 5693634 5694327 0.82299 1.70622 12.954 NPHP4 280790 downstream 316 disjoint 0.03298 chr5 72783428 72783895 1.77856 0.75336 12.954 FOXD1 3321 upstream -85 disjoint 0.03298 chrl 9 53639321 53639891 0.16457 1.03012 12.9524 G IN2D 49378 downstream 0 overlap 0.03299 chrX 150892509 150893268 0.25041 0.94914 12.9522 GABRE 538 inside intron 68 disjoint 0.03299 chrl l 108800602 108801124 2.18494 0.76229 12.9485 LOC399947 2518 inside exon -409 disjoint 0.033 chrl 9 41560806 41561775 -0.0921 0.57975 12.9459 ZFP14 10094 upstream 0 overlap 0.03301 chr5 139468623 139469163 0.89635 -0.0128 12.9455 PURA 4728 upstream -767 disjoint 0.03301 chrl 20082349 20083205 0.40647 1.25996 12.9432 PLA2G2E 39491 downstream -300 disjoint 0.03302 chrl5 90198679 90199431 1.8964 1.05208 12.9431 SLC03A1 730 inside intron 0 overlap 0.03302 chr5 133736093 133736680 -0.0577 0.7516 12.9379 UBE2B 1325 inside intron -302 disjoint 0.03304 chrl 2 45053973 45054518 1.85055 1.06071 12.9285 SLC38A2 1160 promoter -1073 disjoint 0.03306 chr2 118698878 118699315 1.49576 0.41849 12.9272 INSIG2 136359 downstream 0 overlap 0.03307 chrl 3 110015087 110015833 0.29784 1.13631 12.9261 RAB20 3016 upstream -2609 disjoint 0.03307 chrlO 131741763 131742266 0.87935 1.82509 12.9248 TXNL2 82386 upstream -7554 disjoint 0.03307 chrl 35166288 35167307 0.5473 1.29648 12.9241 ZMY 6 102848 downstream 27 disjoint 0.03308 chrl l 103540657 103541430 2.27407 1.51387 12.9208 PDGFD 421 promoter -389 disjoint 0.03308 chrl 84717584 84718520 0.01745 0.54739 12.9194 BXDC5 39 overlaps exon 0 overlap 0.03309 downstream
chr22 30387021 30387753 0.86402 1.86217 12.9148 C22orfi0 50977 downstream 169 disjoint 0.03311 chrlO 74674762 74675503 0.5354 1.54245 12.9102 DNAJC9 1527 inside intron 1132 disjoint 0.03312 chr6 2947004 2947543 0.56666 1.44255 12.9098 NQ02 1775 inside intron -1485 disjoint 0.03312 chr6 41103129 41103701 0.9801 0.19329 12.9097 UNC5CL 11204 inside exon 79 disjoint 0.03312 chr5 140508969 140509409 0.02665 1.08057 12.9084 PCDHB6 613 promoter 1932 disjoint 0.03313 chrl 9 49953540 49953938 1.22542 0.04183 12.9058 BCL3 9670 covers exon(s) 0 overlap 0.03314 chrl l 2640850 2641530 0.47419 1.05838 12.9041 KCNQ1 201591 inside intron 35456 disjoint 0.03314 chrl 154895857 154896417 1.03074 1.79627 12.9008 BCAN 17494 overlaps 3' -1657 disjoint 0.03315 chr4 47532640 47533410 0.04308 0.84161 12.8938 CORIN 1405 inside intron 0 overlap 0.03318 chr5 140995658 140996167 0.65029 1.6499 12.8907 HDAC3 428 inside intron 337 disjoint 0.03319 chrl 9 40088263 40088973 0.71744 1.42122 12.8892 ZNF30 20750 upstream 0 overlap 0.0332 chr7 87402487 87402977 0.01932 0.9242 12.8856 ADAM22 850 inside intron 0 overlap 0.0332 chrl 8 68362765 68363483 0.22718 1.09554 12.8796 CBLN2 224 promoter 0 overlap 0.03322 chr9 130196132 130196816 1.42037 -0.081 12.8716 C9orf74 22672 downstream -388 disjoint 0.03325 chr2 211048605 211048985 0.28516 1.6316 12.8705 LANCL1 690 inside intron 441 disjoint 0.03325 chr9 92920435 92920890 0.40876 1.59698 12.8643 AUH 243105 downstream 0 overlap 0.03327 chrl 7 70660063 70660572 1.06127 0.1638 12.8638 HN1 1796 inside intron 853 disjoint 0.03327 chrl2 50524863 50525507 0.30172 1.02044 12.8615 LOC401720 22389 upstream 1532 disjoint 0.03327 chrlO 14255284 14256063 0.12037 0.73638 12.8611 FRMD4A 156808 inside intron -281094 disjoint 0.03327 chrl 26020046 26020853 0.69638 1.69377 12.8586 FAM54B 776 inside intron -84 disjoint 0.03328 chrl l 66876851 66877387 0.21616 1.13346 12.8564 POLD4 205 covers exon(s) 45 disjoint 0.03329 chr7 155652105 155652506 0.55747 1.72577 12.8512 SHH 354378 upstream -10690 disjoint 0.0333 chr4 175376439 175377047 1.38215 0.42535 12.8497 FBX08 64929 downstream -4368 disjoint 0.03331 chrlO 13555848 13556792 3.74612 3.14118 12.847 ClOorBO 28189 inside intron 0 cover 0.03332 chrl 7 7282621 7283406 0.64337 -0.0401 12.8442 FGF11 6 promoter 147 disjoint 0.03332 chrl 5818804 5819481 0.8025 1.65316 12.8342 NPHP4 155636 downstream 40263 disjoint 0.03336 chr2 9059794 9060228 1.64412 0.57489 12.8305 MB0AT2 1098 inside intron 350 disjoint 0.03337 chr2 161809288 161809700 1.72366 0.13921 12.8264 TANK 107577 downstream 0 overlap 0.03338 chrl6 55229260 55229745 1.30962 0.3419 12.8249 MT1A 333 promoter 0 overlap 0.03338 chr20 3816429 3817376 0.90306 1.58887 12.8195 PANK2 109 promoter 77 disjoint 0.0334 chrl l 117907452 117907919 1.35299 0.38978 12.8125 TMEM25 319 covers exon(s) -173 disjoint 0.03342 chrX 70096613 70097011 0.56909 1.68768 12.8113 SLC7A3 28930 upstream -28886 disjoint 0.03343 chr2 135526326 135527009 0.2664 0.94884 12.8087 RAB3GAP1 4 covers exon(s) -132768 disjoint 0.03344 chrl 33121902 33122756 0.74154 1.3216 12.8059 HPCA 1928 promoter 1517 disjoint 0.03345 chrl7 35549556 35550092 -0.0006 0.90465 12.8026 CASC3 0 overlaps 5' -16526 disjoint 0.03346 chrl 212225605 212226007 1.14237 0.00135 12.8017 PR0X1 2475 promoter 0 overlap 0.03346 chrl 7 26840993 26841532 1.68781 0.81534 12.7972 RAB11FIP4 98226 inside intron -1211 disjoint 0.03348 chrlO 135184066 135184776 0.79743 1.55121 12.7951 CYP2E1 6080 upstream -14 disjoint 0.03348 chrl 179341671 179342348 1.2321 0.519 12.7945 IER5 17411 downstream -46 disjoint 0.03348 chrl 8 57153988 57154458 0.67613 1.61135 12.7934 CDH20 154296 upstream -1316 disjoint 0.03349 chrl 9 12778623 12779204 0.90214 1,69289 12.7915 RNASEH2A 196 covers exon(s) 0 overlap 0.0335 chrl2 54783319 54784015 0.12009 0.81074 12.7893 ERBB3 23161 overlaps 3' 120 disjoint 0.0335 chrl3 111777452 111778829 0.16036 0.75786 12.7824 S0X1 7539 downstream -1032 disjoint 0.03352 chrl 6217310 6218162 0.7729 1.68323 12.7818 ICMT 468 covers exon(s) 0 overlap 0.03352 chr9 95970240 95970910 -0.0776 0.77429 12.7788 PTPDC1 83674 downstream -958 disjoint 0.03353 chr8 110773773 110774384 0.28468 0.98454 12.7772 FLJ20366 48694 upstream -700 disjoint 0.03354 chr!2 47499227 47499628 1.54432 0.27804 12.7728 CACNB3 449 inside intron -318 disjoint 0.03355 chrl 7 43282803 43283201 1.04752 -0.0491 12.7725 SP6 5037 inside intron 9 disjoint 0.03355 chrl l 124135940 124136588 0.668 -0.0317 12.7686 ESAM 796 inside intron 685 disjoint 0.03357 chrl 3 97623895 97624463 0.18832 1.3518 12.7677 FARPl 30461 inside intron 2101 disjoint 0.03357 chr5 31568507 31569549 0.50961 1.45281 12.7671 C5or£22 352 inside intron -213 disjoint 0.03357 chr3 71718241 71719036 -0.0818 0.53603 12.7641 FOXP1 2412 promoter -2337 disjoint 0.03358 chrl 111016142 111016819 0.2343 0.87212 12.759 KCNA3 2358 inside exon 948 disjoint 0.03359 chrl 7 17565707 17566384 1.38861 0.58814 12.7549 RAI1 40196 inside intron 0 overlap 0.03361 chrl 3 112029566 112031751 1.07385 1.75934 12.7545 C13orf28 46918 upstream 1216 disjoint 0.03361 chrl 9 1825246 1826459 0.41691 1.31647 12.7535 FAM108A1 9972 downstream 173 disjoint 0.03361 chr5 140758397 140758939 1.52768 2.37339 12.7499 PCDHGB5 519 inside exon 258 disjoint 0.03363 chrl 151873424 151875380 0.07737 0.93186 12.7466 Clorf77 276 overlaps exon 0 overlap 0.03364 downs&eam
chr9 114858938 114859513 0.0248 0.82762 12.7436 ZFP37 122 promoter 0 overlap 0.03364 chr3 6880918 6881562 0.46956 1.16695 12.7434 GRM7 2992 inside intron -1277 disjoint 0.03364 chr6 3400273 3400776 1.2732 0.35459 12.7418 C6or£85 10057 upstream 284 disjoint 0.03365 chrlO 1729278 1729817 1.2028 2.01714 12.7412 ADARB2 39852 inside intron 1607 disjoint 0.03365 chr3 157877129 157878125 -0.0056 0.51471 12.7369 TIPARP 2057 inside intron -831 disjoint 0.03367 chr8 77747527 77748066 0.92327 -0.0346 12.7335 ZFHX4 30768 upstream 4656 disjoint 0.03368 chr5 155085841 155086678 0.23015 0.94207 12.7325 SGCD 599666 upstream 1019 disjoint 0.03368 chrlS 66309335 66310152 0.19276 0.929 12.7319 CLN6 257 promoter -44 disjoint 0.03368 chrl 53435875 53436676 -0.0858 0.49291 12.7319 CPT2 1 187 inside intron -472 disjoint 0.03368 chr9 16818486 16818887 -0.0687 1.0921 12.722 BNC2 41898 inside intron 48 disjoint 0.03372 chrl4 64242118 64243362 1.02488 0.40525 12.7183 PLEKHG3 1173 inside intron -358 disjoint 0.03373 chr2 171495415 171496276 0.07934 0.64974 12.7135 GORASP2 1459 inside intron -770 disjoint 0.03374 chr20 61183481 61184056 0.93577 1.74277 12.7114 BHLHB4 74695 upstream 4156 disjoint 0.03375 chr8 1324715 1325272 0.64573 1.75485 12.7109 DLGAP2 111703 upstream 3355 disjoint 0.03375 chrlO 61137860 61138561 0.80373 0.1674 12.7094 SLC16A9 27204 inside intron 55 disjoint 0.03376 chrl 95057566 95058178 1.56109 0.37726 12.7036 SLG44A3 586 promoter 12 disjoint 0.03378 chrl l 20359051 2036720 0.73616 1.31509 12.7002 IGF2 80059 downstream -45338 disjoint 0.03379 chr7 30511040 30511780 0.37618 1.13665 12.6969 C7or£24 64 promoter 0 overlap 0.0338 chr9 78816947 78817456 0.8871 -0.0101 12.6948 F0XB2 6934 upstream 1274 disjoint 0.03381 chr2 96897045 96897863 0.63592 1.32155 12.6937 SEMA4C 1571 covers exon(s) 0 overlap 0.03381 chr5 79902452 79905400 0.50796 1.1952 12.6927 DP58 599 promoter -249 disjoint 0.03382 chrl 92725217 92725733 1.56487 0.64154 12.6926 GFI1 197 promoter -20 disjoint 0.03382 chrl 8 24008216 24008863 0.77016 0.18023 12.6862 CDH2 2325 inside intron 549 disjoint 0.03384 chr2 73255471 73256151 1.38852 0.54548 12.6803 SMYD5 38746 upstream 0 overlap 0.03386 chr7 96459997 96460665 0.8112 0.03109 12.6693 DLX6 12560 upstream 8654 disjoint 0.0339 chr2 151825427 151825960 0.28004 1.17156 12.6682 C2or£38 662 inside intron 169 disjoint 0.0339 chrX 114047617 114048264 1.1469 0.42664 12.6664 HTR2C 322811 inside exon 281898 disjoint 0.03391 chrl 179719308 179720167 0.17856 0.66964 12.6538 CACNA1E 0 overlaps 5' 0 cover 0.03395 chr7 139987778 139988248 2.2498 1.10055 12.6528 DENND2A 734 promoter -173 disjoint 0.03395 chrl9 54095725 54096386 0.37273 1.11693 12.6523 NUCB1 0 overlaps 5' -295 disjoint 0.03395 chrl 7 77849077 77849562 0.74097 1.77375 12.646 CD7 19206 downstream -4115 disjoint 0.03397 chr7 29889628 29890098 1.31541 0.33454 12.6438 SCRN1 105803 downstream 309 disjoint 0.03398 chrl 8 18180790 18181293 0.95212 0.05235 12.6433 CTAGE1 70582 downstream 1121 disjoint 0.03398 chr6 10518437 10518976 1.06884 0.19906 12.6378 TFAP2A 1616 overlaps exon 0 overlap 0.03401 upstream
chr5 42987264 42987884 0.70989 1.48177 12.6357 LOC389289 88213 downstream 0 inside 0.03402 chrl 49013016 49013813 0.23414 0.87998 12.6336 Clorfl65 1276 inside intron 1145 disjoint 0.03403 chr6 50873235 50873675 0.64061 1.66108 12.6324 TFAP2B 20866 upstream 21570 disjoint 0.03403 chrl3 112393856 112394467 1.76595 1.05078 12.6318 ATP11A 1213 inside intron -667 disjoint 0.03403 chr2 176696962 176697501 1.6346 0.65026 12.6278 H0XD9 1629 inside exon 82 disjoint 0.03404 chr2 200038083 200038481 1.2491 0.10675 12.6265 FLJ32063 4382 upstream -157 disjoint 0.03405 chrX 46938532 46939422 -0.2236 0.28156 12.6262 UBE1 294 inside intron 0 overlap 0.03405 chrlO 14687211 14687858 0.14927 0.8817 12.6261 FAM107B 169043 inside intron -500 disjoint 0.03405 chr5 80630101 80632641 0.11391 0.83531 12.623 ZCCHC9 536 promoter 297 disjoint 0.03406 chrl 7 72883059 72883571 1.23616 2.1991 12.6222 55863 inside intron -958 disjoint 0.03406 chrl 16345641 16346246 0.62234 1.62821 12.6197 EPHA2 8904 inside intron 1452 disjoint 0.03407 chrlO 120502565 120503155 0.56876 1.37373 12.6186 C10orf46 1592 inside intron 784 disjoint 0.03407 chr3 147361955 147362709 0.40525 1.1185 12.6165 PL0D2 0 overlaps 5' 0 overlap 0.03408 chr3 116986346 116987047 -0.3219 0.40788 12.6164 LSAMP 660020 downstream -78 disjoint 0.03408 chr21 42889197 42889526 1.17778 2.57916 12.6125 SLC37A1 96387 downstream -5647 disjoint 0.03409 ehr3 125233325 125234047 1.87437 1.2285 12.6057 R0PN1 40437 upstream 294 disjoint 0.0341 1 chr2 24001218 24002021 0.05488 0.65028 12.6015 UBXD4 14858 upstream 739 disjoint 0.03412 chrl 3 37966232 37966735 0.90544 1.80525 12.5973 UFM1 144215 downstream -143819 disjoint 0.03414 chrl5 34659598 34660239 2.33052 1.4209 12.5922 C15orf41 14147 upstream -409 disjoint 0.03416 chr4 8492954 8493382 0.03669 1.17512 12.5905 ACOX3 0 overlaps 5' 0 overlap 0.03416 chrl 2 8077862 8078647 -0.2075 0.39762 12.5905 FOXJ2 1237 inside intron -979 disjoint 0.03416 chr4 174683676 174684170 1.14176 0.14887 12.5884 HAND2 3782 downstream 738 disjoint 0.03417 chr6 136913986 136914456 1.53568 0.56909 12.5858 AP7 502 promoter -148 disjoint 0.03418 chrlO 101757107 101757559 0.5031 1.56072 12.5803 CPN1 74024 downstream 57392 disjoint 0.0342 chrX 129134783 129135358 0.2805 1.27185 12.5765 RAB33A 1330 inside intron -675 disjoint 0.03422 chr6 27306150 27306805 1.2329 0.3346 12.5762 PRSS16 16681 upstream 19966 disjoint 0.03422 chrl 212220545 212221044 1.20154 0.15255 12.5753 PROX1 7438 upstream -254 disjoint 0.03422 chr7 39840028 39840933 1.74348 0.74819 12.5736 CDC2L5 115700 upstream -352 disjoint 0.03422 chrl7 35080555 35081199 0.70452 1.49858 12.5685 PERLD1 16636 overlaps 3' -2040 disjoint 0.03424 chrl2 50602956 50603617 0.7971 1.6628 12.5682 ACVRL1 10577 overlaps 3' -7352 disjoint 0.03424 chrl7 72006212 72006977 0.82446 1.59178 12.5648 RHBDF2 2125 inside intron 1610 disjoint 0.03426 chrl2 129516560 129516997 0.48953 1.52768 12.562 RMBP2 51365 inside intron 2582 disjoint 0.03427 chr7 157907498 157907935 0.69141 1.82965 12.5595 PTPRH2 165243 inside intron 2677 disjoint 0.03427 chrl9 9908504 9909001 0.86406 -0.0667 12.5587 OLFM2 435 promoter -26 disjoint 0.03427 chr22 42123381 42124074 0.87231 1.73184 12.5579 MPPED1 13889 upstream 13270 disjoint 0.03427 chrl6 55525078 55525698 0.09435 0.83805 12.5565 HERPUD1 1830 inside intron -1101 disjoint 0.03428 chrl5 39310960 39311676 -0.1113 0.43873 12.5496 CHP 232 inside intron 0 overlap 0.0343 chr6 41445177 41447667 1.07765 0.39109 12.5445 NCR2 33673 downstream 0 overlap 0.03432 chrl5 61584879 61585454 -0.1647 0.61025 12.5429 USP3 1017 inside intron -188 disjoint 0.03432 ohrlO 1766544 1767017 0.48349 1.50267 12.5316 ADARB2 2652 inside intron 1767 disjoint 0.03435 chrl3 1 13914530 113915210 -0.0339 0.7664 12.5299 RASA3 986 inside intron 250 disjoint 0.03436 chrl3 695811 4 69581647 0.55235 1.33173 12.5202 KLHL1 715 promoter -954 disjoint 0.0344 chr2 131439166 131439669 0.9098 1.80342 12.5198 ARHGEF4 48473 inside intron -829 disjoint 0.0344 chr3 140149144 140149662 1.16197 0.29175 12.5196 FOXL2 654 promoter -111 disjoint 0.0344 chrl8 33269643 33270221 0.70683 1.57074 12.5151 BRUNOL4 129719 inside intron -4\ m disjoint 0.03441 chr7 97718203 97718853 0.76494 0.01754 12.5139 DKFZP434B 550 covers exon(s) 215 disjoint 0.03442
0335
chrl5 58075183 58075884 0.59817 -0.0861 12.5092 FOXB1 7828 upstream -228 disjoint 0.03443 chrl8 33402331 33402942 0.18639 0.91285 12.5058 BRUNOL4 2391 promoter -705 disjoint 0.03445 chr4 5947491 5948536 0.87545 1.71541 12.5031 CRMP1 1806 promoter -1474 disjoint 0.03446 chrl9 1158048 1158736 0.2737 1.04181 12.4994 STK11 1251 overlaps exon 0 overlap 0.03447 downstream
chrl 110011399 110011872 0.65695 1.74367 12.4974 GSTM2 341 promoter 232 disjoint 0.03448 chr7 105302914 105303655 0.4867 1.22191 12.4969 ATXN7L4 608 covers exon(s) 425 disjoint 0.03448 chr3 148619015 148619452 1.13816 0.10515 12.4966 ZIC1 9145 downstream 138 disjoint 0.03448 chr8 135911644 135912597 0.15838 0.63587 12.4959 ZFAT1 117182 upstream 283 disjoint 0.03448 chrl 232432118 232432624 1.1941 2.13314 12.4952 SLC35F3 324817 inside intron 1134 disjoint 0.03448 chr8 60192103 60192600 0.7696 -0.2789 12.4913 TOX 1720 inside intron 88 disjoint 0.0345 chr2 74589150 74589551 1.71602 0.56055 12.4902 PCGF1 822 promoter -369 disjoint 0.0345 chr7 27199618 27200300 1.13007 0.44025 12.4882 HOXA13 5949 downstream 0 overlap 0.03451 chr20 3673746 3674433 1.0512 0.1478 12.4879 HSPA12B 12391 covers exon(s) 3891 disjoint 0.03451 chrl 37711731 37712267 0.90251 1.73495 12.4865 ZC3H12A 472 promoter 43 disjoint 0.03451 chr3 158358839 158359459 0.13726 0.87054 12.4857 CCNL1 1716 covers exon(s) 407 disjoint 0.03451 chrl 7 24014197 24014670 -0.3829 0.57477 12.4855 SUPT6H 769 inside intron -679 disjoint 0.03451 chrl6 71638340 71638860 0.76678 -0.3004 12.4853 ATBF1 914 inside intron 231 disjoint 0.03451 chrl 89872290 89872760 1.22372 0.23804 12.4812 LRRC8C 941 inside intron -410 disjoint 0.03453 chrl 9 54280959 54281570 0.05224 0.88088 12.4782 SNRP70 683 overlaps exon -67 disjoint 0.03453 upstream
chrl l 43554045 43555181 -0.2538 0.15599 12.4763 TTC17 216979 downstream -133 disjoint 0.03454 chrl 245870546 245870914 0.68938 1.93656 12.4718 OR13G1 32051 downstream -782 disjoint 0.03456 chr3 38564448 38564915 0.76693 1.71309 12.4711 SCN5A 101251 overlaps 3' -51373 disjoint 0.03456 chrl 3 50695443 50696051 0.89368 0.22225 12.4696 FAM124A 936 inside intron -554 disjoint 0.03456 chr7 86621653 86622435 0.02292 0.58191 12.4652 DMTF1 1794 overlaps exon -1523 disjoint 0.03458 downstream
chrl2 125243137 125243748 0.19181 0.91837 12.4647 TMEM132B 866023 downstream -989 disjoint 0.03458 chrl 5 94714083 94714904 1.75696 1.24866 12.4582 NR2F2 39134 downstream -1271 disjoint 0.0346 chrl 7 4795269 4795949 1.82729 0.85164 12.4535 EN03 111 overlaps exon -617 disjoint 0.03462 upstream chrl4 95411166 95412020 0.6878 1.21751 12.4504 TCL1A 160966 upstream 0 overlap 0.03463 chrl9 55796188 55796885 1.11338 2.06265 12.4465 SYT3 36228 downstream 2352 disjoint 0.03464 chr7 138369833 138370336 0.56988 1.48243 12.4418 ZC3HAV1L 978 overlaps exon 248 disjoint 0.03465 upstream
chr22 48948492 48949886 -0.194 0.48333 12.4404 PANX2 1430 promoter 64 disjoint 0.03466 chr2 109730427 109730894 1.50134 0.49797 12.4399 ANK D57 1228 inside exon 0 overlap 0.03466 chrl 90965384 90966133 0.85622 0.30132 12.4382 BARHL2 10003 upstream 0 overlap 0.03467 chr3 183884045 183884800 0.12301 0.65356 12.4321 ATP11B 109184 upstream -514 disjoint 0.03469 chrl 50652414 50652986 0.9642 1.86417 12.4319 FAF1 545537 downstream 517 disjoint 0.03469 chr3 75916207 75917230 0.58719 1.92475 12.4318 R0B02 1254753 upstream 0 overlap 0.03469 chr5 76974824 76975816 0.63244 0.11665 12.4308 OTP 4547 upstream 1335 disjoint 0.03469 chrl2 94707159 94707695 0.96687 0.03225 12.4304 NTN4 971 inside intron 309 disjoint 0.0347 chr22 39820251 39821122 -0.2604 0.2724 12.4296 EP300 1699 inside intron -1146 disjoint 0.0347 chr3 136000943 136001515 0.37531 1.14011 12.429 EPHB1 3994 inside intron -2276 disjoint 0.0347 chr21 35089610 35090221 0.47142 1.24873 12.4261 RUNX1 92635 inside intron -2806 disjoint 0.03471 chr5 36779409 36780254 0.33458 1.02336 12.4237 SLC1A3 136962 downstream 834 disjoint 0.03472 chr9 130984285 130985469 1.54269 0.9246 12.42 IER5L 3939 upstream -3443 disjoint 0.03474 chrl 3 111773879 111774508 0.76231 -0.0046 12.4198 soxi 3966 overlaps 3' 0 overlap 0.03474 chr2 29995082 29996111 0.53513 1.05141 12.4191 AL 1824 inside intron 224 disjoint 0.03474 chrl l 2636499 2637560 0.5855 1.07354 12.4173 KCNQ1 197240 inside intron 39426 disjoint 0.03475 chrl 3 32060727 32061194 0.03027 0.9854 12.4167 APRIN 2104 inside intron -892 disjoint 0.03475 chrl . 10846716 10847410 1.25991 2.17132 12.4146 Clorfl27 99434 downstream 24068 disjoint 0.03475 chrl2 50523974 50524575 0.65666 1.64455 12.4125 LOC401720 21500 upstream 2464 disjoint 0.03476 chrl 47683415 47683954 0.87799 0.16213 12.4107 F0XD2 9140 downstream 0 overlap 0.03476 chrl 6 76027004 76027721 0.59535 1.3791 12.4095 ADAMTS18 493 promoter -429 disjoint 0.03477 chr9 36979076 36979823 0.57765 1.39027 12.4067 PAX5 44652 inside intron -2152 disjoint 0.03477 chrl2 93659043 93659889 0.12985 0.86775 12.4024 TMCC3 90589 upstream -90600 disjoint 0.03479 chr6 15508421 15509160 0.32983 0.9693 12.4006 JARID2 153916 inside intron 95623 disjoint 0.03479 chr5 72629014 72629762 1.09939 0.446 12.3963 TMEM174 129185 downstream 141 disjoint 0.03481 chrl l 64645004 64645627 0.49403 1.26293 12.3958 FAU 608 covers exon(s) 85 disjoint 0.03481 chrl 9 1711655 1712960 0.21694 0.69882 12.3925 ATP8B3 50309 downstream 412 disjoint 0.03482 chrlO 105200323 105201003 0.57869 1.69863 12.3916 FAM26B 1061 overlaps exon 937 disjoint 0.03482 downstream
chr5 1 13723106 113723796 0.6446 -0.0368 12.3796 CN 2 2118 promoter 619 disjoint 0.03487 chrX 68750921 68751448 -0.0343 0.99713 12.3772 EDA 1187 promoter 925 disjoint 0.03488 chr3 10834846 10835283 0.51006 1.5408 12.3708 SLC6A11 1930 inside intron -1399 disjoint 0.0349 chr5 9600414 9601162 0.41259 1.05285 12.3672 SEMA5A 1257 promoter -699 disjoint 0.03491 chr5 137052038 137052624 0.77465 1.94538 12.365 KXHL3 46737 inside intron 64528 disjoint 0.03493 chr4 165525175 165525780 0.75566 1.52336 12.3615 ANP32C 186863 upstream -548 disjoint 0.03494 chrl 8 55092662 55093132 0.86638 -0.109 12.3607 RAX 1058 promoter -142 disjoint 0.03494 chr9 71476098 71476586 0.80047 1.89738 12.3575 APBA1 455 inside intron 38 disjoint 0.03495 chrl l 63361156 63361800 1.02483 1.6582 12.3462 MARK2 1670 promoter 890 disjoint 0.03499 chrl5 70195578 70196310 0.00719 0.79002 12.3428 MY09A 934 inside intron 606 disjoint 0.035 chrlO 76839586 76840271 1.07891 0.16113 12.3403 ZNF503 8156 upstream 0 overlap 0.03501 chr3 1101 1296 11011802 0.7473 1.69081 12.3378 SLC6A1 1841 inside intron -912 disjoint 0.03502 chr3 69670667 69671308 0.2274 0.93995 12.335 MITF 200014 upstream 2390 disjoint 0.03503 chrl 7 6498253 6498822 1.94598 1.18904 12.333 MED31 2604 upstream 123 disjoint 0.03504 chrl2 100128199 100128990 0.1906 1.01279 12.3329 SLC5A8 80 promoter -135 disjoint 0.03504 chrl2 122721273 122722037 0.52734 1.35375 12.3309 C12orC8 0 overlaps 5' 0 overlap 0.03504 chr9 113464396 113465136 0.30362 0.92134 12.3302 GNG10 715 inside intron -267 disjoint 0.03504 chr5 42460499 42461074 0.1798 1.11755 12.329 GH 717 inside intron 0 overlap 0.03505 chrX 8660948 8661505 1.3133 0.39657 12.327 KALI 722 promoter -448 disjoint 0.03506 chrl4 100362508 100363257 0.3643 0.9579 12.3263 DLK1 99527 downstream 0 cover 0.03506 chr7 66024232 66024843 0.40835 1.13919 12.3133 C7orf42 595 inside intron 0 overlap 0.0351 chr3 183096880 183097513 1.14139 1.8875 12.3127 S0X2 184465 downstream -169189 disjoint 0.0351 chrl2 107719568 107720038 0.42015 1.38413 12.3092 SSH1 55441 inside intron -32717 disjoint 0.03512 chr2 111593188 111593727 1.23234 0.27887 12.3037 BCL2L11 1234 promoter 0 inside 0.03514 chr22 29696207 29696807 1.77364 0.8602 12.299 M0RC2 2021 promoter -632 disjoint 0.03516 chr2 50910589 50911104 1.00905 1.90709 12.2982 NRXN1 198002 inside intron 196922 disjoint 0.03516 chrl9 13068835 13069378 0.78676 -0.2648 12.2958 NFK 101252 inside exon 0 overlap 0.03517 chr6 168558007 168558675 0.9225 1.8502 12.2946 SM0C2 26204 upstream -1116 disjoint 0.03517 chrl l 74627710 74628609 0.56229 1.08083 12.293 ARRB1 111911 downstream 686 disjoint 0.03518 chr20 54634234 54634809 0.76853 0.01739 12.2919 TFAP2C 2955 upstream 0 inside 0.03518 chr4 68092648 68093644 0.11785 0.56565 12.2853 CENPC1 206 inside intron 0 overlap 0.03521 chr3 195403930 195404475 1.60054 0.72477 12.28 HES1 67303 downstream 97 disjoint 0.03523 chr8 71143388 71143973 1.34983 0.28599 12.2745 PRDM14 2142 overlaps exon 454 disjoint 0.03525 downstream
chrl 158136924 158137695 1.48302 0.7021 12.2711 CCDC19 395 promoter -157 disjoint 0.03526 chrl7 70430028 70430531 0.13003 0.98054 12.2676 USH1G 414 inside intron 59 disjoint 0.03527 chrl 166170606 166171425 -0.0707 0.53548 12.267 BRP44 431 inside intron 226 disjoint 0.03527 chrl 7 1411195 1411768 0.72688 1.52249 12.2666 PITPNA 1066 inside intron 141 disjoint 0.03527 chrl 7 5916539 5917219 0.85923 1.58661 12.2664 KIAA0523 1882 inside intron -1366 disjoint 0.03527 chrl 8 70271478 70272273 1.15371 1.91405 12.2656 C18orf51 3885 inside intron 2313 disjoint 0.03528 chr4 102485103 102485882 0.14152 0.76942 12.2599 PPP3CA 1493 inside intron 237 disjoint 0.03529 chrl 9 3325373 3325840 0.55362 1.50995 12.2589 NFIC 7801 inside intron -4460 disjoint 0.0353 chr5 148014443 148014997 0.4377 1.37187 12.2577 HTR4 510 promoter -170 disjoint 0.0353 chrl l 65440072 65441055 0.39132 1.16592 12.2533 Cllorf68 2051 overlaps 3' 621 disjoint 0.03532 chrl 50664327 50664938 0.90278 0.14414 12.2463 FAF1 533585 downstream 87 disjoint 0.03534 chr20 12541 16 1254862 -0.2153 0.40013 12.2447 SDCBP2 2963 inside intron 0 overlap 0.03535 chrl l 73033967 73034473 1.32132 0.47237 12.241 PLEKHBl 397 promoter 14975 disjoint 0.03536 chrlO 124244557 124245096 0.7444 1.5727 12.2322 HTRA1 33511 inside intron -32327 disjoint 0.03539 chrl 3 50314307 50315148 1.6545 0.50707 12.2313 DLEU7 927 inside intron 224 disjoint 0.03539 chr5 131855385 131856068 1.45473 0.86868 12.2199 IRF1 1060 promoter -551 disjoint 0.03544 chrl5 88616642 88617485 0.49916 1.35161 12.2192 NGRN 6744 downstream 1833 disjoint 0.03544 chrl2 45064431 45065441 1.15352 0.50848 12.2139 SLC38A2 11618 upstream -308 disjoint 0.03546 chrl5 64435469 64436062 0.35079 1.08954 12.2128 TIPIN 0 overlaps 5' 0 overlap 0.03546 chrl 177466299 177467017 0.43796 0.98669 12.2091 ABL2 941 promoter -476 disjoint 0.03548 chr3 44492584 44493395 0.26281 0.96523 12.2077 ZNF445 770 inside intron 447 disjoint 0.03548 chrl 9 47465985 47466664 0.44184 1.07923 12.2074 C1C 13992 upstream -620 disjoint 0.03548 chr5 78315163 78315633 2.38246 1.2684 12.1994 ARSB 1888 inside intron 440 disjoint 0.03551 chr20 1705155 1706054 -0.2843 0.30983 12.1978 SIRPA 116758 upstream 0 overlap 0.03552 chr7 157887149 157887824 0.88978 1.52429 12.1912 PTPRN2 185354 inside intron 3482 disjoint 0.03554 chrl6 7294546 7295117 0.01977 0.97719 12.1899 A2BP1 1285414 inside intron 0 overlap 0.03555 chrlO 104163815 104164528 0.89382 1.46762 12.1882 PSD 4362 overlaps exon -2953 disjoint 0.03555 upstream
chrl 21221476 21221946 0.93488 1.83836 12.1855 EIF4G3 153980 inside intron 153756 disjoint 0.03556 chrl9 366693 367361 0.80025 1.46616 12.1824 THEG 39685 upstream 2537 disjoint 0.03558 chr5 81084149 81084877 1.02113 0.53397 12.1821 SSBP2 1322 promoter -544 disjoint 0.03558 chrl l 56849443 56850228 0.47837 0.97198 12.1809 SSRP1 9698 overlaps 3' -36 disjoint 0.03558 chr5 37869561 37870283 1.37583 0.74004 12.1809 GDNF 371 inside intron 145 disjoint 0.03558 chrl2 56299974 56300444 1.27775 0.34074 12.1723 SLC26A10 15 inside exon -55 disjoint 0.03561 chr2 96768747 96769571 0.18083 0.78302 12.1666 LMAN2L 0 overlaps 5' 0 overlap 0.03563 chrl9 47106784 47107284 1.50384 2.34415 12.1579 ARHGEF1 26499 downstream 1548 disjoint 0.03566 chrl6 56576799 56577407 0.76309 -0.0007 12.1559 TEPP 8960 covers exon(s) 0 overlap 0.03566 chrl8 22488215 22489102 -0.2871 0.18471 12.1522 CTD1 13910 upstream 485 disjoint 0.03568 chr6 12772729 12773253 0.63759 1.77059 12.1518 PHACTR1 52565 upstream 84610 disjoint 0.03568 chrl9 63318777 63319462 0.78967 1.86883 12.1518 ZNF329 34497 downstream 1659 disjoint 0.03568 chr7 65217354 65218154 0.33131 0.89838 12.1513 RCP9 115 overlaps exon 0 overlap 0.03568 downstream
chr4 8980054 8980524 0.76165 1.77425 12.145 DUB3 10848 downstream 11302 disjoint 0.0357 chr3 185516748 185517251 1.03921 1.89494 12.1449 EIF4G1 961 inside intron -815 disjoint 0.0357 chrll 6905172 6905642 0.34413 1.28815 12.1421 ZNF215 943 covers exon(s) -384 disjoint 0.03571 chr3 161040187 161040492 2.01048 0.5097 12.1419 SCHIP1 565950 inside intron -74473 disjoint 0.03571 chr6 32836105 32836602 0.15677 1.08408 12.1405 HLA-DQA2 18965 downstream 718 disjoint 0.03571 chr2 208104261 208104771 0.60574 1.5179 12.1371 CREB1 1331 inside intron -992 disjoint 0.03572 chr8 109162428 109163196 0.52239 -0.2123 12.1311 SP02 1545 inside intron 465 disjoint 0.03575 chrl8 45273108 45273510 2.29252 1.17481 12.1294 RPL17 205 promoter -162 disjoint 0.03575 chr9 132557817 132558408 1.13623 0.17342 12.1293 EXOSC2 589 promoter 495 disjoint 0.03575 chrl7 59274350 59275559 0.30584 0.97613 12.1289 SMARCD2 268 promoter 0 overlap 0.03575 chr3 52207808 52208452 0.67924 1.36526 12.1254 ALAS1 625 overlaps two exons -227 disjoint 0.03577 chrl8 8790220 8790657 0.26646 1.32729 12.1234 IAA0802 82852 inside intron -14576 disjoint 0.03578 chrl4 76288501 76289055 0.35621 1.11812 12.1225 VASH1 9229 upstream 8267 disjoint 0.03578 chr2 192766265 192766899 0.27476 1.13068 12.1224 TMEFF2 989 inside intron 341 disjoint 0.03578 chrl 113061092 113061598 0.39537 1.2609 12.1175 PPM1J 1620 promoter 1393 disjoint 0.0358 chr8 37778781 37779720 0.19974 0.74422 12.1153 GPR124 4850 inside intron -3523 disjoint 0.0358 chrl l 8247230 8247772 0.99491 1.76267 12.1126 LMOl 5249 upstream -332 disjoint 0.03581 chr8 116730125 116730515 0.29598 1.46752 12.1071 TRPS1 19886 inside intron -204 disjoint 0.03584 chrl5 76721133 76721696 1.34026 0.59875 12.1065 CHRNB4 492 promoter -257 disjoint 0.03584 chrl5 91433927 91434679 1.19558 0.57958 12.1023 RGMA 491 promoter 0 overlap 0.03585 chr3 38469228 38469970 1.09988 0.35818 12.1008 ACVR2B 823 promoter 122 disjoint 0.03586 chr8 19842973 19843588 0.74583 1.69139 12.1006 LPL 1916 inside intron -687 disjoint 0.03586 chr4 53423817 53424431 0.97824 0.32278 12.0979 RASLl lB 566 covers exon(s) -60 disjoint 0.03587 chrl l 131263525 131264149 0.58751 1.42381 12.0949 HNT 517945 inside intron 21389 disjoint 0.03588 chr3 25806629 25807557 0.28085 0.85808 12.0866 OXSM 55 overlaps two exons -6169 disjoint 0.03591 chrlO 134651109 134651729 0.73691 1.74122 12.0778 C10orf93 45056 upstream 2482 disjoint 0.03594 chr4 6321509 6322012 0.42016 1.32079 12.0771 FS1 465 promoter 169 disjoint 0.03594 chrX 24622830 24623372 0.37654 1.42509 12.0752 POLA1 854 inside intron -625 disjoint 0.03595 chr7 145026796 145027305 0.99216 1.83019 12.0709 CNTNAP2 417080 upstream 416658 disjoint 0.03597 chr7 36156154 36156630 1.05692 2.02827 12.0688 KIAA1706 2730 upstream 2486 disjoint 0.03597 chr4 46085231 46086026 0.03601 0.8045 12.0628 GABRA2 675 covers exon(s) 634 disjoint 0.036 chrl5 76206582 76207520 0.40247 1.10313 12.0576 CD32 3412 inside intron 3128 disjoint 0.03602 chr3 185432218 185433154 0.39199 1.1449 12.056 ALG3 16285 downstream -726 disjoint 0.03602 chrl 9 44526479 44527159 0.494 1.13034 12.055 SAMD4B 1532 inside intron -966 disjoint 0.03603 chrl l 17052561 17053217 0.129 1.48932 12.0509 RPS13 2578 overlaps exon 2198 disjoint 0.03604 upstream
chrl7 34809412 34810038 0.49442 1.20034 12.0404 FBXL20 1363 inside intron 854 disjoint 0.03609 chr8 133756854 133757678 0.16358 0.81382 12.039 LR C6 0 overlaps 5' 0 overlap 0.03609 chrl3 113849050 113849877 0.78369 1.36721 12.0386 RASA3 66319 inside intron 4291 disjoint 0.03609 chrX 51503929 51504716 0.82133 0.06164 12.032 GSPT2 663 inside exon -179 disjoint 0.03612 chrI9 37764564 37765221 0.15993 0.98057 12.032 PDCD5 621 covers exon(s) 0 overlap 0.03612 chrlO 72102810 72103593 0.47013 1.21484 12.0199 ADAMTS14 246 inside intron -66 disjoint 0.03617 chr7 128287130 128289657 0.64691 1.27003 12.0195 ATP6V1F 476 promoter 294 disjoint 0.03617 chrlO 49481766 49482311 0.76232 1.38505 12.0188 ARHGAP22 832 inside intron 547 disjoint 0.03617 chrl 26985806 26986473 0.24616 0.88701 12.0148 PIGV 599 promoter 204 disjoint 0.03619 chr2 1976527 1977321 1.09872 1.84584 12.0139 MYT1L 336730 inside intron -55960 disjoint 0.03619 chrl 207447832 207448695 0.51094 1.2313 12.0126 CAMK1G 374972 upstream 22773 disjoint 0.03619 chr2 160834471 160834905 0.18703 1.06589 12.0122 RBMS1 223645 downstream 0 overlap 0.03619 chrl 2 97811070 97811870 0.06163 0.77203 12.0094 ANKS1B 260732 inside intron 483 disjoint 0.0362 chr8 97727469 97728011 0.06789 1.00358 12.0079 PGCP 795 inside intron -350 disjoint 0.03621 chrl 39648283 39648858 0.33749 1.19869 12.0044 MACF1 78887 inside intron -457 disjoint 0.03623 chrl2 92357876 92358625 0.20024 0.87021 12.0042 UBE2N 1531 inside intron 441 disjoint 0.03623 chr8 1326011 1326481 1.08505 2.05969 11.9978 DLGAP2 110494 upstream 2146 disjoint 0.03625 chr7 32303110 32303860 0.24573 1.0327 11.9964 LSM5 192641 downstream 648 disjoint 0.03625 chrl 4 72771801 72772451 1.05491 0.37838 11.9927 PAPLN 1556 promoter 1356 disjoint 0.03627 chr8 76367304 76367705 0.26956 1.35941 11.9884 HNF4G 247052 upstream 114300 disjoint 0.03628 chrl7 71649451 71650173 0.75634 0.14774 11.9864 R FI57 97811 downstream -54 disjoint 0.03629 chr4 3265135 3265692 0.54508 1.62148 11.9835 RGS12 19979 upstream -742 disjoint 0.0363 chrlO 98580345 98580956 1.11456 0.5366 11.983 LCOR 1770 promoter 741 disjoint 0.0363
Chrl 151898002 151898616 1.09964 1.80717 11.9788 SNAPAP 179 covers exon(s) -9 disjoint 0.03632 chr7 4782072 4782584 0.38689 1.37784 11.9752 IAA0415 283 inside intron -4 disjoint 0.03633 chr20 54011293 54011691 -0.2631 0.83712 11.975 CBLN4 1727 inside intron 319 disjoint 0.03633 chrX 16796601 16797287 0.31657 1.25879 11.974 RBBP7 1090 covers exon(s) 376 disjoint 0.03634 chrl2 113586986 113587457 1.13001 0.13231 11.9724 TBX3 18894 downstream 0 overlap 0.03634 chr4 40912317 40912878 1.88056 0.6424 11.9714 APBB2 1073 promoter 193 disjoint 0.03634 chrl l 2732152 2732832 0.59491 1.37165 11.9593 CNQ1 292893 inside intron 36159 disjoint 0.03639 chr6 131498851 131499527 0.32072 0.91462 11.9536 AKAP7 8626 upstream -1 disjoint 0.0364 chrl 2 48017495 48018258 1.03503 0.13513 11.9509 C1QL4 258 promoter -66 disjoint 0.03642 chr4 21558225 21558872 1.26874 1.93142 11.9502 KCNIP4 599 inside intron 311 disjoint 0.03642 chrlO 102782371 102783024 -0.1053 0.59726 11.9447 SFXN3 1386 inside intron -115 disjoint 0.03644 chrl 203583511 203584218 0.34712 1.17315 11.9366 KLHDC8A 8443 inside intron -3312 disjoint 0.03647 chr6 43844667 43845134 0.28836 1.12602 11.9351 VEGFA 796 promoter 476 disjoint 0.03648 chrl l 73176357 73177097 0.57165 1.28908 11.9321 MRPL48 349 overlaps exon 0 cover 0.03649 downstream
chr5 171548747 171549345 1.12544 0.3325 11.926 ST 10 883 promoter -203 disjoint 0.03651 chrl 7 44015683 44016084 0.79953 -0.2662 11.9258 HOXB4 4942 upstream -681 disjoint 0.03651 chr4 185695250 185696707 0.10901 0.63338 11.9238 IRF2 62554 upstream -62075 disjoint 0.03652 chrlO 21503775 21504348 1.19688 -0.0937 11.9215 NEBL 654 promoter 0 overlap 0.03653 chrS 67504975 67506162 0.66581 -0.1014 11.9196 RRS1 1159 overlaps 3' -310 disjoint 0.03654 chrl 9 42553301 42553879 -0.1193 0.57352 11.9191 HKR1 35882 downstream 0 overlap 0.03654 chrS 675627 676517 0.94973 1.75388 11.9165 ERICHl 4402 upstream 313 disjoint 0.03655 chrl 7 38576961 38578010 -0.0497 0.61272 11.9103 NBR1 190 inside intron -72 disjoint 0.03657 chr21 32027270 32027632 0.44829 1.592 11.9086 SFRS15 1138 promoter -424 disjoint 0.03658 chrl l 0249388 6250035 1.36881 2.03158 11.9066 CCKBR 11847 overlaps 3' -119 disjoint 0.03659 chrlO 105410346 105410817 0.07781 0.99463 11.9047 SH3PXD2A 194336 overlaps exon 0 overlap 0.03659 downstream
chrlO 63299260 63299799 0.57337 1.39137 11.904 ARID5B 31649 upstream 33093 disjoint 0.0366 chr2 183440531 183441389 1.06717 0.37327 11.9003 FRZB 789 promoter -193 disjoint 0.03661 chrB 32487165 32487912 2.08295 1.34453 11.8931 KL 658 promoter 16 disjoint 0.03664 chrl l 71633228 71634225 0.57896 -0.0719 11.8907 PHOX2A 377 promoter 0 overlap 0.03665 chrl4 76679415 76680317 0.24385 0.79503 11.8899 ZDHHC22 1529 promoter -1358 disjoint 0.03665 chr7 27159876 27160277 1.99774 0.94847 11.8896 HOXA7 2543 inside exon 831 disjoint 0.03665 chr22 44849575 44850416 0.3371 1.10842 11.8833 FLJ27365 10130 upstream -2383 disjoint 0.03667 chrl 149428682 149429431 0.2512 0.80082 11.8813 VPS 72 0 overlaps 5' 8040 disjoint 0.03668 chr7 50318895 50319503 1.06073 1.76046 11.8802 IKZF1 3972 inside intron -3830 disjoint 0.03668 chrl 6 65797 66369 0.39001 1.12036 11.8779 MPG 648 promoter 1079 disjoint 0.03669 chrl 149438277 149439766 0.13361 0.49955 11.8759 PEP5K1A 582 inside intron -121 disjoint 0.0367 chrl l 65236575 65237048 0.67137 1.8945 11.8753 HTATIP 511 covers exon(s) 0 overlap 0.0367 chr5 74379770 74380631 1.01514 1.91521 11.8726 GCNT4 17291 upstream 3366 disjoint 0.03671 chr6 36499296 36499835 0.48459 1.3219 11.8725 KCTD20 18686 upstream 0 overlap 0.03671 chr4 115740420 115741028 0.61478 -0.1284 11.8697 UGT8 21943 upstream -39 disjoint 0.03673 chrl 152198040 152198938 0.56261 1.03727 11.8666 SLC39A1 7873 overlaps 3' -286 disjoint 0.03674 chr2 236743961 236744782 0.45187 -0.0293 11.864 GBX2 2571 upstream 145 disjoint 0.03675 chr5 170765448 170766023 0.33131 1.06701 11.8581 PM1 18046 overlaps exon 12342 disjoint 0.03677 upstream
chrl l 123548045 123548560 0.4871 1.4903 11.8487 L0H11CR2A 56725 downstream -430290 disjoint 0.0368 chr3 12574150 12574972 0.00324 0.6268 11.8478 MKRN2 557 inside intron -99 disjoint 0.03681 chr3 126575032 126575887 0.69547 1.32061 11.8419 ZNF148 897 inside intron 468 disjoint 0.03683 chrl3 100428059 100428562 0.96521 1.95932 11.8412 VGCNL1 438251 downstream -302335 disjoint 0.03683 chrl 7 5343206 5343676 1.8629 0.84545 11.8409 NALP1 84876 overlaps 3' 179 disjoint 0.03683 chrX 70672731 70673021 0.093 1.63425 11.8369 OGT 3074 covers exon(s) -3041 disjoint 0.03684 chr3 162304810 162305208 0.87174 1.9926 11.8368 B3GALNT1 168 overlaps exon 0 overlap 0.03684 upstream
chr3 188400827 188401558 1.19321 1.84615 11.8345 RTP1 2860 inside exon -380 disjoint 0.03685 chrl l 107843062 107843604 0.17405 0.99473 11.8286 Cl lorf65 0 overlaps 5' 30104 disjoint 0.03687 chr7 1292041 14 129204479 1.48016 0.28599 11.8274 NRF1 146960 downstream 1043 disjoint 0.03687 chrl5 71812304 71812843 0.49234 1.27973 11.8217 LOC388135 18025 downstream 18771 disjoint 0.03689 chrl 47551001 47552215 -0.0536 0.45798 11.8203 STIL 190 inside intron 79 disjoint 0.0369 chrl4 53755330 53756037 1.46473 0.75997 11.8141 CDKN3 177438 upstream 177136 disjoint 0.03692 chrlO 125417681 125418433 0.93241 1.40056 11.8137 GPR26 1821 inside intron -1049 disjoint 0.03693 chrl l 44289242 44290041 1.05719 0.28418 11.8022 ALX4 951 promoter 0 overlap 0.03697 chr5 112072621 112073211 0.26572 0.95508 11.7991 APC 28271 upstream -805 disjoint 0.03698 chrl 6 71658491 71658994 1.14936 -0.0274 11.7988 ATBF1 18717 upstream -199 disjoint 0.03698 chrl2 14023240 14023922 -0.1098 0.533 11.7971 GRIN2B 396 inside intron 1971 disjoint 0.03699 chr5 16233768 16234565 0.65351 1.36266 11.7927 FBXL7 680464 downstream -348 disjoint 0.03701 chr5 177565551 177566447 0.61642 1.64347 11.791 HNRPAB 1438 overlaps two exons -437 disjoint 0.03701 chr6 36672048 36672820 0.06731 0.74407 11.7893 SFRS3 1905 covers exon(s) -1658 disjoint 0.03702 chr6 128881285 128881893 0.30742 1.06408 11.7833 PTPRK 1522 inside intron 0 overlap 0.03704 chr3 47398185 47398757 0.50246 1.2497 11.7816 PTPN23 691 inside intron -2 disjoint 0.03705 chrl 69808338 69808900 1.04712 0.22429 11.779 LRRC7 189545 upstream -1255 disjoint 0.03706 chrl l 62098991 62099392 0.34139 1.54305 11.7772 TUT1 16199 overlaps 3' -720 disjoint 0.03706 chr7 27118656 27119126 0.79995 -0.0483 11.7766 H0XA3 1014 inside intron 586 disjoint 0.03707 chrl7 5913287 5913953 0.42732 1.45799 11.771 IAA0523 704 promoter 86 disjoint 0.03709 chrl6 66424153 66424798 0.0845 0.83357 11.7681 CENPT 502 inside intron 361 disjoint 0.0371 chrl4 23874374 23874985 1.74985 1.01258 11.7663 RIPK3 4096 downstream -181 disjoint 0.0371 1 chr6 108598357 108598970 0.81457 0.1083 11.7663 NR2E1 4403 inside intron -254 disjoint 0.03711 chr8 143218854 143219534 0.88019 1.73559 11.7647 TSNARE1 262909 downstream -18079 disjoint 0.03711 chrl l 22645348 22645994 0.38309 1.10421 11.7614 GAS2 235 promoter -155 disjoint 0.03713 chr9 94894424 94895778 0.93211 1.59145 11.7601 C9orf89 2492 promoter 1778 disjoint 0.03714 chr7 1538704 1539394 0.65911 1.43274 11.7598 MAF 1811 inside intron -1042 disjoint 0.03714 chr4 174688551 174689231 0.96641 0.34454 11.7574 HAND2 599 promoter 0 inside 0.03715 chr4 5948878 5950238 0.67245 1.3523 11.7557 CRMP1 3193 upstream -2861 disjoint 0.03715 chrl2 52709645 52710262 0.87363 0.17544 11.7521 H0XC6 1185 overlaps exon 0 cover 0.03717 upstream
chrl4 80491499 80492035 1.1704 0.35117 11.7492 TSHR 0 overlaps 5' -185 disjoint 0.03718 chrl l 1 19702262 119702834 0.73506 1.44579 11.7487 TMEM136 1037 inside intron -680 disjoint 0.03718 chrl7 35854372 35855566 0.08723 0.68571 11.7482 1GFBP4 1171 inside intron -540 disjoint 0.03718 chr8 61756101 61756427 1.15505 -0.1399 11.7428 CHD7 2209 inside intron -367 disjoint 0.03721 chrl9 63612375 63612845 -0.0041 0.79081 11.7394 Z F584 501 inside intron -34 disjoint 0.03723 chrlS 52058042 52058671 0.01987 0.83556 11.7332 WDR72 218892 upstream -218746 disjoint 0.03725 chrl5 21363163 21363561 0.94713 2.04666 11.7327 M RN3 1617 inside exon 119091 disjoint 0.03725 chrl5 63435483 63436061 1.06658 0.31647 11.728 PUNC 21317 inside intron 0 overlap 0.03726 chrl7 4832119 4832778 0.1901 0.80107 11.727 INCA1 8850 overlaps 3' -404 disjoint 0.03727 chrX 74062931 74063503 0.60549 1.33842 11.7268 KIAA2022 1223 promoter -1030 disjoint 0.03727 chrlO 101760040 101760402 0.13782 1.26039 11.7231 CPN1 71181 downstream 54549 disjoint 0.03729 chrl 99241835 99242266 1.26357 0.24931 11.7154 PAP2D 770 inside intron 254 disjoint 0.03731 chr5 1 11117904 111118494 0.14771 0.88008 11.7128 C5orfl3 2359 inside intron 2843 disjoint 0.03733 chr3 75753724 75754974 0.9084 1.75055 11.7125 CNTN3 1100692 upstream -1970 disjoint 0.03733 chrl 7 6864234 6864846 0.46554 1.15918 11.703 BCL6B 2246 promoter 1278 disjoint 0.03737 chrl 6 65757745 65758320 0.84541 0.02227 11.6983 HSF4 2888 covers exon(s) -256 disjoint 0.03738 chr9 98423784 98424284 2.01928 0.70814 11.694 CDC14B 1852 promoter -1727 disjoint 0.0374 chrl 7 43458643 43459212 0.24508 1.11608 11.692 COPZ2 10938 overlaps exon -740 disjoint 0.03741 upstream
chr3 185803723 185804571 1.02489 0.32492 11.6899 EPHB3 41443 downstream 0 overlap 0.03742 chr9 35835752 35836223 1.45468 0.26585 11.6872 C9orfl27 16531 covers exon(s) 87 disjoint 0.03743 chrl 6 55208116 55208586 1.13082 0.16493 11.6871 MT2A 8105 downstream 0 overlap 0.03743 chrX 48866007 48866759 0.33199 1.04142 11.6844 GP OW 263 overlaps exon 29 disjoint 0.03744 upstream
chr20 48033475 48033891 0.07361 1.16252 11.6824 SNAI1 542 overlaps exon -411 disjoint 0.03744 upstream
chrl 3 22309771 22310259 -0.1367 1.0512 11.6821 SGCG 342831 upstream 0 overlap 0.03744 chrl 9 3935232 3935945 -0.2092 0.40729 11.6811 EEF2 515 overlaps exon 17 disjoint 0.03745 upstream
chrl 9 10165359 10165933 0.34836 1.18565 11.6794 DNMT1 877 inside intron 33 disjoint 0.03746 chrl 7 7094313 7095032 0.09357 0.81728 11.6689 DULLARD 950 inside intron 116 disjoint 0.03749 chrl 8 42167109 42167576 0.60049 1.41762 11.6579 RNF165 608 promoter 0 overlap 0.03753 chrl l 16585706 16586781 0.31879 -0.2389 11.6502 Cl lorf58 129988 upstream 0 overlap 0.03756 chr5 140399561 140400345 0.58165 0.05667 11.6451 PCDHB1 10817 upstream 55438 disjoint 0.03758 chr22 48634717 48635328 0.67898 1.52275 11.6451 ZBED4 1185 inside intron -570 disjoint 0.03758 chrl 6 1 1741965 11743053 0.53522 1.60208 11.6417 TXNDC11 1095 inside intron 521 disjoint 0.0376 chrl 4 70346528 70347100 0.96211 0.12899 11.6408 MAP3 9 888 promoter -204 disjoint 0.0376 chrl7 77130729 77131409 0.05427 0.80511 11.6362 C17orf70 886 promoter -443 disjoint 0.03762 chrl 48224964 48225470 0.35051 1.12401 11.6336 SLC5A9 235520 upstream -2233 disjoint 0.03763 chrl5 88695794 88696436 1.14539 0.51935 11.6324 ZNF774 109 promoter 40 disjoint 0.03764 chrX 111211423 111212208 0.60164 0.0119 11.63 TRPC5 451 overlaps exon 0 cover 0.03764 downstream
chr2 237142786 237143842 0.13771 0.49461 11.6266 CXCR7 0 overlaps 5' -784 disjoint 0.03766 chr3 140740202 140740814 1.37754 0.68089 11.6171 RBP1 365 covers exon(s) 0 cover 0.03769 chrlO 42750346 42750998 1.15979 1.85979 11.6167 B S1L 152082 downstream -880 disjoint 0.03769 chr7 94901476 94902012 0.2504 1.03346 11.6158 P0N2 307 inside intron 0 overlap 0.0377 chrl 6 87639271 87639879 0.90532 1.61712 11.613 LOC197322 47945 upstream 2151 disjoint 0.03771 chrl5 87757630 87758242 0.01526 0.83252 11.6126 RHCG 82560 downstream -1444 disjoint 0.03771 chrl 221967426 221968108 0.04241 0.67041 11.611 CAPN2 603 inside intron 0 overlap 0.03772 chrl 174124162 174124706 2.32681 1.21805 11.6079 RFWD2 318286 downstream -288731 disjoint 0.03773 chr5 92961868 92962697 0.3775 -0.1067 11.6055 NR2F1 17070 downstream 2854 disjoint 0.03774 chrl3 52071356 52071976 0.44111 1.34104 11.6022 LOC144983 17629 upstream 53 disjoint 0.03775 chr6 139392585 139393571 1.1707 0.28448 11.6002 REPS1 41495 upstream -152 disjoint 0.03775 chr3 497998 498624 0.08502 0.78279 11.597 CHL1 284349 downstream -172105 disjoint 0.03777 chrlO 7495331 7495924 0.6697 -0.0826 11.5951 SFMBT2 1876 promoter 0 overlap 0.03777 chr6 117909422 117909859 1.62958 0.56512 11.5936 DCBLD1 653 promoter 331 disjoint 0.03778 chr2 144806891 144807436 1.10715 0.31357 11.5901 GTDC1 393 promoter -24 disjoint 0.03779 chrl5 21361048 21361443 0.97335 2.12741 11.5878 MKRN3 103 promoter 121209 disjoint 0.0378 chr6 36961967 36962531 0.03335 0.72221 11.5847 C6orf89 350 inside intron -62 disjoint 0.03781 chrl3 112034490 112034960 1.01254 1.93648 11.5841 C13orf28 43709 upstream -756 disjoint 0.03781 chr7 102575855 102576658 -0.1231 0.54623 11.5817 NAPE-PLD 80 overlaps exon 0 overlap 0.03782 downstream
chrl 7 43403472 43404023 0.19458 1.02332 11.5793 CDK5RAP3 45 covers exon(s) 0 overlap 0.03783 chr5 140190451 140191134 -0.0502 0.59791 11.5783 PCDHA6 2618 inside intron -310 disjoint 0.03784 chr9 131409275 131409911 0.661 1.45848 11.5771 C9orf50 12964 downstream 2253 disjoint 0.03784 chrl l 69597308 69598097 0.77316 1.29387 11.5754 TMEM16A 4196 upstream 3889 disjoint 0.03785 chr7 29814368 29815312 1.04575 1.69584 11.5744 SC N1 180589 downstream -1092 disjoint 0.03785 chr7 2639523 2640101 0.467 1.19223 11.5735 TTYH3 1395 inside intron -1060 disjoint 0.03785 chr2 64536285 64537129 0.16342 0.83507 11.5716 HSPC159 1120 covers exon(s) -544 disjoint 0.03786 chrlO 1599277 1599747 1.18292 2.02653 11.5715 ADARB2 169922 inside intron -13485 disjoint 0.03786 chrl2 113586250 113586756 1.0755 0.29298 11.5698 TBX3 19595 downstream 314 disjoint 0.03787 chr3 33235923 33236354 1.70988 0.65343 11.5691 FBXL2 57583 upstream -156 disjoint 0.03787 chr9 76084384 76084683 0.61966 1.99638 11.5652 RORB 217388 upstream 216915 disjoint 0.03789 chrl5 57736104 57736642 -0.1334 0.70999 11.5632 GTF2A2 342 inside intron 26 disjoint 0.0379 chrl 7 71293573 71294181 1.0724 1.77187 11.5549 H3F3B 6119 upstream -670 disjoint 0.03793 chr7 27250575 27251012 1.0457 0.11352 11.5491 EVX1 1887 inside intron 152 disjoint 0.03795 chrl 8 45266539 45267302 0.61488 1.50745 11.5486 LOC497661 296 inside intron 17 disjoint 0.03795 chrl 7 6863010 6863375 0.73482 1.82851 11.5447 C17orf49 4163 downstream 2749 disjoint 0.03796 chrl 13949347 13949856 0.01377 0.95497 11.5414 PRDM2 885 inside intron -302 disjoint 0.03798 chrl2 49704727 49705610 -0.0532 0.59483 11.538 SLC11A2 798 inside intron 297 disjoint 0.03799 chr2 161804395 161804761 1.58334 0.4299 11.5344 TANK 102684 downstream 0 overlap 0.03801 chrl l 20574152 20574904 0.66167 1.11692 11.5336 SLC6A5 2617 upstream 0 overlap 0.03801 chrl 9 14468413 14469157 0.61908 1.48439 11.5325 GIPCl 470 promoter -28 disjoint 0.03801 chr5 92959353 92959938 1.17978 0.35551 11.5316 NR2F1 14555 downstream -2767 disjoint 0.03802 chr22 18130681 18131217 1.1507 0.45966 11.5313 TBX1 6456 covers exon(s) 436 disjoint 0.03802 chrX 12063667 12065084 0.25584 1.05676 11.5148 FRMPD4 1421 promoter 1441 disjoint 0.03808 chr2 229846438 229847190 0.25269 0.80877 11.5141 FLJ20701 2214 promoter -2190 disjoint 0.03808 chrl8 10443546 10444154 0.89227 0.17963 11.5126 APCDD1 470 promoter 0 overlap 0.03809 chrl4 87860863 87861785 0.67998 1.20836 11.5118 CN 10 1218 inside intron -617 disjoint 0.03809 chrl4 73960952 73961561 0.40354 1.31523 11.5039 NPC2 68275 downstream 658 disjoint 0.03813 chr2 26921838 26922816 0.23475 0.74555 11.502 DPYSL5 1650 promoter 990 disjoint 0.03814 chr9 34568506 34569099 0.9574 0.1835 11.5011 CNTFR 10622 inside intron -248 disjoint 0.03815 chrll 125733992 125734803 0.94757 2.00706 11.4899 ST3GAL4 2687 inside intron -2709 disjoint 0.0382 chrl l 2741894 2742429 0.59051 1.50996 11.4874 KCNQ1 302635 inside intron 26562 disjoint 0.03821 chr9 124019113 124021027 1.14828 0.45825 11.4831 LHX6 9777 covers exon(s) 0 cover 0.03823 chr8 101928543 101929115 1.05549 1.69015 11.4703 Y HAZ 104331 downstream 102705 disjoint 0.03828 chrl 181652178 181652927 0.5928 0.01747 11.47 MNAT2 1432 inside intron 0 overlap 0.03828 chr8 38875724 38876350 0.22499 1.11004 11.465 TACC1 111787 downstream 1264 disjoint 0.03831 chrl l 116610086 116610565 1.17073 2.48287 11.4626 D FZp547C 1425 covers exon(s) -935 disjoint 0.03832
195
chr9 109438748 109439583 0.33201 1.08643 11.4602 KLF4 147173 upstream 0 overlap 0.03833 chr5 7902373 7902879 1.38602 0.54082 11.4589 FAST D3 19235 downstream 66 disjoint 0.03834 chrlO 11829351 11829854 0.63122 1.46526 11.4578 ECHDC3 4963 covers exon(s) -4408 disjoint 0.03834 chrl2 54980539 54981173 0.69813 1.49878 11.4556 CS 98 promoter 0 overlap 0.03835 chr7 157501977 157502480 0.30468 1.16191 11.4488 PTPRN2 570698 inside intron 80937 disjoint 0.03838 chrl l 65842239 65842806 0.38556 1.63282 11.4482 CD248 1149 promoter -1128 disjoint 0.03838 chrl 38004362 38005180 0.36938 0.88878 11.4474 EPHA10 987 promoter -887 disjoint 0.03839 chr2 69824294 69824731 1.06007 2.13073 11.447 ANXA4 1510 inside intron -1198 disjoint 0.03839 chrS 153549029 153549466 1.29425 0.47124 11.4469 GALNTIO 1021 promoter 272 disjoint 0.03839 chr2 119306301 119306735 1.37844 0.46046 11.4454 EN1 15493 downstream 2337 disjoint 0.0384 chrl 3 34942641 34943291 0.74503 0.09275 11.445 NBEA 528186 inside intron 0 overlap 0.0384 chrl 9 6227606 6228052 0.99806 1.94655 11.4424 MLLT1 2906 inside intron 2431 disjoint 0.03841 chr20 24922274 24922648 0.26293 1.3988 11.4421 C20orf3 850 promoter -574 disjoint 0.03841 chr2 54563617 54564018 0.32491 1.46399 11.4408 SPTBN1 26660 inside intron -25739 disjoint 0.03842 chrl4 70359391 70359969 1.11045 0.33976 11.4382 MAP3 9 13751 upstream -681 disjoint 0.03843 chr9 34980841 34981242 1.87478 0.83499 11.4377 DNAJB5 1057 inside intron -966 disjoint 0.03843 chrl 2832513 2832923 0.20433 1.23765 11.4371 ACTRT2 94982 upstream 3993 disjoint 0.03843 chr3 32830599 32831198 1.63068 0.89677 11.4301 TRIM71 3315 upstream 2000 disjoint 0.03846 chrlO 74842616 74843191 0.22366 1.04779 11.4272 ANXA7 617 inside intron 226 disjoint 0.03847 chrl2 120457529 120458534 0.56612 1.23642 11.4188 FBXL10 44212 inside intron 877 disjoint 0.03851 chr9 137300915 137301439 1.18084 2.32229 11.4145 0LFM1 193924 downstream -4111 disjoint 0.03853 chr5 138561052 138561693 0.46869 1.25941 11.4057 SBL1 270 inside intron 76 disjoint 0.03857 chrl2 6287846 6288557 0.59057 1.35011 11.4051 PLEKHG6 1305 promoter 1307 disjoint 0.03857 chrlO 42882505 42882942 1.08987 1.96303 11.4039 RET 9590 upstream 9003 disjoint 0.03858 chrl 7 40653708 40654374 1.48171 0.57753 11.4027 F NL1 700 promoter 134 disjoint 0.03859 chr7 5601656 5602490 0.08605 0.82484 11.398 FSCN1 2677 inside intron -575 disjoint 0.0386 chrl 9 62761851 62762285 -0.0602 0.83373 11.3976 ZNF550 2315 promoter 80 disjoint 0.0386 chr22 40108764 40109285 1.10457 1.88359 11.3947 TEF 856 inside intron -537 disjoint 0.03862 chrl 7 76989292 76989935 0.76401 -0.0894 11.3932 TMEM105 70224 upstream 0 overlap 0.03862 chrl 3 59870438 59871228 0.52902 1.25649 11.3845 TDRD3 1316 inside intron -392 disjoint 0.03867 chrl 7 34814181 34814630 0.03495 0.97856 11.3844 PPARBP 46399 downstream -1673 disjoint 0.03867 chr2 37572 38118 0.72089 1.7192 11.3815 FAM110C 1188 promoter -1013 disjoint 0.03868 chr9 137139448 137140020 0.83315 1.52366 11.3776 0LFM1 32457 inside intron -2039 disjoint 0.03869 W 201
111
Figure imgf000112_0001
Figure imgf000113_0001
Figure imgf000114_0001
Figure imgf000115_0001
chrlO 102975688 102976671 0.38406 -0.0366 10.8696 LBX1 2035 close to 3' 0 inside 0.04091 chrl9 18561596 18562553 0.63811 -0.0453 10.8683 FLJ20850 989 inside intron -42 disjoint 0.04092 chr6 108542090 108542809 0.71659 0.18216 10.8671 0STM1 39457 upstream 0 overlap 0.04092 chrl9 12986685 12987011 0.95184 -0.3169 10.8611 NFDi 19102 inside intron -426 disjoint 0.04095 chrl5 74417932 74418228 1.75433 0.3967 10.861 ISL2 1731 inside intron 0 overlap 0.04095 chrlS 44754759 44755262 1.07326 0.33045 10.8567 S AD7 23681 upstream 360 disjoint 0.04098 chr4 82610433 82611044 0.1868 0.8918 10.8531 RASGEF1B 1040 inside intron 590 disjoint 0.04099 chr3 128204029 128204502 0.70097 1.51652 10.8522 PLXNA1 13838 inside intron 11153 disjoint 0.041 chr8 38767702 38768241 0.49019 1.28971 10.8515 TACC1 3765 inside intron -2785 disjoint 0.041 chrl2 48003463 48004245 -0.3417 0.15681 10.8508 TROAP 135 covers exon(s) -178 disjoint 0.04101 chrl 182621178 182622014 1.13422 0.35485 10.8495 Clorf21 758 promoter 24 disjoint 0.04101 chrl9 12988583 12989134 0.72622 -0.2417 10.8491 NFK 21000 inside intron -2324 disjoint 0.04101 chr3 62338178 62338671 0.96387 0.15537 10.849 FEZF2 4118 upstream -59 disjoint 0.04101 chrl 2 119386971 119387619 0.66847 1.47511 10.8484 SFRS9 4321 inside intron 3442 disjoint 0.04102 chrl5 58557273 58558025 -0.2593 0.26554 10.8445 NARG2 610 covers exon(s) 335 disjoint 0.04103 chrl 50260778 50261886 0.20976 0.63032 10.8407 ELAVL4 85338 upstream 118 disjoint 0.04105 chrl6 53919311 53920146 0.8769 0.18396 10.8379 IRX6 3340 overlaps exon 92 disjoint 0.04106 upstream
chr5 74383204 74383979 1.09422 0.46402 10.8368 GC T4 20725 upstream 18 disjoint 0.04106 chr3 137951530 137952316 0.03681 0.81591 10.8362 STAG1 1618 inside intron 804 disjoint 0.04107 chr5 3907996 3908538 0.68117 1.40462 10.8357 IRX1 258829 downstream -200 disjoint 0.04107 chr5 140691383 140691934 1.11517 1.89829 10.8342 PCDHGA1 948 inside exon 47 disjoint 0.04108 chr7 27164421 27164783 2.13425 1.05795 10.8294 HOXA7 1601 promoter 0 overlap 0.0411 chr4 186553194 186553698 0.59164 1.34626 10.8291 ANKRD37 1135 promoter 439 disjoint 0.0411 chr2 45087265 45087669 1.5791 0.36604 10.8281 SK2 2356 inside intron -1211 disjoint 0.0411 chr3 42031310 42032164 0.58035 1.1501 10.8253 TRAK1 75585 upstream -377 disjoint 0.04112 chrl2 50070725 50071156 1.60083 0.60054 10.8228 GALNT6 310 covers exon(s) 390 disjoint 0.04112 chr9 35481108 35481645 0.13233 0.85364 10.8203 RUSC2 985 inside intron -408 disjoint 0.04114 chrl2 52734910 52735206 1.37049 -0.0041 10.8143 HOXC4 983 inside exon -552 disjoint 0.04117 chrl l 119939439 119940010 1.07499 0.39707 10.8102 ARHGEF12 226284 downstream 22 disjoint 0.04119 chr20 16154143 16154583 0.59324 1.5138 10.8083 C20orf23 347494 downstream 347253 disjoint 0.0412 chr7 149730373 149731071 1.79175 1.13876 10.8045 ZNF775 23035 downstream 1768 disjoint 0.04121 chrl 9 45483796 45484816 0.61017 1.61437 10.8035 AKT2 763 promoter -349 disjoint 0.04122 chr9 101171033 101171465 1.15633 2.32714 10.8033 SEC61B 146643 downstream -71999 disjoint 0.04122 chrl l 47564760 47565230 0.79986 1.69033 10.8031 NDUFS3 7553 downstream 2484 disjoint 0.04122 chrl 9 23945588 23946202 -0.0755 0.71251 10.7956 ZNF254 115613 upstream 95 disjoint 0.04125 chrl 7 46586034 46587188 -0.3619 0.17529 10.7954 NME1 116 covers exon(s) 0 overlap 0.04126 chr4 88031560 88032189 0.88983 1.44463 10.7853 C4orf36 381 covers exon(s) 7 disjoint 0.0413 chrlO 135194496 135194969 0.98607 1.85298 10.7853 CYP2E1 3640 inside intron -1945 disjoint 0.0413 chrl 8 43919289 43919969 0.69802 1.25292 10.7844 ZBTB7C 97798 upstream -1771 disjoint 0.04131 chrl 180628458 180629447 1.49161 0.89854 10.7778 GLUL 886 promoter -272 disjoint 0.04134 chr3 123997184 123997585 0.07141 1.0342 10.7626 DIRC2 588 inside intron -20 disjoint 0.04142 chrl l 60435886 60437699 0.26526 0.90449 10.76 T EM109 553 promoter 429 disjoint 0.04142 chr5 171641427 171642215 0.13032 0.63061 10.759 UBTD2 1184 inside intron 570 disjoint 0.04143 chrl 84929635 84930030 1.74652 0.76382 10.7584 SSX2IP 868 promoter -473 disjoint 0.04143 chr3 54132542 54133291 0.03632 0.5326 10.7582 CACNA2D3 810 covers exon(s) -477 disjoint 0.04143 chr5 139504976 139505587 1.33194 0.79326 10.755 LOC492311 19272 downstream 134 disjoint 0.04144 chr7 27113363 27113901 1.13633 0.24448 10.754 HOXA3 6239 inside exon 213 disjoint 0.04145 chrl3 51598981 51599799 0.06175 0.66178 10.7537 NE 5 1415 covers exon(s) 975 disjoint 0.04145 chrl l 2791590 2792596 0.45579 1.14729 10.7516 KCNQ1 352331 inside intron -6130 disjoint 0.04146 chr21 37658981 37659387 1.74814 0.83357 10.7498 DYRK1A 2341 promoter -96620 disjoint 0.04147 c i6 24397619 24398053 0.96458 1.77767 10.7477 DCDC2 68205 inside intron 67645 disjoint 0.04148 chrl9 15389399 15389689 -0.0541 1.29564 10.7455 A AP8L 1143 inside intron 601 disjoint 0.04149 chr5 151133740 151134525 -0.0186 0.61202 10.7446 G3BP1 2072 inside intron -1461 disjoint 0.04149 chrlO 15941466 15942093 0.08017 0.7053 10.7429 C10orf97 431 inside intron 0 overlap 0.04149 chrl8 33107498 33108146 0.90255 1.61513 10.74 B UN0L4 291794 inside intron 99 disjoint 0.04151 chrl 43770632 43771135 1.01488 0.27481 10.7398 PTPRF 1499 inside intron -453 disjoint 0.04151 chrl3 110604579 110605190 0.28441 0.93814 10.7386 ARHGEF7 494 inside intron -47 disjoint 0.04152 chrlO 95317218 95318128 0.20971 0.84627 10.7379 GPR120 807 inside intron -120 disjoint 0.04152 chr3 186698092 186699058 0.83696 1.42268 10.7377 TMEM41A 437 inside intron 0 overlap 0.04152 chr20 61284866 61285303 0.52339 1.38079 10.7372 YTHDF1 32679 downstream -3554 disjoint 0.04153 chr20 2616345 2617091 1.75593 0.86131 10.7316 EDH3B 23503 upstream 3813 disjoint 0.04155 chr3 61210738 61211349 1.58212 0.82348 10.7295 FHIT 814 inside intron 294 disjoint 0.04156 chrl 9 46459449 46460315 0.08372 0.58757 10.7261 AXL 42787 overlaps 3' 740 disjoint 0.04158 chr2 193316 193788 0.51154 1.59656 10.7232 SH3YL1 52552 downstream ^781 disjoint 0.04159 chrlO 122699543 122700082 1.02539 0.29466 10.7202 BRWD2 98859 downstream -654 disjoint 0.0416 chrl 9 50285917 50286595 0.65501 1.14094 10.7197 GEMIN7 11548 inside exon 0 overlap 0.04161 chr2 104640964 104641644 1.25744 0.67004 10.7173 POU3F3 196756 upstream 376 disjoint 0.04162 chrl l 124245710 124246282 0.52801 1.34228 10.7115 ROB03 5219 covers exon(s) -1489 disjoint 0.04164 chrl l 64978541 64979116 0.78506 1.44452 10.7107 F SG44 67843 downstream 0 overlap 0.04165 chrl 9 52452863 52453538 0.04675 0.67226 10.7084 CCDC9 1232 covers exon(s) -7 disjoint 0.04166 chr6 75970166 75970918 -0.0089 0.57785 10.7069 COL12A1 1424 inside intron 507 disjoint 0.04167 chr3 101601363 101601950 0.50771 1.19802 10.7046 TOMM70A 964 inside intron 241 disjoint 0.04168 chr6 168663675 168664210 1.12326 1.84936 10.701 SMOC2 78796 inside intron -1924 disjoint 0.0417 chr3 48257189 48257590 1.1415 0.15266 10.7009 ZNF589 58 promoter 0 overlap 0.0417 chrl l 662011 15 66201646 0.13012 0.73551 10.6981 RBM4B 204 overlaps exon 0 overlap 0.04171 upstream
chrl l 31798501 31799053 0.95943 0.19859 10.6971 PAX6 9047 upstream 0 overlap 0.04172 chr9 123399639 123400372 0.85678 0.19165 10.6953 DAB2IP 30420 inside intron 0 overlap 0.04172 chrl2 14108204 14108674 1.2521 2.15836 10.6921 GRIN2B 83886 upstream -81695 disjoint 0.04174 chr20 17500498 17501036 0.72839 1.4911 10.6897 DSTN 1900 inside intron -1181 disjoint 0.04175 chrl 211291534 211292178 -0.0442 0.55633 10.6854 RPS6KC1 315 inside intron -44 disjoint 0.04177 chr8 128819692 128820360 0.23012 0.87172 10.6721 MYC 2195 inside exon 0 inside 0.04183 chrl4 37136396 37137222 0.60026 0.01221 10.6676 FOXA1 2157 promoter 0 overlap 0.04185 chrl 4 100992850 100993284 1.31937 0.40247 10.6671 DI03 104156 upstream 44 disjoint 0.04185 chrl l 2687173 2687994 0.65693 1.29576 10.6603 CNQ1 247914 inside intron -8510 disjoint 0.04188 chr6 1560835 1561266 1.1422 0.18538 10.655 FOXC1 5156 downstream 0 overlap 0.0419 chr9 136674691 136675455 0.19495 0.94274 10.6515 COL5A1 1219 inside intron -473 disjoint 0.04192 chr9 78821562 78822104 0.79547 0.12689 10.6509 FOXB2 2286 promoter 0 overlap 0.04193 chrlO 101283689 101284162 1.44084 0.59198 10.6506 N X2-3 990 inside intron 271 disjoint 0.04193 chr9 34580677 34581183 0.99162 0.21117 10.6426 CNTFR 956 promoter 0 inside 0.04197 chr6 14320141 14320575 2.07107 1.11697 10.6331 CD83 94298 downstream -418 disjoint 0.04201 chrlO 116154742 116155284 1.08746 0.42689 10.6318 KIAA1914 238 promoter -153 disjoint 0.04201 chr2 11399736 11400626 0.22058 0.6498 10.626 ROC 2 1535 inside intron 784 disjoint 0.04204 chr3 130450233 130451091 0.27097 1.20617 10.6258 COPG 51 promoter 0 overlap 0.04204 chrl 201160683 201161228 0.74736 1.49181 10.6212 LHL12 1765 covers exon(s) 1599 disjoint 0.04206 W
117
chrl6 49744751 49745323 0.47728 -0.1148 10.6165 SALL1 2099 promoter 0 inside 0.04208 chrl5 77512317 77512856 1.06945 0.33974 10.6137 KIAA1024 405 inside intron 0 overlap 0.04209 chrl l 31782613 31783083 0.856 -0.0509 10.6081 PAX6 6350 inside intron 0 inside 0.04212 chr9 132548267 132549026 0.44951 0.95641 10.6063 PRDM12 18466 downstream -801 disjoint 0.04213 chr9 34369552 34370199 0.63055 0.0666 10.6056 C9orf24 1398 covers exon(s) 0 overlap 0.04214 chrlO 135190290 135190832 0.81106 1.53801 10.6053 CYP2E1 24 promoter 413 disjoint 0.04214 chr2 219245295 219245942 0.32578 0.85285 10.6052 ST 36 243 covers exon(s) -238 disjoint 0.04214 chrl3 94208401 94209015 0.50596 1.40713 10.6033 S0X21 46012 upstream -44349 disjoint 0.04215 chr20 37023085 37024004 0.80899 0.14647 10.6004 DHX35 409 promoter 27 disjoint 0.04216 chr9 138566444 138566986 0.70452 1.40372 10.5974 N0TCH1 6386 upstream -5248 disjoint 0.04217 chrl4 56335448 56336113 0.57842 0.00267 10.5956 OTX2 5984 downstream -134 disjoint 0.04218 chrl5 88546409 88547161 1.11463 0.59144 10.5926 SEMA4B 844 inside intron -82 disjoint 0.04219 chr20 2623982 2624488 2.42461 1.58985 10.5924 IDH3B 31140 upstream -1284 disjoint 0.04219 chrX 125511357 125511755 -0.327 0.80959 10.5894 WDR40B 2759 inside exon 1637 disjoint 0.04221 chrlO 103579622 103580128 0.87582 0.08359 10.5888 KCNIP2 9472 inside intron 148 disjoint 0.04221 chrl7 44019189 44019659 0.73255 -0.0905 10.5812 HOXB5 6442 downstream -4187 disjoint 0.04225 chr5 76148202 76149046 0.33879 1.01607 10.5807 F2RL1 1563 promoter 1272 disjoint 0.04225 chrX 30162237 30162599 0.33866 1.38947 10.5779 MAGEB3 3764 inside intron 12494 disjoint 0.04227 chr21 16882221 16883147 -0.1754 0.32437 10.5777 C21orf34 393652 inside intron -857350 disjoint 0.04227 chr3 174068612 174069176 0.69596 1.45142 10.5765 SPATA16 272518 downstream -117076 disjoint 0.04227 chrl7 34284609 34285288 0.45964 1.22252 10.5764 LASP1 4716 inside intron -3979 disjoint 0.04228 chr20 61160022 61160528 0.61778 1.40528 10.5748 BHLHB4 51236 upstream 5498 disjoint 0.04228 chrl7 56838609 56839199 0.83938 -0.0074 10.5723 TBX2 6571 inside intron -561 disjoint 0.0423 chrl6 83765392 83766186 0.538 1.17133 10.5698 FAM92B 61778 upstream -2860 disjoint 0.04231 chr3 187985321 187986064 -0.1665 0.41226 10.5686 EIF4A2 1267 covers exon(s) -582 disjoint 0.04232 chr3 181984939 181985409 1.01332 1.83947 10.5685 FXR1 127736 upstream 43448 disjoint 0.04232 chr8 24911995 24912751 0.2922 0.96681 10.5618 NEFL 41953 upstream 675 disjoint 0.04236 chrl4 52086729 52087322 0.93338 1.67542 10.5615 IAA1344 1640 inside intron 1466 disjoint 0.04236 chr4 5946232 5946988 1.45648 2.16051 10.5604 CR P1 547 promoter -215 disjoint 0.04237 chrl9 7600953 7601699 0.50691 1.10698 10.5586 XAB2 515 promoter -356 disjoint 0.04237 chrl2 56201583 56202188 1.03366 0.37975 10.5577 MBD6 737 promoter 401 disjoint 0.04238 chrX 139160165 139160566 0.83896 1.85588 10.5572 SOX3 254324 downstream -158732 disjoint 0.04238 chr6 33504121 33504570 0.47039 1.35949 10.5557 SYNGAP1 8297 inside intron 0 overlap 0.04239 chrl 151922405 151923339 1.51047 1.94428 10.5554 NPR1 4669 covers exon(s) -3406 disjoint 0.04239 chrl4 83936769 83937272 0.90172 1.67459 10.5552 FLRT2 1128968 upstream 1128975 disjoint 0.04239 chrl 9 42777801 42778352 -0.0843 0.69862 10.5523 ZNF540 43654 inside intron -150 disjoint 0.0424 chrl 7 46597802 46598338 1.08869 0.18607 10.5522 NME2 0 overlaps 5' 281 disjoint 0.0424 chrl4 34942032 34942715 0.43683 1.06758 10.5476 NFKBIA 979 covers exon(s) 83 disjoint 0.04242 chrl2 50548413 50548778 2.0027 0.91867 10.546 ANKRD33 19232 upstream 116 disjoint 0.04243 chr2 130060228 130060816 0.18937 0.91876 10.5435 RAB6C 392888 upstream 697 disjoint 0.04244 chr22 30126085 30126800 -0.2042 0.6876 10.5424 DRG1 547 covers exon(s) -127 disjoint 0.04244 chrl 7 4922633 4923139 0.1925 1.2781 10.5396 ZFP3 156 inside intron 0 overlap 0.04246 chrl 6 83822743 83823108 0.8019 1.88766 10.5378 FAM92B 119129 upstream 3585 disjoint 0.04247 chr2 42131019 42131451 0.79558 1.66852 10.531 LOC91461 1763 inside intron 50353 disjoint 0.04251 chr8 71480055 71480596 1.85283 0.70611 10.5307 NCOA2 1482 promoter -731 disjoint 0.04251 chr6 20319143 20319730 0.81634 0.15966 10.528 E2F3 190646 upstream 517 disjoint 0.04252 chrl 9 13066301 13066847 0.94428 0.25317 10.5244 NF 98718 overlaps exon 1528 disjoint 0.04253 upstream chr7 13998070 13998504 0.18213 1.0634 10.5198 ETV1 2782 upstream -332 disjoint 0.04256 chrl6 30347855 30348662 -0.1313 0.47784 10.5151 XTP3TPA 211 covers exon(s) 0 overlap 0.04258 chrl l 92250583 92257442 0.35254 1.09723 10.5133 MTNR1B 84994 upstream -267 disjoint 0.04259 chr6 31815011 31815654 0.21061 0.88609 10.5116 MSH5 98 promoter 0 overlap 0.0426 chr8 134649882 134650313 0.93346 1.76695 10.5115 ST3GAL1 3030 inside intron 838 disjoint 0.0426 chrl5 21673697 21674281 0.37644 1.12794 10.5078 NDN 190155 upstream 43 disjoint 0.04262 chrl2 50729766 50730262 1.59724 0.65196 10.5053 NR4A1 6004 inside intron 558 disjoint 0.04263 chrl 1285741 1286685 0.79313 1.85231 10.4997 MXRA8 1964 promoter -4752 disjoint 0.04266 chr2 3362968 3363734 0.3555 1.04989 10.4988 TTC15 516 inside intron 0 overlap 0.04266 chr3 189353108 189354054 0.98618 0.49452 10.4947 LPP 59360 upstream 115 disjoint 0.04269 chrl2 31703504 31703977 0.20221 0.84122 10.4943 MGC50559 117 overlaps exon -42737 disjoint 0.04269 downstream
chrl 239587526 239588078 0.38028 1.20373 10.4936 RGS7 426 promoter -113 disjoint 0.04269 chr2 54410456 54411106 0.01392 0.57411 10.4919 FLJ40298 468 promoter 28 disjoint 0.0427 chrll 73035319 73035756 2.58809 1.53313 10.4916 PLEKHB1 449 inside intron 13692 disjoint 0.0427 chr5 179037601 179038047 1.14481 1.98917 10.4857 CANX 20488 upstream 0 overlap 0.04273 chr2 74521745 74522251 0.94075 0.18027 10.4748 RTKN 316 inside intron 0 inside 0.04279 chr7 157245733 157246167 0.71439 1.64958 10.4732 PTPRN2 827011 inside intron -1947 disjoint 0.04279 chrl l 2103092 2105149 0.56451 1.11896 10.472 IGF2 11630 downstream 5460 disjoint 0.0428 chr2 111592086 111592884 0.82076 0.25667 10.4703 BCL2L11 2077 promoter 0 inside 0.04281 chrl 5 71713104 71713830 0.28477 0.88994 10.4622 NPTN 299 promoter -126 disjoint 0.04285 chr4 166520409 166520846 1.61879 0.75737 10.4621 CPE 866 inside intron -291 disjoint 0.04285 chrl9 13768536 13769189 0.49708 1.19239 10.4617 ZSWIM4 1263 inside intron -887 disjoint 0.04285 chr2 120233007 120233390 1.02404 -0.0219 10.4598 PTPN4 286 promoter 146 disjoint 0.04286 chrl 111791902 111792563 0.35416 0.90384 10.4564 WDR77 789 inside intron 264 disjoint 0.04288 chrl 9 3875286 3875753 1.00598 2.02685 10.4563 ATCAY 43648 overlaps exon 8720 disjoint 0.04288 upstream
chrl l 2463868 2464974 0.18861 0.82296 10.4523 KC Q1 24609 inside intron -40474 disjoint 0.0429 chr2 72230668 72231279 0.00735 0.65968 10.4474 CYP26B1 2198 promoter 0 overlap 0.04292 chr2 239860899 239861264 1.14502 2.25635 10.4468 HDAC4 126315 inside intron 441 disjoint 0.04292 chrX 151750755 151751189 -0.0356 0.83545 10.4377 NSDHL 589 inside intron -348 disjoint 0.04297 chrl 245563062 245563568 1.909 1.18727 10.4354 ZNF496 1395 promoter -599 disjoint 0.04298 chr!2 124235767 124236270 0.93128 0.14224 10.4313 AACS 119890 downstream 0 overlap 0.04301 chrl l 2594197 2595013 0.44026 0.98427 10.4302 CNQ1 154938 inside intron -34152 disjoint 0.04301 chr2 161991122 161991802 1.09633 0.51369 10.429 TBR1 10257 downstream 25 disjoint 0.04302 chr2 26059335 26059736 1.64596 0.65635 10.4273 KIF3C 429 promoter -182 disjoint 0.04302 chr4 120351829 120352384 1.89763 1.06556 10.4267 MY0Z2 75361 downstream 628 disjoint 0.04302 chr8 22517137 22517846 0.47042 1.55854 10.4253 C8orf58 4071 overlaps 3' 191 disjoint 0.04303 chrl3 46024110 46024610 1.52651 0.8217 10.4199 LRCH1 693 promoter 361 disjoint 0.04306 chr7 27191794 27192297 1.06605 0.31681 10.418 H0XA11 435 promoter 0 overlap 0.04307 chr2 220058809 220059351 1.99668 1.07312 10.4169 GMPPA 12505 upstream -781 disjoint 0.04307 chrlO 130090853 130091320 0.53466 1.26141 10.4152 MKI67 276209 upstream 97529 disjoint 0.04308 chrl 226395152 226395652 0.41467 1.2271 10.4149 GUK1 548 covers exon(s) 0 overlap 0.04308 chrl 7 44792570 44793309 0.05924 0.60332 10.4144 ZNF652 1524 inside intron 596 disjoint 0.04308 chr22 41093634 41094140 1.09342 0.30734 10.4132 NFAM1 64199 downstream 193 disjoint 0.04309 chr9 71623907 71624404 0.83265 1.81448 10.4118 C9orfl35 1146 promoter -58984 disjoint 0.04309 chr2 66505618 66506851 0.60609 0.26428 10.4082 EIS1 9184 upstream 0 overlap 0.04311 chrl 9 15440847 15441314 1.02335 1.89389 10.4015 PGLYRP2 9997 inside exon 68 disjoint 0.04314 chrl9 44446157 44446558 0.86296 1.80851 10.401 IL28A 4438 upstream 255 disjoint 0.04315 chrl 3 24010894 24011660 0.17388 1.25198 10.4009 PARP4 25947 upstream 1944 disjoint 0.04315 chr7 158466775 158468327 1.02112 1.75728 10.3999 WDR60 124746 downstream -6614 disjoint 0.04315 chrl9 53935924 53936460 1.85609 1.21532 10.397 IZUM01 5517 overlaps 3' -1150 disjoint 0.04317 chr6 36099600 36100276 1.48822 0.81917 10.3954 SLC26A8 0 overlaps 5' 2947 disjoint 0.04318 chrl l 2804667 2805275 0.926 1.62211 10.3903 KCNQ1 365408 inside intron -19207 disjoint 0.0432 chrl l 76860929 76861716 0.42798 -0.0729 10.39 PAK1 864 inside intron 125 disjoint 0.0432 chr5 6898368 6899048 0.5716 1.13546 10.3892 POLS 130651 downstream -22091 disjoint 0.0432 chr2 72224160 72224916 1.44458 0.34419 10.384 CYP26B1 3554 covers exon(s) 0 overlap 0.04323 chr2 54639368 54639978 0.65682 0.04626 10.3796 SPTBN1 334 overlaps exon 0 overlap 0.04325 downstream
chr3 159294253 159294759 0.96279 0.23725 10.3726 SHOX2 8760 downstream 0 overlap 0.04328 chrl8 43711884 43712514 1.09578 0.15229 10.3724 SMAD2 664 promoter 0 overlap 0.04329 chr3 62330416 62331132 0.55325 -0.01 10.3723 FEZF2 2928 overlaps exon 0 overlap 0.04329 upstream
chrl8 53169443 53169772 0.07823 1.24875 10.3689 ST8SIA3 946 promoter 933 disjoint 0.0433 chrl 165154952 165155458 0.77489 1.50207 10.3684 ClorS2 55726 overlaps exon 942 disjoint 0.04331 upstream
chrl 171711549 171712244 0.23665 1.28958 10.3639 PRDX6 864 promoter 357 disjoint 0.04333 chrl l 1893866 1894234 0.75939 1.67608 10.3638 TNNT3 3210 upstream 9873 disjoint 0.04333 chrl l 118471800 118472824 0.68138 1.3705 10.3628 DPAGT1 5170 overlaps 3' -126 disjoint 0.04333 chrl l 810463 810966 0.58917 1.27711 10.3618 PNPLA2 1562 inside intron -192 disjoint 0.04334 chrX 122139487 122139792 0.18749 0.63937 10.3604 GRIA3 6046 upstream 6641 disjoint 0.04334 chr22 26530326 26530724 2.18067 1.26866 10.3563 MN1 2841 upstream -1734 disjoint 0.04336 chrl l 65000701 65001358 0.34549 1.05349 10.3538 SCYL1 47765 upstream 0 overlap 0.04338 chr20 54932635 54933211 0.7759 -0.0097 10.3532 BMP7 341496 downstream 543 disjoint 0.04338 chrl 61317401 61318197 0.75476 0.27092 10.3478 NFIA 2685 upstream -1936 disjoint 0.04341 chrl 2 130428318 130428720 1.03042 2.0827 10.3347 LOC338797 11802 downstream 54719 disjoint 0.04347 chr5 154296752 154297300 0.33571 1.30776 10.3332 OEMIN5 585 covers exon(s) 352 disjoint 0.04348 chr2 117530612 117531013 0.70798 1.78329 10.3205 DDX18 757711 upstream 757569 disjoint 0.04354 chr9 1 15956597 115957244 -0.1354 0.41444 10.318 COL27A1 807 promoter 0 overlap 0.04355 chrl 2155013 2155519 0.69444 1.42192 10.3176 SKI 5020 inside intron -3980 disjoint 0.04356 chr6 168597647 168598150 1.29223 1.89417 10.316 SMOC2 12768 inside intron -11698 disjoint 0.04356 chrl 8 75367686 75368030 0.57405 1.62631 10.313 NFATC1 106373 inside intron 3751 disjoint 0.04358 chr5 140709964 140710470 1.29672 2.12866 10.3093 PCDHGB1 0 overlaps 5' 953 disjoint 0.04359 chrl 9 54213778 54214581 0.54828 1.36384 10.3082 LHB 1620 promoter 0 overlap 0.0436 chr7 4147193 4147591 1.12476 2.03018 10.3054 SDK1 839588 inside intron -10914 disjoint 0.04361 chr6 132311094 132311574 0.06862 1.13354 10.3052 CTGF 2636 inside exon 1475 disjoint 0.04361 chrl 7 38369528 38370303 0.39135 1.05794 10.3005 AARSD1 15242 covers exon(s) 0 cover 0.04364 chr2 174916104 174916541 0.87599 0.09509 10.2967 CIR 52147 downstream 120 disjoint 0.04366 chr5 93472282 93472911 0.52723 1.09347 10.2899 C5or£21 36062 upstream 0 overlap 0.0437 chr5 178705526 178705996 1.51729 0.75953 10.2848 ADAMTS2 592 promoter -126 disjoint 0.04372 chr8 1491978 1492502 0.99143 1.70955 10.2831 DLGAP2 55003 inside intron -2900 disjoint 0.04373 chr8 1259989 1260387 0.9146 1.82982 10.2773 DLGAP2 176588 upstream -6244 disjoint 0.04376 chr4 111757920 111758409 0.93607 0.09026 10.2754 PITX2 5293 overlaps 3' 268 disjoint 0.04377 chr6 27890663 27891301 0.01327 0.68691 10.2741 HIST1H2BM 0 covers -199 disjoint 0.04378 chrl 153369696 153370340 1.07021 0.44297 10.2734 EFNA1 2724 inside intron -2621 disjoint 0.04378 chr2 122122149 122122761 -0.2248 0.63632 10.2734 CLASP1 760 inside intron 107 disjoint 0.04378 chrl2 118075929 118076330 1.03233 0.15645 10.2712 KIAA1853 172151 inside intron 0 overlap 0.04379 chrl9 45463371 46463874 0.06481 0.79844 10.2708 HNRPUL1 1296 inside intron -418 disjoint 0.04379 chr22 49024380 49024919 0.91428 1.64895 10.2697 TUBGCP6 607 inside exon 68 disjoint 0.04379 chr4 140435491 140436230 0.58046 1.31437 10.2685 NDUFC1 176 covers exon(s) 0 overlap 0.0438 chrI9 8306746 8311662 0.69739 1.61201 10.2653 ANKRD47 2483 covers exon(s) -285 disjoint 0.04382 chrl5 68554470 68554883 0.53032 1.47915 10.2626 UACA 226790 downstream 109551 disjoint 0.04384 chr7 20784759 20785662 1.13637 0.44114 10.2604 SP8 7367 downstream -7 disjoint 0.04385 chr6 96571591 96572166 0.57737 1.218 10.2518 FUT9 1002 inside intron -734 disjoint 0.04389 chr2 230493033 230493632 0.03891 0.57077 10.2474 TRIP12 1266 inside intron 524 disjoint 0.04391 chrl l 2020719 2021360 -0.1779 0.48374 10.2415 IGF2 95419 downstream -30152 disjoint 0.04394 chr3 49670745 49671176 0.86886 1.77999 10.2394 BSN 103820 inside intron -5412 disjoint 0.04395 chr8 22604280 22604927 0.80557 0.33222 10.2394 EGR3 1832 inside exon 0 inside 0.04395 chr9 132990145 132990579 0.04798 0.92302 10.2391 NUP214 222 promoter 26 disjoint 0.04395 chrl9 12265060 12265671 0.35025 0.95662 10.2378 ZNF44 965 overlaps exon 543 disjoint 0.04395 upstream
chrX 9391085 9391600 0.82163 0.12456 10.2355 TBL1X 1438 promoter 1230 disjoint 0.04397 chrl l 2079880 2080503 0.69461 1.54664 10.2338 IGF2 36276 downstream 30106 disjoint 0.04397 chrl2 54760828 54761480 0.80256 0.08797 10.2287 ERBB3 670 inside intron -168 disjoint 0.044 chrl5 43358473 43359202 0.12536 0.62648 10.2262 SLC28A2 26748 downstream -79929 disjoint 0.04401 chr4 172202321 172202695 1.04156 2.06893 10.2218 GALNT17 768536 upstream 767614 disjoint 0.04403 chrl9 38358712 38359179 0.57699 1.33842 10.2218 PQWD 43875 downstream 103 disjoint 0.04403 chr7 157888302 157888757 0.9883 1.93833 10.22 PTPRN2 184421 inside intron 2549 disjoint 0.04404 chrl8 7028662 7029169 0.50051 1.31178 10.2192 LAMA1 78643 covers exon(s) -27174 disjoint 0.04404 chr8 60195273 60195779 1.02074 0.40661 10.2189 TOX 953 promoter 0 overlap 0.04404 chrl5 42791523 42792197 -0.018 0.73622 10.216 B2M 547 inside intron 0 overlap 0.04406 chrlO 132749748 132750403 0.92153 1.77659 10.2102 TCERG1L 249570 downstream 13243 disjoint 0.0441 chr7 28414030 28414884 1.34576 0.77771 10.2043 CREB5 108566 inside intron 357 disjoint 0.04412 chr2 159535509 159536081 0.11907 0.74614 10.202 TANC1 2118 inside intron -862 disjoint 0.04413 chr5 122462537 122463036 1.19276 0.34273 10.2003 PPIC 62214 upstream 0 inside 0.04414 chrlO 124881149 124881586 0.07246 0.92054 10.1993 HMX2 16041 upstream 670 disjoint 0.04415 chrlO 95742573 95743001 1.95361 0.98764 10.195 PLCE1 734 promoter 336 disjoint 0.04417 chrl9 18820116 18820622 0.43966 1.24493 10.191 UPF1 16373 inside intron 6013 disjoint 0.04419 chrlS 33092753 33093157 0.49011 1.4862 10.1899 BRUNOL4 306783 overlaps exon -4149 disjoint 0.04419 downstream
chr3 173242344 173242919 0.32133 1.05512 10.1894 FNDC3B 1265 inside intron -929 disjoint 0.0442 chrl4 20992822 20993541 0.26552 0.85611 10.1828 RAB2B 21419 downstream 541 disjoint 0.04423 chr2 81279077 81279475 1.22371 2.14884 10.1808 CTNNA2 1685444 downstream -3034 disjoint 0.04424 chrl6 24279837 24280236 0.93885 2.06344 10.1766 CACNG3 105461 overlaps exon -104809 disjoint 0.04426 upstream
chrl5 99236055 99236696 1.12119 0.67685 10.1758 ALDH1A3 887 promoter 88 disjoint 0.04426 chr20 38752910 38753560 0.86395 0.28319 10.1716 AFB 1621 promoter 0 overlap 0.04428 chr4 46689234 46689781 0.69287 1.50912 10.1697 GABRA4 555 covers exon(s) 104 disjoint 0.04429 chrl3 50693451 50694042 0.99795 0.21569 10.1694 FAM124A 465 promoter 451 disjoint 0.04429 chr4 24412880 24413883 0.46469 1.34595 10.1677 SOD3 7728 downstream -1880 disjoint 0.0443 chr3 129687777 129688211 1.04268 0.19381 10.1673 GATA2 6506 overlaps exon 0 overlap 0.0443 upstream
chr6 168335674 168336091 0.98084 1.89071 10.1665 FRMD1 112987 upstream -1431 disjoint 0.04431 chr2 119316242 119316834 0.85577 0.16956 10.1642 EN1 5394 inside exon 0 inside 0.04432 chr2 47653053 47653595 0.86234 1.67178 10.1635 KCNK12 2080 promoter -383 disjoint 0.04433 chr3 73130222 73130584 0.1404 1.1088 10.1634 PPP4R2 1414 inside intron -1018 disjoint 0.04433 chrl 154527670 154528038 0.398 1.42274 10.16 TMEM79 8308 overlaps exon 0 overlap 0.04435 upstream
chrl9 16601129 16601494 0.57196 1.64457 10.1572 CRSP7 1115 promoter -450 disjoint 0.04436 chrl 4 36187212 36187889 0.44505 -0.1151 10.1528 PAX9 12766 upstream 0 overlap 0.04438 chrl l 71630813 71631283 1.56793 0.74346 10.1522 PH0X2A 1568 inside intron -637 disjoint 0.04439 chrl 18575424 18575789 1.07607 2.02463 10.1518 IGSF21 268598 overlaps exon 93 disjoint 0.04439 downstream
chr3 170865761 170866093 1.14878 0.02375 10.1512 MDS1 1594 promoter -2014 disjoint 0.04439 chr5 1706187 1706708 0.77808 1.52014 10.1485 AYTL2 129112 upstream 272 disjoint 0.04441 chr9 29200904 29201646 0.02251 0.5808 10.1463 LR N6C 491602 upstream 525 disjoint 0.04442 chr6 105507399 105508046 0.84924 0.17761 10.1436 LIN28B 3569 upstream 0 cover 0.04444 chr2 101457560 101458136 0.38198 1.33229 10.1436 CREG2 87072 upstream 0 overlap 0.04444 chrl 200420172 200420535 0.4052 1.60165 10.1432 LGR6 9205 upstream 9046 disjoint 0.04444 chrlO 71009329 71010045 0.21825 0.72538 10.1426 EUR0G3 6202 upstream -648 disjoint 0.04444 chr6 160103713 160104288 0.9897 1.78594 10.1403 ACAT2 639 covers exon(s) 0 overlap 0.04446 chrl 60311772 60312348 1.21274 0.62058 10.1392 Clorf87 0 overlaps 5' 0 cover 0.04446 chr8 135794905 135795380 0.85707 1.94495 10.1357 ZFAT1 443 promoter -158 disjoint 0.04448 chr6 157139259 157139834 0.15298 0.84346 10.1343 ARID1B 943 promoter -56182 disjoint 0.04448 chrH 88513962 88514603 0.75446 -0.0195 10.1336 TTC8 153232 downstream 48285 disjoint 0.04449 chr9 134984815 134985249 0.68212 1.56984 10.1298 RALGDS 1132 inside intron 541 disjoint 0.04451 chr4 36924949 36925386 0,81232 1.6757 10.127 C4orfl9 336863 upstream -1575 disjoint 0.04453 chrX 119035313 119035848 -0.13 0.65119 10.124 PEPP-2 59886 downstream -1551 disjoint 0.04454 chrlO 62883310 62883803 0.77284 0.06082 10.1238 TMEM26 97 promoter -295 disjoint 0.04454 chr7 142696528 142696926 0.00127 0.92162 10.1238 CASP2 1005 inside intron -596 disjoint 0.04454 chr3 37008264 37009016 0.16036 0.68345 10.1221 EPM2ADP1 782 inside exon 216 disjoint 0.04455 chrl 7 70396672 70398015 1.24743 1.84518 10.1183 FADS6 3284 inside intron 2929 disjoint 0.04458 chrl 214533453 214533890 1.1334 1.7935 10.1153 USH2A 129470 inside intron 307072 disjoint 0.0446 chrl 7 35550669 35551466 -0.215 0.40189 10.1138 CASC3 637 covers exon(s) -17639 disjoint 0.0446 chrl 7 76421055 76421630 0.73029 1.33826 10.1123 KIAA1303 287836 inside intron -7300 disjoint 0.04461 chr5 72628111 72628926 1.70434 1.11031 10.1082 TMEM174 128282 downstream 977 disjoint 0.04463 chrX 74882540 74883454 0.40719 1.17343 10.1038 MAGEE2 38341 downstream -222698 disjoint 0.04465 chr4 85724414 85724873 1.66527 0.58372 10.1029 CDS1 1334 inside intron -497 disjoint 0.04466 chrl 5 61120483 61121207 1.78608 1.02436 10.1023 TPM1 683 promoter 79 disjoint 0.04466 chr20 32161965 32162399 0.1914 1.07084 10.0998 EIF2S2 1346 inside intron 519 disjoint 0.04467 chrl 32311554 32312090 0.23821 0.97206 10.0997 TMEM39B 439 inside intron 0 overlap 0.04467 chr9 138639687 138640262 1.26555 1.90089 10.0958 EGFL7 36935 upstream 6459 disjoint 0.0447 chrl 9 48770878 48771345 -0.3097 0.45017 10.094 XRCC1 209 covers exon(s) 77 disjoint 0.04471 chr3 5000436 5000904 1.01926 1.98333 10.0933 BHLHB2 4229 inside exon -469 disjoint 0.04471 chrl9 9981288 9981833 -0.1815 0.58674 10.0899 COL5A3 313 inside intron 0 overlap 0.04473 chrl l 1 15411046 115411378 1.40672 2.45737 10.087 IGSF4 530722 upstream -274719 disjoint 0.04475 chrl 228270857 228271510 0.42299 0.97947 10.086 GALNT2 1207 inside intron -25 disjoint 0.04475 chr3 1 1012134 1 1012535 1.14355 1.99687 10.0855 SLC6A1 2679 inside intron -1750 disjoint 0.04475 chr3 187986152 187986610 0.12173 1.09723 10.0832 EIF4A2 2098 covers exon(s) -1413 disjoint 0.04477 chrl 196154971 196155651 0.4757 0.01222 10.0801 LHX9 1832 inside intron -557 disjoint 0.04478 chr5 174077445 174078438 0.03482 0.53073 10.0711 MSX2 5742 upstream 2037 disjoint 0.04483 chrl 9 40321848 40322481 0.84229 1.41994 10.068 FXYD1 277 inside intron 1715 disjoint 0.04485 chr7 54794674 54795429 0.30452 0.97466 10.0606 SEC61G 242 promoter 0 overlap 0.04489 chrl 6 66674813 66675511 0.85836 0.15912 10.0581 NFATC3 1364 promoter 554 disjoint 0.0449 chr21 45882748 45883218 0.76249 1.5369 10.0531 SLC19A1 95970 upstream -500 disjoint 0.04493 chrlO 42367869 42368420 0.00655 0.69712 10.0502 ZNF33B 85577 downstream 0 inside 0.04494 chr8 949053 949553 1.07289 1.69426 10.0486 ERICH1 277828 upstream 169 disjoint 0.04495 chr22 48483295 48483657 0.43271 1.44777 10.0479 C22orS4 46106 upstream 415 disjoint 0.04496 chr6 10830535 10831023 0.41362 1.241 10.0456 TMEM14C 300 promoter 0 overlap 0.04497 chrl6 1300673 1301284 0.29909 0.85569 10.0452 UBE2I 1035 inside intron -440 disjoint 0.04498 chrl7 64106041 64106511 0.23485 1.00753 10.0449 FAM20A 2178 inside intron 1156 disjoint 0.04498 chr2 70384177 70384788 0.816 1.37693 10.0397 FLJ14668 1473 promoter -1336 disjoint 0.045 chrl9 18386344 18386954 0.50479 1.44322 10.0395 SSBP4 4181 upstream 1656 disjoint 0.045 chr2 205119566 205120069 0.35333 1.06725 10.0392 PARD3B 806 inside intron -411 disjoint 0.04501 chrX 56274838 56275275 0.6733 -0.1491 10.0361 KLF8 356 promoter 401 disjoint 0.04502 chr20 44073525 44074028 1.11828 1.80521 10.036 MMP9 2572 covers exon(s) 0 overlap 0.04502 chrlO 38305564 38305995 0.14441 0.98131 10.0345 ZNF25 106 promoter 0 overlap 0.04503 chr2 86523161 86523737 -0.0191 0.6508 10.032 JMJD1A 1208 inside intron -203 disjoint 0.04504 chrl l 32066539 32067207 0.08136 0.75012 10.0315 RCN1 2059 promoter 1 63 disjoint 0.04504 chrl l 2414735 2415445 0.88533 1.4128 10.0243 KCNQ1 7351 upstream 6302 disjoint 0.04508 chrl9 11345103 11345879 1.12815 1.78709 10.024 C19orf39 503 promoter 407 disjoint 0.04508 chr5 134390492 134390965 1.3448 0.5789 10.0219 ΡΓΓΧ1 6921 downstream 26 disjoint 0.04509 chr6 28149227 28149628 1.30719 2.21819 10.021 ZNF165 4922 upstream 30815 disjoint 0.0451 chr2 172665441 172666046 0.54441 -0.0554 10.0187 DLX1 6988 downstream 1467 disjoint 0.04511 chr9 135455552 135456130 1.00724 1.59705 10.0185 ADAMTSL2 65757 downstream 7861 disjoint 0.04511 chrl7 34085286 34086135 1.1513 0.52876 10.0164 MLLT6 29265 upstream -260 disjoint 0.04512 chrl 47951921 47952636 0.75724 1.45849 10.0149 F0XD2 277646 downstream -2815 disjoint 0.04513 chrl 226699894 226700577 0.90593 0.34752 10.0149 HIST3H2A 11605 downstream 0 overlap 0.04513 chrl l 34417349 34417809 -0.0596 0.98347 10.0142 CAT 296 inside intron 0 overlap 0.04513 chr5 73970372 73970999 -0.1584 0.44914 10.0099 ENC1 1273 inside intron 482 disjoint 0.04515 chr9 136359227 136360147 0.53921 1.06781 10.0036 RXRA 997 inside intron -438 disjoint 0.04519 chrl 8 26877750 26878253 0.24204 0.98192 10.0027 DSC3 1064 promoter -635 disjoint 0.0452 chr21 33938444 33938988 0.34399 1.05828 10.0001 rrsNi 1791 inside intron -782 disjoint 0.04521 chr6 24826109 24826689 0.07601 0.72281 9.99545 C6orf62 692 inside intron 1677 disjoint 0.04523 chrll 67130174 67130749 0.53187 1.26565 9.99321 Cl lorf72 3 overlaps exon 0 overlap 0.04524 downstream
chrl 9 49023637 49023969 0.84112 1.92747 9.99264 LYPD5 7012 upstream -6788 disjoint 0.04525 chrl l 59138466 59139005 0.21259 0.88183 9.99106 OSBP 1187 inside intron 258 disjoint 0.04525 chr7 100398484 100398984 0.31237 1.02067 9.99061 MUC17 51099 upstream -1971 disjoint 0.04526 chr2 176698813 176699280 1.04925 0.17915 9.98569 HOXD9 3480 downstream -980 disjoint 0.04528 chrl 7 4404264 4404980 0.33318 0.79S26 9.98192 MYBBP1A 412 overlaps two exons 0 overlap 0.0453 chrl 148126311 148127372 -0.0647 0.27136 9.98162 HIST2H2AB 222 promoter -217 disjoint 0.0453 chr5 180565221 180566392 0.73737 0.05838 9.98012 TRI 7 439 promoter -46 disjoint 0.04531 chrlO 98335061 98335781 0.08136 0.61941 9.97641 TM9SF3 1017 inside intron 258 disjoint 0.04532 chr8 17314554 17314991 1.96671 0.98882 9.97604 MTMR7 215 inside intron 0 overlap 0.04533 chr4 5938602 5939069 1.36578 2.11833 9.97501 CR P1 2146 inside intron 1035 disjoint 0.04533 chrl 9 58960996 58961439 1.16251 2.03609 9.96992 NALP12 57965 downstream 2113 disjoint 0.04536 chr9 126068939 126069409 0.88836 1.6916 9.96762 NE 6 8870 inside intron -8377 disjoint 0.04537 chrl 7 23670917 23671629 0.06082 0.61298 9.96607 TMEM97 670 inside intron -185 disjoint 0.04538 chrl3 32489585 32489989 1.07422 0.12464 9.95927 KL 1015 inside intron -157 disjoint 0.04542 chr2 222877489 222878069 0.79701 0.05287 9.9577 FLJ32447 6380 inside exon -237 disjoint 0.04542 chr3 73022478 73022914 0.57275 1.41266 9.95644 SHQ1 42191 upstream 37772 disjoint 0.04543 chrl6 33841802 33842788 0.01863 0.54683 9.95193 LOC649159 27215 downstream 1 113 disjoint 0.04546 chrl l 6458220 6458873 0.52213 1.388 9.95056 ARFIP2 297 overlaps exon 126 disjoint 0.04546 upstream
chr22 19728700 19729843 0.4718 1.30367 9.94924 LOC400891 426 promoter 136 disjoint 0.04547 chrl 8 45342733 45343341 0.7654 0.01134 9.94666 LIPG 309 overlaps exon -207 disjoint 0.04548 downstream
chr20 17611540 17612013 1.37498 0.61115 9.9465 R BP1 613 promoter -84 disjoint 0.04548 chrl9 10844450 10844956 0.67491 1.41406 9.94365 CARM1 1198 inside intron -184 disjoint 0.04549 chr20 56858042 56858804 0.83196 0.05993 9.94194 GNAS 9853 inside intron 1320 disjoint 0.0455 chrl l 2522675 2523712 -0.1913 0.1152 9.94178 KCNQ1 83416 inside intron -10481 disjoint 0.0455 chrl 154808516 154809265 -0.1187 0.40864 9.94054 IQGAP3 0 overlaps 5' 0 cover 0.04551 chr8 97577097 97577777 -0.234 0.28823 9.93888 SDC2 2040 inside intron -314 disjoint 0.04552 chrl 2 47867377 47868404 0.00832 0.51802 9.93395 TUB A3 723 inside intron 0 overlap 0.04555 chrll 3774109 3774836 0.14058 0.8391 9.93156 NUP98 631 inside intron 187 disjoint 0.04556 chr6 27745061 27745561 0.64741 -0.0408 9.93107 HIST1H2BL 138126 downstream 10211 disjoint 0.04556 chrl 150078160 150078594 0.808 -0.0031 9.92814 THEM5 14202 downstream 0 overlap 0.04558 chrl 151909016 151909732 0.2317 0.67214 9.92661 ILF2 370 covers exon(s) 210 disjoint 0.04559 chr8 101730241 101730747 1.10661 0.36182 9.9219 MGC39715 321 overlaps exon 100 disjoint 0.04561 downstream
chr21 26866292 26866729 0.46442 -0.2551 9.91932 CYYR1 722 inside intron 152 disjoint 0.04562 chr7 139577981 139578615 2.14848 1.18157 9.91778 IAA1718 54772 upstream -1156 disjoint 0.04563 chr8 94307622 94308059 0.58142 1.53251 9.91603 RBM12B 514304 downstream -259977 disjoint 0.04564 chrl 9 60321747 60322283 1.37972 0.67837 9.91477 PPP1R12C 1009 promoter -830 disjoint 0.04565
Chrl 6 1998404 1998963 0.35674 1.24316 9.91399 ZNF598 800 inside intron 364 disjoint 0.04565 chrl 110952586 110953336 0.51944 1.11579 9.91299 KCNA2 2719 upstream -877 disjoint 0.04566 chr4 2935759 2936873 0.66307 1.37028 9.9091 GRK4 619 inside intron 0 overlap 0.04568 chrl 9 42033721 42034569 -0.2605 0.29268 9.90074 ZNF345 615 overlaps exon 0 overlap 0.04572 upstream
chr21 41134179 41134646 0.99617 1.72717 9.89947 DSCAM 6262 inside intron 734 disjoint 0.04573 chrlS 90739392 90739859 1.17311 0.3907 9.8989 ST8SIA2 1249 inside intron 0 overlap 0.04574 chr3 37879135 37879725 0.36443 0.95377 9.8974 CTDSPL 463 inside intron -92 disjoint 0.04574 chrl l 8887769 8888416 0.91503 0.34346 9.8961 ST5 657 inside intron 733 disjoint 0.04575 chr22 28442060 28442799 0.71603 1.47998 9.89125 CABP7 3544 upstream 3282 disjoint 0.04577 chr22 39544677 39545078 0.09384 0.9924 9.88416 SLC25A17 259 inside intron 3 disjoint 0.04582 chr2 72943537 72944112 1.53746 0.89958 9.88236 SPR 23943 upstream -13 disjoint 0.04582 chrl 9 52044402 52045079 -0.0086 0.67448 9.87787 AP2S1 963 inside intron 375 disjoint 0.04585 chrl2 2870862 2871191 0.04518 1.14255 9.8763 TULP3 569 inside intron 0 overlap 0.04586 chr9 34371708 34372214 1.69545 1.00591 9.87328 C9orf24 15634 inside intron -557 disjoint 0.04587 chrl 2 54652783 54653591 0.07436 0.70805 9.87195 CDK2 5958 overlaps 3' 312 disjoint 0.04588 chr2 160973519 160973992 1.20224 0.48872 9.8712 RBMS1 84558 inside intron -813 disjoint 0.04588 chr9 97319509 97319979 0.92354 0.17852 9.86941 PTCH1 8858 upstream 0 overlap 0.04589 chr5 1245690 1246235 0.34025 1.03173 9.8639 SLC6A19 8530 upstream 488 disjoint 0.04592 chr9 129369401 129370036 0.37251 1.10775 9.86342 C9or£88 1139 inside intron 325 disjoint 0.04593 chrl 7 34609435 34609908 0.315 1.02198 9.85942 RPL19 153 promoter 104 disjoint 0.04595 chr4 41443103 41443858 0.66485 0.22343 9.85821 PH0X2B 1885 inside intron 83 disjoint 0.04595 chrl 154862139 154862873 0.17434 0.67706 9.85491 HAPLN2 6430 overlaps 3' -232 disjoint 0.04597 chrlO 82202984 82203460 1.433 0.51485 9.85299 TSPAN14 586 promoter 76 disjoint 0.04597 chrl 8 27334123 27334668 0.21757 0.92862 9.85173 DSG2 1954 inside intron -1599 disjoint 0.04598 chr2 169992269 169992703 1.36918 2.28269 9.85154 BBS5 51548 upstream 51424 disjoint 0.04598 chrX 152851307 152852927 0.77329 1.55903 9.85057 ARD1A 734 covers exon(s) 219 disjoint 0.04599 chrl6 49720561 49727037 1.21711 0.45407 9.84965 SALL1 15615 downstream 0 overlap 0.04599 chrl9 11392855 11393289 0.93842 0.17425 9.84673 MGC20983 13690 overlaps exon -265 disjoint 0.04601 upstream
chrl8 10717173 10717860 1.28838 1.95919 9.84456 FAM38B 29360 upstream -506 disjoint 0.04602 chrlO 118885513 118886089 0.92372 0.33738 9.84292 VAX1 1712 overlaps exon 0 overlap 0.04603 downstream
chrl7 67631804 67632387 1.78111 1.01971 9.84195 S0X9 3049 inside exon 0 overlap 0.04603 chrX 53045202 53045639 0.38172 1.14298 9.84098 TMEM29 42302 upstream 794 disjoint 0.04604 chr20 15408674 15408931 0.91819 2.38864 9.83995 C20orfl33 283171 inside intron 1092905 disjoint 0.04604 chrl3 18818550 18819377 0.67165 1.40912 9.8363 TPTE2 189525 downstream -1329 disjoint 0.04606 chr3 151607828 151608438 0.30363 0.94287 9.83217 TSC22D2 1039 promoter 221 disjoint 0.04608 chr8 21836465 21837050 0.41131 0.93338 9.83102 XP07 3338 inside intron -2577 disjoint 0.04609 chrl2 56289379 56289894 1.01403 0.2552 9.82753 DTX3 4509 overlaps 3' 253 disjoint 0.04611 chr2 63136829 63137407 0.94146 0.32487 9.82509 0TX1 5361 inside exon 33 disjoint 0.04613 chrl2 21817559 21817921 1.13078 0.27268 9.81615 KCNJ8 1092 overlaps exon -115526 disjoint 0.04618 upstream
chrX 72585507 72586061 -0.2044 0.42024 9.80947 CDX4 1693 inside intron -1192 disjoint 0.04621 chrl 210941274 210941885 0.34816 0.93796 9.80795 SNFT 1325 promoter -603 disjoint 0.04622 chr8 61985615 61985992 1.22755 0.2058 9.80621 CHD7 231723 downstream -33 disjoint 0.04623 chrl9 63646611 63647117 1.54419 2.27555 9.79866 ZNF132 3211 upstream -2549 disjoint 0.04628 chrl 53457779 53458427 0.10064 0.61931 9.79851 Clorfl23 449 inside intron 106 disjoint 0.04628 chrl 218618384 218618818 0.75662 1.65317 9.79562 RAB3GAP2 106010 upstream -105828 disjoint 0.0463 chr3 135606919 135607422 1.33019 0.64574 9.79172 AM0TL2 30824 upstream 752 disjoint 0.04632 chrl l 6588996 6589466 0.49422 1.12506 9.79112 TAF10 554 covers exon(s) 0 overlap 0.04632 chr6 168723341 168723778 1.21038 2.18791 9.7873 SM0C2 138462 inside intron -6383 disjoint 0.04634 chrl l 118162165 118162752 0.60938 1.36218 9.78646 DDX6 4329 overlaps exon 3763 disjoint 0.04635 upstream
chrl 7 35338554 35338952 -0.1136 0.73364 9.78596 0RMDL3 1175 promoter -976 disjoint 0.04635 chr8 37874159 37874521 2.04003 1.08908 9.78588 RAB11FIP1 1639 inside intron 1091 disjoint 0.04635 chrl5 64335331 64336400 -0.0822 0.36649 9.78393 MEGF11 2203 promoter -2143 disjoint 0.04636 chr3 32859938 32860336 0.83788 -0.1052 9.7819 TR1M71 25425 inside intron -21519 disjoint 0.04637 chrl 5 38517306 38517776 1.52085 0.66537 9.78049 BAHD1 2926 upstream -1548 disjoint 0.04638 chrl 9 45481608 45482009 0.31931 1.22133 9.7788 AKT2 1024 inside intron 568 disjoint 0.04639 chr6 43005783 43006592 0.46404 1.04718 9.77854 TNRC5 863 inside intron -179 disjoint 0.04639 chr22 18131446 18131955 1.47634 0.65103 9.7782 TBX1 7221 covers exon(s) 0 cover 0.04639 chr6 14109491 14110033 1.45961 2.12006 9.77528 R F182 76310 downstream -76002 disjoint 0.0464 chrlO 65627570 65627941 0.22593 1.2394 9.77504 REEP3 676442 downstream -26674 disjoint 0.0464 chrl 4 94304416 94304745 1.22041 0.11723 9.77423 GSC 1506 overlaps exon 0 inside 0.04641 upstream
chr8 17313402 17313833 0.20998 0.98272 9.7736 MT RV 1373 inside intron 1141 disjoint 0.04641 chr2 196742931 196743540 0.3086 0.97644 9.77359 STK17B 979 inside intron 294 disjoint 0.04641 chrX 136338725 136339300 0.61785 0.01833 9.77268 ZIC3 136711 upstream -145 disjoint 0.04641 chrl 6 3170492 3171230 0.97443 0.37007 9.76752 OR1F1 23017 upstream 1606 disjoint 0.04645 chrl l 14883905 14884339 1.46952 0.7769 9.76732 CYP2R1 13579 upstream 0 inside 0.04645 chr4 100788852 100789358 0.29693 1.0626 9.76706 MTTP 73849 downstream 2724 disjoint 0.04645 chrlO 7489527 7489931 1.01544 0.12775 9.76454 SFMBT2 3524 inside intron 0 inside 0.04646 chrl 6 76024699 76025205 0.14263 0.81544 9.75842 ADAMTS18 1306 inside intron 605 disjoint 0.0465 chr20 55272233 55272908 1.05183 0.40446 9.75746 B P7 1799 inside intron 0 overlap 0.0465 chrlO 112242482 112243469 0.0301 0.44181 9.75606 DUSP5 4145 upstream 3684 disjoint 0.04651 chr8 26299116 26299763 0.53885 1.1081 9.75524 BNEP3L . 2677 inside intron -2182 disjoint 0.04651 chr2 31658054 31658769 0.18213 0.79529 9.74797 SRD5A2 774 inside intron 28 disjoint 0.04655 chrl5 92576194 92576805 0.90083 0.28439 9.74757 MCTP2 65693 upstream -211 disjoint 0.04656 chrl 22803077 22803696 0.68463 1.52222 9.74616 EPHA8 40487 downstream -2948 disjoint 0.04656 chr2 37236911 37237348 -0.1644 0.61324 9.74543 EIF2AK2 7005 upstream 57 disjoint 0.04657 chrl 9 61679845 61680228 0.4931 1.53101 9.744 ZNF667 326 inside intron 0 overlap 0.04657 chrl 7 42253499 42254035 0.8631 0.19444 9.74242 WNT3 2419 promoter -1475 disjoint 0.04658 chr20 47236408 47236982 0.42442 1.11398 9.74193 STAU1 1328 inside intron 778 disjoint 0.04658 chrl 149403977 149404342 0.1911 1.08987 9.73682 LYSMD1 617 overlaps exon -17980 disjoint 0.04662 downstream
chr2 104850885 104851460 0.97787 0.35063 9.73233 POU3F3 12485 downstream -27 disjoint 0.04665 chrl 85513786 85514331 -0.038 0.55052 9.73139 BCL10 1839 inside intron 122 disjoint 0.04665 chrl2 131267260 131267589 0.85239 1.93363 9.73118 GALNT9 10735 upstream -3583 disjoint 0.04665 chr2 24252121 24252415 0.35215 1.56564 9.7305 FLJ30851 646 inside intron 0 overlap 0.04666 chr7 76881860 76882472 1.99536 1.0547 9.72843 LOC54103 8500 upstream 304 disjoint 0.04667 chr9 106035553 106035918 -0.0322 0.87865 9.72755 SMC2 138902 downstream -138939 disjoint 0.04668 chrl 7 40401554 40402060 0.62738 -0.0969 9.72144 C1QL1 385 promoter 0 overlap 0.04671 chr21 43185676 43186113 0.69969 1.57248 9.72107 NDUFV3 333 promoter 0 overlap 0.04671 chrl l 32407847 32408446 1.01256 0.32638 9.721 WT1 5216 inside intron 274 disjoint 0.04671 chr5 176758128 176758457 1.53403 2.61698 9.71844 SLC34A1 14068 overlaps 3' 1230 disjoint 0.04672 chr8 142502654 142503274 1.90175 2.4846 9.71635 PTP4A3 1466 inside intron 2941 disjoint 0.04673 chr7 117296427 117297349 0.23865 0.68756 9.71459 CTTNBP2 3447 inside intron 2829 disjoint 0.04675 chr3 22387296 22387691 1.2029 2.13371 9.71432 ZNF659 619477 upstream 805 disjoint 0.04675 chrl l 2408270 2409088 1.20288 1.71365 9.71431 TRPM5 7420 upstream -9292 disjoint 0.04675 chr22 48370882 48371211 0.85126 1.8224 9.71219 C22orf34 65978 downstream 23751 disjoint 0.04676 chr5 134910105 134910818 1.1689 0.58058 9.70987 NETJR0G1 10568 upstream -2387 disjoint 0.04677 chrl 6 30286662 30287194 0.4491 1.21197 9.70855 TBC1D10B 1207 inside intron 1384 disjoint 0.04678 chrlO 83673592 83673888 0.6567 1.84247 9.70777 NRG3 48516 inside intron -47883 disjoint 0.04678 chrl 27756661 27757131 0.6362 1.38357 9.70646 AHDC1 45559 inside intron -9436 disjoint 0.04679 chrl l 66645669 66646077 0.13025 1.09889 9.70497 FBXL11 1596 inside intron -1763 disjoint 0.0468 chr7 158496490 158497080 1.79979 2.3937 9.70322 VIPR2 133329 downstream -4295 disjoint 0.04681 chr4 190802733 190803134 1.34425 2.14473 9.70198 FRG1 295833 upstream 409 disjoint 0.04681 chr5 39459657 39460438 -0.0399 0.3961 9.69185 DAB2 264 inside intron 211 disjoint 0.04687 chrl 154528405 154528921 0.89657 1.64034 9.68727 TMEM79 9043 overlaps 3' -356 disjoint 0.0469 chr2 136560524 136561132 1.02025 1.66126 9.68288 CXCR4 29150 downstream 29424 disjoint 0.04692 chrl 224805833 224806630 0.84377 1.40415 9.68283 Clorf95 2710 inside intron -1798 disjoint 0.04692 chrl9 62320776 62321177 0.91254 1.77812 9.6727 USP29 2143 promoter 974 disjoint 0.04698 chr8 76483746 76484204 0.88919 1.57563 9.66223 HNF4G 130493 upstream -995 disjoint 0.04703 chrl 8 28603065 28603641 0.77689 -0.0632 9.66214 KLHL14 3330 overlaps exon 47 disjoint 0.04703 downstream
chrl 92122687 92123463 0.16594 0.86003 9.65453 TGFBR3 779 inside intron 38 disjoint 0.04708 chr4 89837197 89837971 0.52748 1.1554 9.6533 NAP1L5 31 inside exon -103693 disjoint 0.04708 chrlO 126423990 126424493 0.17662 0.90023 9.64799 FAM53B 1071 promoter -715 disjoint 0.04711 chr9 95663409 95664085 0.79655 1.48293 9.64604 BARX1 93337 downstream -107 disjoint 0.04712 chrl 4 75516110 75516475 0.88674 1.81685 9.64421 TGFB3 766 inside intron 1901 disjoint 0.04713 chrl l 116704114 116704824 -0.3902 0.19429 9.64361 CEP164 334 inside intron 0 overlap 0.04714 chrl4 99136543 99137225 0.41226 1.42757 9.63851 KIAA1822 44007 upstream 2003 disjoint 0.04716 chr3 89238541 89239014 1.67457 0.92553 9.637 EPHA3 349 promoter 7308 disjoint 0.04717 chrl6 49145386 49145787 1.03993 1.95938 9.62722 D1 5645 inside intron -4420 disjoint 0.04722 Chr6 170303693 170303953 0.5104 1.85851 9.62573 DLL1 137668 downstream -6833 disjoint 0.04723 chrl 33420827 33421560 0.84883 1.49834 9.62447 TRJ 62 974 promoter -362 disjoint 0.04723 chrl7 14147657 14148055 0.83447 -0.0931 9.62289 HS3ST3B1 2427 inside intron 0 inside 0.04724 chrl9 12637664 12638408 0.34809 1.17115 9.61712 MAN2B1 419 overlaps exon 0 overlap 0.04728 downstream
chrl5 41872599 41873126 0.47006 1.32213 9.61316 SERF2 792 inside intron -35 disjoint 0.0473 chr3 137393991 137394647 0.07966 0.72792 9.61252 MSL2L1 2730 inside intron 2237 disjoint 0.0473 chrl 7 52690597 52691199 0.42244 -0.1816 9.6097 MSI2 1225 covers exon(s) -1353 disjoint 0.04731 chrl3 111122322 111122927 1.08237 1.80469 9.6056 C13orfl6 351307 downstream -3192 disjoint 0.04734 chr5 114626709 114627319 1.51289 0.94035 9.60195 PGGT1B 261 promoter -153 disjoint 0.04736 chrl7 7077773 7078276 -0.14 0.52643 9.60127 DVL2 310 overlaps exon 0 overlap 0.04736 downstream
chr2 219562967 219563734 0.48739 0.94991 9.59766 CRYBA2 2630 overlaps 3' 2192 disjoint 0.04739 chr5 168662085 168662511 0.55881 1.51348 9.59652 SLIT3 1532 promoter -1232 disjoint 0.04739 chr9 130046474 130046767 0.29292 1.46245 9.59249 DNM1 40991 inside intron 5508 disjoint 0.04741 chr5 11958961 11959659 0.26834 0.8406 9.59244 CTNND2 1852 promoter -1258 disjoint 0.04741 chrl 120057223 120057765 0.69893 -0.1195 9.58979 PHGDH 1191 inside intron -201 disjoint 0.04743 chrl 219121127 219121489 0.99704 0.11201 9.58922 HLX1 1746 covers exon(s) 0 overlap 0.04743 chrl 2 129764033 129764780 0.38454 1.03912 9.58243 STX2 124983 downstream 997 disjoint 0.04747 chrl 3 97592099 97592674 1.10046 0.51699 9.57923 FARP1 760 promoter 0 overlap 0.04749 chr3 42553383 42553789 0.40767 1.40861 9.57673 VIPR1 34263 inside exon -481 disjoint 0.0475 chr8 73080160 73080558 1.21638 0.48291 9.57627 TRPA1 69814 downstream 0 overlap 0.04751 chr9 70511575 70511976 -0.0447 0.82581 9.5756 PIP5 1B 1140 inside intron -818 disjoint 0.04751 chr2 176747638 176748249 1.02974 0.38677 9.57047 H0XD3 10588 downstream 0 cover 0.04755 chrX 30158366 30158800 0.34146 1.18652 9.56949 MAGEB3 0 overlaps 5' 16293 disjoint 0.04755 chr20 57308251 57308721 -0.0031 0.74672 9.56811 EDN3 172 promoter 0 overlap 0.04756 chrl 7 34281450 34282036 0.16208 0.98978 9.56795 LASP1 1557 inside intron -820 disjoint 0.04756 chrl2 44949971 44950369 1.13932 0.29762 9.5655 SLC38A1 497 promoter -296 disjoint 0.04757 chr2 173001744 173002418 0.75814 0.10932 9.56481 ITGA6 1129 inside intron -315 disjoint 0.04758 chr6 26341404 26342423 0.44909 0.93138 9.55918 HIST1H1D 771 overlaps 3' 6253 disjoint 0.04761 chr9 4652922 4653389 2.17699 1.30844 9.55748 PPAPDC2 625 inside exon 0 overlap 0.04762 chrl 7 14142742 14143071 0.74161 -0.2975 9.55661 HS3ST3B1 2159 promoter 0 overlap 0.04763 chrl 7 24529803 24530309 0.71306 0.02744 9.55576 MY018A 1223 inside intron 706 disjoint 0.04763 chr6 30760680 30761186 0.50074 1.30553 9.55457 NPvM 5561 downstream 1185 disjoint 0.04764 chr9 138602307 138602948 0.91744 0.39652 9.55185 N0TCH1 42249 upstream -41111 disjoint 0.04765 chr7 158057279 158057934 0.48903 1.05727 9.54344 PTPRN2 15244 inside intron -1548 disjoint 0.04769 chrlO 102371588 102372154 0.52458 1.68931 9.54308 HIFIAN 85903 downstream 32261 disjoint 0.04769 chr8 142209047 142209514 0.92041 1.59781 9.54194 DE ND3 1146 inside intron -523 disjoint 0.0477 chrl 2 9993872 9994626 -0.1752 0.4348 9.54088 FLJ46363■ 2576 overlaps exon 160716 disjoint 0.04771 upstream
chr8 124618263 124618781 0.07653 0.83326 9.54076 FBX032 3845 inside intron 2939 disjoint 0.04771 chrl 9 15807362 15808371 0.31329 1.02343 9.53882 OR10H1 27516 upstream 0 overlap 0.04772 chrX 134012670 134013218 0.2311 0.85804 9.53457 FAM127B 668 inside exon 11 disjoint 0.04775 chr8 4426774 4427416 0.95622 1.49251 9.53259 CSMD1 412319 inside intron 408960 disjoint 0.04776 chrl 208491688 208492775 1.09625 0.36314 9.53038 SERTAD4 18871 downstream -17428 disjoint 0.04777 chrlO 1628812 1629210 0.60785 1.56508 9.52947 ADARB2 140459 inside intron -43020 disjoint 0.04778 chr8 25369455 25370055 0.62043 1.25572 9.52936 KCTD9 1781 inside intron 1148 disjoint 0.04778 chr2 176672197 176672601 1.1134 0.24715 9.52871 HOXD12 174 promoter 0 overlap 0.04778 chr9 17895425 17895933 0.2002 1.01221 9.52834 SH3GL2 326232 downstream 486 disjoint 0.04778 chr9 33636296 33636664 1.22474 2.17751 9.52555 AN RD18B 122084 downstream 103855 disjoint 0.04779 chr20 39200601 39200999 -0.3139 0.46492 9.52542 PLCG1 1027 inside intron -355 disjoint 0.0478 chrl8 59968035 59968502 0.77211 1.49285 9.52437 SERPINB8 179793 downstream -146800 disjoint 0.0478 chrl3 94752227 94752595 0.60731 1.58116 9.52366 ABCC4 544 promoter -15 disjoint 0.04781 chr8 19362440 19362844 0.56803 1.43872 9.52282 ChGn 221529 inside intron 466 disjoint 0.04781 chrl4 56339510 56340014 -0.0566 0.60687 9.52268 0TX2 2083 inside intron -4196 disjoint 0.04781 chrl8 18009475 18009912 0.43428 -0.3641 9.51337 GATA6 6062 inside intron 880 disjoint 0.04786 chrX 152343030 152343503 0.44574 1.13898 9.5125 TREX2 21635 downstream -2637 disjoint 0.04787 chr5 140596483 140596913 0.34504 1.19807 9.50832 PCDHB15 8417 upstream 0 overlap 0.04789 chr20 22966041 22966475 -0.1973 0.58604 9,49981 SST 4 1921 close to 3' -1162 disjoint 0.04794 chr22 48361745 48362215 0.4294 1.19834 9.49907 FLJ44385 33413 downstream 32747 disjoint 0.04795 chr22 36999136 36999534 0.03089 0.8907 9.49894 C22orf5 175 promoter 0 overlap 0.04795 chr8 75425803 75426276 0.59837 -0.132 9.4949 GDAP1 596 covers exon(s) -204 disjoint 0.04797 chr5 72630132 72630467 1.20951 0.17018 9.4935 TMEM174 130303 downstream 0 inside 0.04798 chr7 155131005 155131859 0.27478 1.07979 9.4927 PRR8 26475 upstream -427 disjoint 0.04799 chrl3 71335630 71336244 0.66953 0.06059 9.49139 DACH1 3086 inside intron 1119 disjoint 0.04799 chr5 140751990 140752505 0.62058 1.19551 9.48982 PCDHGA8 324 inside exon 64 disjoint 0.048 chrl7 68817176 68817751 0.44807 1.03509 9.48792 CDC42EP4 1986 inside intron 819 disjoint 0.04801 chrl 41899311 41899886 0.47275 1.056 9.48645 HIVEP3 256895 inside intron 81 disjoint 0.04802 chrl7 45108826 45109491 -0.0847 0.46878 9.48579 SPOP 1032 inside intron 378 disjoint 0.04803 chr2 124896552 124897073 0.75511 1.71647 9.48222 CNTNAP5 397219 inside intron -396827 disjoint 0.04804 chr5 122450201 122450923 0.90679 0.21055 9.48046 PPIC 49878 upstream 1313 disjoint 0.04806 chr9 129934502 129935129 1.15437 2.0995 9.47527 LOC389791 3855 downstream -3592 disjoint 0.04809 chrH 22361251 22361753 1.07884 0.36556 9.47237 SLC7A7 6400 upstream 0 overlap 0.04811 chrl 119976133 119976606 1.24011 1.97464 9.47219 PHGDH 79426 upstream -7984 disjoint 0.04811 chr7 27163715 27164048 1.82758 0.81085 9.47011 HOXA7 895 promoter -623 disjoint 0.04812 chrlO 33334241 33334639 0.08793 0.97369 9.46748 ITGB1 47038 upstream -24365 disjoint 0.04813 chr6 35288709 35289140 1.29963 0.72657 9.46714 SCUBE3 1027 promoter 0 overlap 0.04813 chrl 116170816 116171358 0.14161 0.70954 9.46637 NHLH2 13911 downstream 975 disjoint 0.04814 chrl4 67356130 67356601 0.54335 1.21711 9.45751 RAD51L1 0 overlaps 5' -144495 disjoint 0.04819 chr6 99383620 99384201 0.76653 0.07897 9.45453 POU3F2 5099 upstream -861 disjoint 0.04821 chr3 139793925 139794468 0.63325 1.26953 9.44797 CEP70 1350 inside intron 1199 disjoint 0.04824 chrl 75852120 75852659 0.32214 0.94494 9.44777 SLC44A5 2764 upstream 383 disjoint 0.04825 chr5 133537819 133538187 0.7461 1.67657 9.44601 SKP1A 2395 inside intron 1683 disjoint 0.04826 chrl 234295609 234296148 1.10162 0.56965 9.44328 NIDI 506 promoter -169 disjoint 0.04828 chr2 473870 474268 0.34552 1.3153 9.44314 TMEM18 193170 downstream 10925 disjoint 0.04828 chrS 179429444 179429879 1.64952 0.71363 9.43878 RNF130 1835 inside intron 1018 disjoint 0.04829 chrl 7 40402219 40402722 0.73612 0.05347 9.4321 C1QL1 1050 promoter -269 disjoint 0.04833 chr20 3705838 3706344 1.62036 0.94805 9.42737 C20orf28 3757 overlaps 3' 0 overlap 0.04836 chrl 7 8032232 8033053 0.53699 0.9909 9.4263 C1 orf59 1061 overlaps 3' 90 disjoint 0.04837 chr7 35260990 35261625 0.74022 0.20587 9.42413 TBX20 1224 promoter 0 overlap 0.04838 chr20 59875045 59875446 0.89725 1.74417 9.42382 CDH4 614092 inside intron 6724 disjoint 0.04838 chrl 204047403 204048013 0.42003 1.23801 9.42232 SLC41A1 770 inside intron 480 disjoint 0.04839 chr7 157065703 157066701 1.10868 1.89969 9.42113 PTPRN2 1006477 inside intron -3548 disjoint 0.0484 chr7 149732284 149732932 0.47544 1.52641 9.42034 ZNF775 24946 downstream 0 overlap 0.04841 chrl 3 99446973 99447551 0.84063 0.19836 9.4191 ZIC2 14654 downstream 0 overlap 0.04841 chrl 90967967 90968371 0.82899 -0.0357 9.41849 BARHL2 12586 upstream -2575 disjoint 0.04842 chrl5 82947949 82948278 1.9815 0.98772 9.41719 ZSCAN2 2697 overlaps exon -2334 disjoint 0.04843 upstream
chr2 173309360 173309866 1.26716 0.56277 9.41654 RAPGEF4 508 inside intron -144 disjoint 0.04843 chr4 154824173 154824610 1.2221 0.45176 9.41019 TLR2 280 promoter 0 overlap 0.04846 chrl9 47120766 47121236 0.12821 0.85183 9.40707 ARHGEF1 40481 downstream 2520 disjoint 0.04848 chrl7 112S946 1126314 0.6254 1.63604 9.40591 TUSC5 3392 upstream -4463 disjoint 0.04848 chr7 27128109 27128438 1.60331 0.54409 9.40354 HOXA3 4725 inside introii 174 disjoint 0.04849 chr5 178356674 178357174 1.75022 2.43072 9.40233 GRM6 1945 promoter -1731 disjoint 0.0485 chrlO 22806967 22807473 0.93464 0.26009 9.40174 PIP5 2A 236016 downstream 0 overlap 0.0485 chr3 33732720 33733085 0.69526 1.61763 9.40091 CLASP2 1766 inside intron 1125 disjoint 0.04851 chrl 240752103 240752684 0.4955 1.12083 9.39953 PLD5 1936 inside intron 855 disjoint 0.04852 chr7 56520490 56521224 0.95888 1.76393 9.39932 LOC401357 326439 downstream -1283 disjoint 0.04852 chr3 148594998 148595396 0.91836 0.06416 9.39619 ZIC4 11700 inside intron -608 disjoint 0.04854 chrl5 87759521 87760024 0.63871 1.31043 9.39542 RHCG 80778 downstream 722 disjoint 0.04854 chrll 77809226 77809801 1.24554 1.80817 9.39357 GAB2 2813 upstream -2178 disjoint 0.04855 chrX 69589449 69590064 0.32042 0.74995 9.3933 DLG3 7906 inside intron 1460 disjoint 0.04855 chr7 150299553 150300062 1.34982 2.02075 9.39302 KCNH2 5884 inside intron 2677 disjoint 0.04856 chrl l 271822 272357 1.22434 2.03641 9.39237 NALP6 3253 overlaps exon -122 disjoint 0.04856 downstream
chr4 40954889 40955503 1.32665 0.78182 9.39132 UCHL1 1204 inside intron -265 disjoint 0.04856 chrlO 42571857 42572513 0.89274 1.46374 9.38879 BMS1L 25751 upstream -939 disjoint 0.04858 chrl 7 33920924 33921412 1.20868 0.42304 9.38675 SNIP 94296 downstream -164 disjoint 0.04859 chrl 7 69708441 69708917 1.07719 1.78064 9.38381 RPL38 2472 promoter 2610 disjoint 0.04861 chrl4 70179420 70179959 0.82681 0.2202 9.38342 MED6 42284 upstream -335 disjoint 0.04861 chrl 8 32018645 32019115 1.29571 0.54563 9.38226 MOCOS 2364 promoter 1274 disjoint 0.04862 chr20 5537389 5537739 -0.1012 0.93588 9.38044 KIAA1434 1932 inside intron 1751 disjoint 0.04862 chr9 36248709 36249074 0.32887 1.22416 9.37452 GNE 309 promoter 0 overlap 0.04867 chrl3 90623248 90623682 0.97463 1.75583 9.3745 GPC5 225205 upstream 1568 disjoint 0.04867 chr5 134394611 134395087 0.85956 0.1089 9.37277 PITX1 2799 overlaps exon 0 overlap 0.04868 downstream
chrl 9 63598806 63599243 1.34007 0.51123 9.37054 RPS5 8359 downstream 22 disjoint 0.04869 chr9 29099536 29100114 0.45255 0.95212 9.36983 LRKN6C 390234 upstream 102057 disjoint 0.04869 chr3 130199907 130200377 0.31601 1.05749 9.3694 CCDC48 31604 upstream 2175 disjoint 0.04869 chrl7 70556120 70556653 0.35162 1.27177 9.36906 K.CTD2 1247 inside intron -1209 disjoint 0.0487 chrl 2 130718396 130718755 1.31652 2.31633 9.36829 SFRS8 42832 upstream -5633 disjoint 0.0487 chrl 7 44150808 44151314 0.53731 -0.0803 9.36558 P AC 3566 downstream 0 overlap 0.04872 chrl9 53366314 53366820 0.63967 1.31716 9.36325 LOC374920 554 inside intron 57 disjoint 0.04873 chr6 45494477 45494935 1.21406 0.28074 9.35934 RUNX2 90446 inside intron 389 disjoint 0.04875 chrl 36170366 36170861 0.43828 1.14392 9.35683 EIF2C3 1008 inside intron -517 disjoint 0.04877 chr3 193338542 193339275 0.78915 1.68156 9.35334 FGF12 269430 downstream 269237 disjoint 0.04879 chrl 9 15872605 15873099 0.27589 0.99863 9.35324 CYP4F2 2722 upstream 1530 disjoint 0.04879 chr9 1040642 1040974 1.31723 0.24926 9.35322 DMRT2 639 promoter -132 disjoint 0.04879 chrl 6 31390203 31390640 0.32814 1.20881 9.34951 TGFB1I1 344 promoter 137 disjoint 0.04882 chrl l 59079588 59079989 1.66337 0.67456 9.34876 OSBP 60203 downstream 4724 disjoint 0.04882 chr2 122209582 122210122 0.66266 1.378 9.34766 MKI67IP 815 covers exon(s) 456 disjoint 0.04883 chrl5 91059451 91059865 0.36009 1.28653 9.3418 LOC400451 59417 upstream -225 disjoint 0.04886 chrl 6 66677967 66678716 -0.4688 -0.0134 9.33586 NFATC3 1092 inside intron -480 disjoint 0.04889 chrl4 69304452 69305096 0.08614 0.70078 9.33584 SFRS5 866 covers exon(s) -31 disjoint 0.04889 chr6 1563766 1564174 1.44413 0.46117 9.33094 GMDS 626670 downstream 0 overlap 0.04892 chr3 62331295 62331872 0.65399 0.02366 9.3307 FEZF2 2188 inside intron 0 overlap 0.04892 chrl3 113901869 113902270 0.23382 1.18953 9.33034 RASA3 13926 inside intron -4237 disjoint 0.04892 chr7 112514479 112514916 0.0912 0.82083 9.32848 GP 85 98 overlaps exon -147026 disjoint 0.04894 downstream
chrl2 26165555 26165925 1.08731 0.23901 9.32781 BHLHB3 3187 inside exon 391 disjoint 0.04894 chrl2 6830269 6830910 0.58778 -0.0305 9.32414 CDC A3 0 overlaps 5' 356 disjoint 0.04896 chrl l 7229084 7229482 1.12234 0.25343 9.32072 SYT9 274 promoter 0 overlap 0.04899 chrl 10194252 10194746 -0.2179 0.49895 9.31953 KIF1B 835 inside intron -359 disjoint 0.04899 chrl 201564334 201564875 1.78193 0.91069 9.31566 FMOD 22036 downstream -782 disjoint 0.04902 chr7 3985140 3985828 1.10219 1.92214 9.31082 SDK1 677535 inside intron 134343 disjoint 0.04904 chr3 115150250 115150717 0.1731 0.92378 9.31059 ZDHHC23 813 covers exon(s) -173 disjoint 0.04904 chrl 7 55396038 55396685 -0.4275 0.08338 9.30713 LOC51136 213 inside intron 0 overlap 0.04907 chr3 37193633 37194208 -0.0912 0.55268 9.30642 LRRFIP2 2548 upstream -500 disjoint 0.04907 chr5 77175052 77175420 1.65208 0.66601 9.30538 TBCA 67112 upstream 878 disjoint 0.04908 chrl3 23376419 23376865 1.47448 0.69037 9.30388 LOC387 11 7295 upstream -366 disjoint 0.04909 chrl l 118497944 118498502 0.25507 0.91101 9.30301 MIZF 447 inside intron 0 overlap 0.04909 chr6 134258990 134259630 1.07744 0.46267 9.30291 TCF21 7021 downstream -17 disjoint 0.04909 chr22 36406833 36407675 0.54005 1.16522 9.30207 LGALS1 5275 downstream -3475 disjoint 0.0491 chrl 5 81276635 81277432 -0.1376 0.67176 9.30169 FSD2 4761 upstream -308 disjoint 0.0491 chr2 172673880 172674431 0.99968 0.39049 9.29938 DLX2 1292 overlaps exon 0 inside 0.0491 1 upstream
chr20 57946904 57947284 0.03352 1.01187 9.29667 PPP1R3D 1462 inside exon 182 disjoint 0.04913 chrl 9 12652982 12653416 0.86672 1.67757 9.29598 DHPS 260 overlaps exon 0 overlap 0.04913 downstream
chrl2 52695787 52696372 0.43868 -0.0588 9.29446 HOXC6 536 promoter -807 disjoint 0.04914 chrl 2 4256001 4256855 0.17318 0.65835 9.28881 CCND2 2803 inside intron -1335 disjoint 0.04917 chr3 69143973 69144305 0.9611 1.97841 9.28822 C3orf64 1158 inside intron 541 disjoint 0.04918 chrlO 91284578 91285048 0.82126 0.1979 9.28596 SLC16A12 244 inside intron 0 overlap 0.04919 chr5 17961064 17961574 1.22054 1.99432 9.28529 BASPl 690315 downstream -272592 disjoint 0.0492 chrl3 36144753 36145220 1.20358 2.04749 9.28295 LOC400120 828 promoter 729 disjoint 0.04921 chr5 11742997 11743467 0.25477 1.1141 9.27192 CTN D2 213642 inside intron 213083 disjoint 0.04928 chr!9 60878879 60879600 -0.0371 0.7793 9.26773 EPN1 476 inside intron -183 disjoint 0.0493 chr2 219567151 219569003 0.38544 1.16146 9.25915 CRYBA2 781 promoter 0 overlap 0.04936 chr6 17209591 17210025 0.45292 1.17041 9.25549 RBM24 180885 upstream 263 disjoint 0.04938 chrl 25817363 25817692 1.25319 0.22487 9.2549 MAN1C1 818 overlaps exon -4 disjoint 0.04938 downstream
chrX 39892071 39892502 0.82281 0.04797 9.2546 BCOR 50472 upstream -61 disjoint 0.04938 chrl 117009710 117010180 1.77459 2.45888 9.25107 IGSF3 1656 inside intron 1 167 disjoint 0.04941 chrl 37873825 37874623 0.2282 0.98624 9.24761 RSPOl 748 promoter -374 disjoint 0.04943 chrl2 105874912 105875656 -0.0803 0.5954 9.24328 C12or£23 1078 covers exon(s) -693 disjoint 0.04945 chr8 20204860 20205402 0.93238 0.29418 9.24138 LZTS1 47778 upstream 0 overlap 0.04946 chr8 25953328 25953834 0.64231 0.04341 9.23813 EBF2 4474 covers exon(s) 0 overlap 0.04948 chrl 9 38866174 38866544 0.51268 1.8324 9.23804 CHST8 729 promoter 640 disjoint 0.04948 chr3 42923083 42923638 1.15795 2.39401 9.23728 ZNF662 678 inside intron 0 overlap 0.04948 chr7 27216025 27216462 1.72156 0.96858 9.23633 HOXA13 9776 upstream 2744 disjoint 0.04949 chr6 15799159 15799491 0.86444 1.8339 9.23576 DTNBPl 27910 upstream -27768 disjoint 0.04949 chrl 7 38086896 38087402 1.25612 0.65078 9.23325 CCRIO 0 overlaps 5' 915 disjoint 0.0495 chrlO 102961800 102962360 0.81636 1.63777 9.23249 LBX1 16346 downstream 1130 disjoint 0.0495 chr7 102874660 102875238 0.49473 1.16089 9.23055 SLC26A5 827 promoter -584 disjoint 0.04952 chrl 5 48843769 48844342 -0.1022 0.52588 9.22857 SPPL2A 859 inside intron 553 disjoint 0.04953 chr6 33530421 33530924 0.01721 0.70601 9.22836 ZBTB9 88 overlaps two exons 0 overlap 0.04953 chr8 48337047 48337481 0.11409 0.86329 9.22453 CEBPD 475841 downstream -418 disjoint 0.04955 chi9 114291048 114291431 1.43494 0.60718 9.22225 KIAA1958 1980 inside intron -1483 disjoint 0.04956 chr2 171722809 171723464 1.49039 0.78237 9.2221 TLK1 1741 inside intron 1320 disjoint 0.04956 chrl7 77262139 77262507 0.88112 1.76115 9.22181 HGS 715 inside intron -287 disjoint 0.04956 chr8 80741030 86741666 0.46837 1.34213 9.21993 REXOILI 156134 downstream 262 disjoint 0.04957 chrl5 94690465 94691029 0.5325 -0.0879 9.21203 NR2F2 15516 downstream -44 disjoint 0.04962 chrX 68643797 68644318 1.12988 1.7769 9.20991 TMEM28 1995 inside intron -1021 disjoint 0.04963 chrl7 8220892 8221260 0.15145 1.07204 9.20594 RPL26 6029 downstream -58 disjoint 0.04965 chrl 159274588 159275028 1.40047 0.63494 9.20493 FUR 306 inside intron 0 overlap 0.04965 chrl2 3801184 3801726 1.71549 0.88489 9.20463 PARP11 51136 covers exon(s) 16457 disjoint 0.04966 chrl3 32009558 32010261 1.76704 0.95189 9.20462 PFAAP5 657 inside intron 48023 disjoint 0.04966 chrl 3 109587516 109588089 0.80441 0.27011 9.20181 COL4A1 169369 downstream 440 disjoint 0.04967 chr5 119829477 119829985 0.01758 0.65665 9.20097 PRR16 1560 inside intron -384 disjoint 0.04968 chr4 88531132 88531577 0.35986 1.18466 9.20029 DHRS8 0 overlaps 5' 31124 disjoint 0.04968 chrl 209374491 209374964 1.05398 1.76156 9.19855 KCNH1 412 promoter -193 disjoint 0.04969 chrl 7 45994782 45995345 0.6948 0.08751 9.19467 CACNA1G 1335 inside intron -504 disjoint 0.04971 chrl 235897858 235898295 0.60419 1.42088 9.1926 RYR2 625534 overlaps exon 115515 disjoint 0.04972 downstream
chrX 118708883 118709458 0.72868 1.34083 9.19249 1902 inside intron 1022 disjoint 0.04972 chr4 90446622 90447152 2.55265 1.8928 9.1883 GPRJN3 1031 inside intron 585 disjoint 0.04975 chr5 88021299 88021841 0.61157 -0.001 9.18808 MEF2C 192938 downstream 0 overlap 0.04975 chr20 61477279 61477695 0.82053 1.66728 9.188 CHRNA4 14088 upstream -3802 disjoint 0.04975 chrl 65387779 65388180 0.80959 -0.0079 9.18249 AK3L2 1101 inside intron -293 disjoint 0.04979 chrl 7 45560093 45560766 0.93987 0.41026 9.18193 SAMD14 1399 inside intron 896 disjoint 0.04979 chr8 143400176 143400469 1.24148 2.2912 9.17959 TSNARE1 81974 inside intron -3492 disjoint 0.04981 chrl l 46221693 46222160 0.2078 0.95925 9.17813 CREB3L1 33643 upstream 0 overlap 0.04982 chr7 24984754 24985296 1.46621 0.88869 9.17775 OSBPL3 988 inside intron 228 disjoint 0.04982 chr5 1033972 1034338 0.50361 1.40615 9.177 NKD2 27829 upstream -21800 disjoint 0.04982 chr7 73146380 73147030 0.42052 0.95062 9.17692 LIM 1 10289 inside intron -9747 disjoint 0.04982 chr7 139122347 139122984 0.11907 0.56184 9.17627 TBXAS1 52436 upstream 891 disjoint 0.04983 chrl2 6926222 6926584 2.19199 1.2341 9.17431 PTPN6 222 inside intron -2034 disjoint 0.04984 chrl5 41590667 41591137 0.98046 0.12586 9.17003 TP53BP1 640 promoter 0 overlap 0.04986 chrl6 85909289 85909789 -0.3542 0.35105 9.16861 FBX031 65074 downstream -218 disjoint 0.04987 chrl4 100265605 100266129 1.19726 1.99765 9.16242 DLK1 2600 inside intron -2353 disjoint 0.04991 chrl5 47041514 47041981 1.93609 1.23515 9.15602 SHC4 951 overlaps exon 295 disjoint 0.04995 downstream
chr6 34966181 34966594 0.56238 1.52146 9.15576 AN S1A 1163 inside intron -539 disjoint 0.04995 chrl 7 34116469 34117469 0.8161 0.44096 9.15554 MLLT6 1069 covers exon(s) -1246 disjoint 0.04996 chr2 16708633 16709362 0.89128 1.57406 9.15118 FAM49A 1214 inside intron -155330 disjoint 0.04998
[0121] Table 3. Gene ontology functional categories enriched in reprogramming
differentially methylated regions (R-DMRs).
Columns are methylation, GO ID, term, count, percentage, fold enrichment, P Value, and false discovery rate (FDR). Fold
ethvlation GO ID Term Count % Enrichment P Value FDR
Hypermethylated
R-DM s GO:0050789 regulation of biological process 607 30.46% 1.285 1.13E-14 2.17E-11
GO:0065007 biological regulation 657 32.97% 1.263 1.35E-14 2.59E-11
GO:0050794 regulation of cellular process 566 28.40% 1.289 1.10E-13 2.10E-10
GO:0007275 multicellular organismal development 332 16.66% 1.424 1.29E-12 2.48E-09
GO:0032502 developmental process 434 21.78% 1.34 1.73E-12 3.30E-09
GO:0007399 nervous system development 140 7.02% 1.808 2.60E-12 4.98E-09
GO:0048856 anatomical structure development 306 15.35% 1.432 7.02E-12 1.34E-08
GO:0048731 system development 256 12.84% 1.465 5.95E-11 1.14E-07
GO:0022610 biological adhesion 133 6.67% 1.731 2.17E-10 4.15E-07
GO:0007155 cell adhesion 133 6.67% 1.731 2.17E-10 4.15E-07
GO:0048523 negative regulation of cellular process 176 8.83% 1.566 7.52E-10 1.44E-06
GO:0016337 cell-cell adhesion 64 3.21% 2.231 1.31E-09 2.50E-06 cellular component organization and
GOtOO 16043 biogenesis 358 17.96% 1.324 1.71E-09 3.27E-06
GO:0048519 negative regulation of biological process 179 8.98% 1.527 3.89E-09 7.43E-06
GO:0007156 homophilic cell adhesion 40 2.01% 2.741 6.74E-09 1.29E-05
GO:0043283 biopolymer metabolic process 634 31.81% 1.191 9.07E-09 1.74E-05
GO:0009987 cellular process 1359 68.19% 1.055 2.21E-08 4.23E-05
GO:0019222 regulation of metabolic process 377 18.92% 1.276 4.58E-08 8.75E-05
GO:0016070 RNA metabolic process 378 18.97% 1.261 1.77E-07 3.39E-04
GO:0010468 regulation of gene expression 349 17.51% 1.274 2.26E-07 4.33E-04
GO:0031323 regulation of cellular metabolic process 361 18.11% 1.266 2.58E-07 4.93E-04 regulation of transcription, DNA-
GO:0006355 dependent 311 15.60% 1.288 4.90E-07 9.37E-04
GO:0006350 transcription 339 17.01% 1.267 6.26E-07 0.0012
GO:0006351 transcription, DNA-dependent 316 15.86% 1.28 7.16E-07 0.00137
GO:0045449 regulation of transcription 328 16.46% 1.272 7.52E-07 0.00144
GO:0032774 RNA biosynthetic process 316 15.86% 1.278 7.90E-07 0.00151 regulation of nucleobase, nucleoside,
nucleotide and nucleic acid metabolic
GO:0019219 process 334 16.76% 1.266 8.50E-07 0.00163
GO:0009653 anatomical structure morphogenesis 162 8.13% 1.44 1.09E-06 0.00209 transcription from RNA polymerase II
GO:0006366 promoter 105 5.27% 1.581 1.99E-06 0.00381
GO:0019226 transmission of nerve impulse 63 3.16% 1.823 3.50E-06 0.0067
GO:0007268 synaptic transmission 57 2.86% 1.889 3.67E-06 0.00702
GO:0010467 gene expression 438 21.98% 1.197 5.29E-06 0.01012 regulation of transcription from RNA
GO:0006357 polymerase II promoter 79 3.96% 1.672 5.66E-06 0.01083 nucleobase, nucleoside, nucleotide and
GO:0006139 nucleic acid metabolic process 471 23.63% 1.171 2.19E-05 0.0418
GO:0007242 intracellular signaling cascade 196 9.83% 1.32 2.43E-05 0.04644
Hypornethylated
RDMRs GO:0007275 multicellular organismal development 326 32.93% 2.642 9.95E-71 I.90E-67 regulation of transcription, DNA-
GO:0006355 dependent 316 31.92% 2.473 6.18E-61 1.18E-57
GO:0032502 developmental process 374 37.78% 2.182 3.56E-60 6.81E-57
GO:0006351 transcription, DNA-dependent 317 32.02% 2.426 3.74E-59 7.15E-56
GO:0032774 RNA biosynthetic process 317 32.02% 2.423 5.00E-59 9.56E-56
GO.0045449 regulation of transcription 324 32.73% 2.374 1.77E-58 3.39E-55 GO:0010468 regulation of gene expression 333 33.64% 2.296 5.76E-57 1.10E-53 regulation of nueleobase, nucleoside,
nucleotide and nucleic acid metabolic
GO:00I9219 process 325 32.83% 2.327 1.30E-56 2.48E-53
GO:0048856 anatomical structure development 287 28.99% 2.537 1.58E-56 3.02E-53
GO:0006350 transcription 327 33.03% 2.309 3.03E-56 5.79E-53
GO:0031323 regulation of cellular metabolic process 337 34.04% 2.233 8.42E-55 1.61E-51
GO:0048731 system development 252 25.45% 2.725 2.07E-54 3.96E-51
GO:0019222 regulation of metabolic process 342 34.55% 2.188 1.12E-53 2.15E-50
GO:0050794 regulation of cellular process 431 43.54% 1.855 2.87E-51 5.49E-48
GO-.0050789 regulation of biological process 451 45.56% 1.804 3.67E-51 7.03E-48
GO:0065007 biological regulation 473 47.78% 1.719 2.10E-48 4.01E-45
GO:0048S13 organ development 197 19.90% 2.925 8.03E-46 1.54E-42
GO:0016070 RNA metabolic process 329 33.23% 2.074 1.30E-45 2.49E-42
GO:0032501 multicellular organismal process 374 37.78% 1.894 6.36E-44 1.22E-40
GO:0009653 anatomical structure morphogenesis 179 18.08% 3.007 5.96E-43 1.14E-39
GO:0010467 gene expression 357 36.06% 1.843 1.74E-38 3.32E-35 nueleobase, nucleoside, nucleotide and
GO:0006139 nucleic acid metabolic process 364 36.77% 1.71 3.97E-32 7.59E-29
GO.0007399 nervous system development 127 12.83% 3.099 3.79E-31 7.25E-28
GO:0009790 embryonic development 76 7.68% 4.838 3.92E-31 7.50E-28
GO:0043283 biopolymer metabolic process 435 43.94% 1.544 5.82E-30 1.11E-26
GO:0009887 organ morphogenesis 84 8.48% 3.853 5.77E-27 1.10E-23
GO:0007389 pattern specification process 51 5.15% 6.183 3.12E-26 5.96E-23
GO:0030154 cell differentiation 202 20.40% 2.095 4.48E-26 8.57E-23
GO:0048869 cellular developmental process 202 20.40% 2.095 4.48E-26 8.57E-23 transcription from RNA polymerase II
GO.0006366 promoter 108 10.91% 3.073 4.59E-26 8.78E-23
GO:0048598 embryonic morphogenesis 43 4.34% 6.444 5.99E-23 1.15E-19 regulation of transcription from RNA
GO:0006357 polymerase II promoter 84 8.48% 3.359 8.13E-23 1.56E-19
GO:0048522 positive regulation of cellular process 127 12.83% 2.427 3.12E-21 5.97E-18
GO:0045941 positive regulation of transcription 65 6.57% 3.795 1.49E-20 2.85E-17
GO:0003002 regionalization 38 3.84% 6.516 1.67E-20 3.19E-17 positive regulation of nueleobase,
nucleoside, nucleotide and nucleic acid
GO:0045935 metabolic process 65 6.57% 3.682 7.66E-20 1.47E-16
GO:0048518 positive regulation of biological process 132 13.33% 2.272 1.46E-19 2.78E-16 positive regulation of transcription,
GO:004S893 DNA-dependent 56 5.66% 4.053 3.94E-19 7.54E-16
GO:0045165 cell fate commitment 33 3.33% 7.057 4.85E-19 9.29E-16
GO:0007420 brain development 42 4.24% 4.996 6.86E-18 1.31E-14 positive regulation of transcription from
GO:0045944 RNA polymerase II promoter 42 4.24% 4.675 8.82E-17 2.11E-13 positive regulation of cellular metabolic
GO:0031325 process 68 6.87% 3.111 8.96E-17 2.11E-13
GO:0035270 endocrine system development 20 2.02% 11.196 3.28E-16 6.33E-13
GO:0007417 central nervous system development 51 5.15% 3.733 8.28E-16 1.49E-12
GO:0022008 neurogenesis 56 5.66% 3.416 1.41E-15 2.76E-12
GO:0048732 gland development 23 2.32% 8.584 1.90E-15 3.61E-12
GO:0030182 neuron differentiation 49 4.95% 3.731 3.15E-15 5.95E-12
GO:0009893 positive regulation of metabolic process 68 6.87% 2.908 3.88E-15 7.44E-12 (30:0043170 raacromolecule metabolic process 486 49.09% 1.282 8.07E-15 1.55E-11
GO:0001501 skeletal development 46 4.65% 3.84 8.29E-15 1.59E-11
GO:0060173 limb development 22 2.22% 8.546 9.85E-15 1.89E-11
GO:0048736 appendage development 22 2.22% 8.546 9.85E-15 1.89Ε-Π
GO:0035108 limb morphogenesis 22 2.22% 8.546 9.85E-15 1.89E-11
GO:0035107 appendage morphogenesis 22 2.22% 8.546 9.85E-15 1.89E-11
00:0048699 generation of neurons 52 5.25% 3.425 1.51E-14 2.89E-11
GO:0044237 cellular metabolic process 538 54.34% 1.238 2.48E-14 4.76E-11
GO:0044238 primary metabolic process 536 54.14% 1.23 1.43E-13 2.74E-10
GO:0030326 embryonic limb morphogenesis 20 2.02% 8.459 2.60E-13 4.97E-10
GO:0035113 embryonic appendage morphogenesis 20 2.02% 8.459 2.60E-13 4.97E-10
GO:0007423 sensory organ development 28 2.83% 5.551 3.01E-13 5.76E-10
GO:0007S07 heart development 32 3.23% 4.758 4.46E-13 8.53E-10
GO.0048523 negative regulation of cellular process 118 11.92% 1.984 5.13E-13 9.82E-10
GO:0035295 tube development 34 3.43% 4.402 7.78E-13 1.49E-09
GO:0048519 negative regulation of biological process 121 12.22% 1.95 8.07E-13 1.54E-09
GO:0030900 forebrain development 21 2.12% 7.267 1.76E-12 3.36E-09
GO.0048468 cell development 124 12.53% 1.896 2.78E-12 5.31E-09
GO:0009888 tissue development 52 5.25% 2.92 8.77E-12 1.68E-08
GO:0001822 kidney development 19 1.92% 7.534 1.24E-11 2.38E-08
GO:0001655 urogenital system development 20 2.02% 7.049 1.25E-11 2.39E-08
GO:0009952 anterior/posterior pattern formation 22 2.22% 6.069 2.51E-11 4.79E-08 embryonic development ending in birth
GO:0009792 or egg hatching 28 2.83% 4.634 3.16E-11 6.04E-08
GO:0043009 chordate embryonic development 28 2.83% 4.634 3.16E-11 6.04E-08
GO:0048666 neuron development 36 3.64% 3.55 9.94E-11 1.90E-07 negative regulation of cellular metabolic
GO:0031324 process 53 5.35% 2.607 3.86E-10 7.38E-07
GO:0008152 metabolic process 565 57.07% 1.171 4.32E-10 8.26E-07
GO:0009892 negative regulation of metabolic process 57 5.76% 2.488 4.50E-10 8.60E-07 negative regulation of transcription,
GO:0045892 DNA-dependent 37 3.74% 3.276 5.45E-10 1.04E-06
GO:0016481 negative regulation of transcription 45 4.55% 2.855 5.58E-10 1.07E-06
GO:0007409 axonogenesis 29 2.93% 3.971 6.24E-10 1.19E-06
GO:0009987 cellular process 737 74.44% 1.082 2.30E-09 4.39E-06
GO:0048812 neurite morphogenesis 29 2.93% 3.755 2.37E-09 4.54E-06 neuron morphogenesis during
GO:0048667 differentiation 29 2.93% 3.755 2.37E-09 4.54E-06
GO:0031175 neurite development 31 3.13% 3.533 2.74E-09 5.25E-06
GO:0001656 metanephros development 14 1.41% 8.327 2.85E-09 5.45E-06 cellular morphogenesis during
GO:0000904 differentiation 30 3.03% 3.614 3.02E-09 5.77E-06
GO:0001654 eye development 17 1.72% 6.105 6.80E-09 1.30E-05 negative regulation of nucleobase,
nucleoside, nucleotide and nucleic acid
GO:0045934 metabolic process 45 4.55% 2.611 9.34E-09 1.79E-05
GO:0048332 mesoderm morphogenesis 12 1.21% 9.517 1.03E-08 1.98E-05
GO.0048754 branching morphogenesis of a tube 15 1.52% 6.64 2.03E-08 3.87E-05 cell projection organization and
GO:0030030 biogenesis 36 3.64% 2.916 2.20E-08 4.21E-05
GO:0048858 cell projection morphogenesis 36 3.64% 2.916 2.20E-08 4.21E-05 GO:0032990 cell part morphogenesis 36 3,64% 2.916 2.20E-08 4.21E-05
GO:0016477 cell migration 39 3.94% 2.739 2.94E-08 5.62E-05
00:0007411 axon guidance 18 1.82% 5.038 5.28B-08 1.01E-04
GO:0045595 regulation of cell differentiation 28 2.83% 3.352 5.81E-08 1.11E-04
GO:0001763 morphogenesis of a branching structure 15 1.52% 6.075 7.25E-08 1.39E-04
GO:0043010 camera-type eye development 13 1.31% 7.277 7.56E-08 1.45E-04
GO:0009953 dorsal/ventral pattern formation 13 1.31% 7.277 7.S6E-08 1.45E-04
GO:0048568 embryonic organ development 11 1.11% 9.103 9.18E-08 1.76E-04
GO:0007498 mesoderm development 16 1.62% 5.537 9.18E-08 1.76E-04
GO:0016055 Wnt receptor signaling pathway 24 2.42% 3.625 1.43E-07 2.74E-04
GO:0035239 tube morphogenesis 22 2.22% 3.877 1.63E-07 3.13E-04
GO:0030324 lung development 15 1.52% 5.71 1.72E-07 3.29E-04
GO:0030323 respiratory tube development 15 1.52% 5.598 2.26E-07 4.32E-04 negative regulation of transcription from
GO:0000122 RNA polymerase 11 promoter 26 2.63% 3.299 2.60E-07 4.97E-04
GO:0002009 morphogenesis of an epithelium 19 1.92% 4.305 2.71E-07 5.19E-04
GO:0021536 diencephalon development 8 0.81% 12.689 6.71E-07 0.00128
GO:0001707 mesoderm formation 10 1.01% 8.652 7.73E-07 0.00148
GO:0000902 cell morphogenesis 54 5.45% 2.06 7.87E-07 0.0015
GO:0032989 cellular structure morphogenesis 54 5.45% 2.06 7.87E-07 0.0015
GO:0042476 odontogenesis 12 1.21% 6.526 1.01E-06 0.00194
GO:0009880 embryonic pattern specification 12 1.21% 6.526 1.01E-06 0.00194 odontogenesis of dentine-containing
GO:0042475 teeth 11 1.11% 7.22 1.20E-06 0.0023
GO:0007369 gastrulation 13 1.31% 5.754 1.36E-06 0.00261
GO:0048565 gut development 8 0.81% 11.713 1.39E-06 0.00265
GO:0035282 segmentation 12 1.21% 6.344 1.39E-06 0.00266
GO:0048566 embryonic gut development 7 0.71% 14.804 1.50E-06 0.00287
GO:0042127 regulation of cell proliferation 53 5.35% 2.022 1.78E-06 0.0034
GO:0001704 formation of primary germ layer 10 1.01% 7.931 1.85E-06 0.00354
GO:0001657 ureteric bud development 10 1.01% 7.931 1.85E-06 0.00354
GO:0042471 ear morphogenesis 12 1.21% 6.011 2.53E-06 0.00484
GO:0001709 cell fate determination 11 1.11% 6.543 3.36E-06 0.00643 negative regulation of developmental
GO:0051093 process 18 1.82% 3.807 3.70E-06 0.00708
GO:0043583 ear development 13 1.31% 5.265 3.83E-06 0.00733
GO.0045596 negative regulation of cell differentiation 16 1.62% 4.115 5.54E-06 0.01059
GO:0051216 cartilage development 12 1.21% 5.571 5.75E-06 0.01101
GO:0050793 regulation of developmental process 33 3.33% 2.425 5.89E-06 0.01127
GO:0042472 inner ear morphogenesis 11 1.11% 6.158 6.21E-06 0.01188
GO:0021983 pituitary gland development 7 0.71% 12.112 7.54E-06 0.01443
GO:0001944 vasculature development 27 2.73% 2.691 7.70E-06 0.01473
GO:0048839 inner ear development 12 1.21% 5.312 9.51E-06 0.0182
GO:0040007 growth 35 3.54% 2.289 1.04E-05 0.01986
GO:0003007 heart morphogenesis 8 0.81% 8.957 1.31E-05 0.02498
GO:0007548 sex differentiation 17 1.72% 3.636 1.37E-05 0.02626
GO:0008283 cell proliferation 71 7.17% 1.698 1.40E-05 0.02673
GO:0048646 anatomical structure formation 25 2.53% 2.658 2.20E-05 0.04216 (30:0003006 reproductive developmental process 17 1.72% 3.479 2.43E-05 0.04655
GO:0048562 embryonic organ morphogenesis 7 0.71% 10.249 2.56E-05 0.04893
[0122] Table 4. Reprogramming differentially methylated regions (R-DMRs) overlap with bivalent domains. Overlap is significant in hypomethylated R-DMRs but not in hypermethylated R-DMRs.
Figure imgf000136_0001
*P values based on 10,000 permutations. Random values are averages over all 10,000 iterations.
[0123] Table 5. Reprogramming differentially methylated regions (R-DMRs) overlap with POU5F1, NANOG AND SOX2 binding sites. Overlap is significant in hypomethylated R-DMRs but not in hypermethylated R-DMRs.
Figure imgf000136_0002
* Data from Boyer et al. Cell. 122, 947-56 (2005).
**P values based on 10,000 permutations. Random values are averages over all 10,000 iterations. [0124] Table 6. Regions of differential methylation between 3 additional iPS lines and the fibroblasts from which they were derived.
These DMRs were defined by using a absolute area cutoff of 10.0 which corresponds in magnitude to the 5% FDR cutoff of the R-DMRs (n=6).
Columns are chromosome, start, end, fibroblast M value, iPS M value, absolute area, gene, distance to gene, relation to gene, distance to CGI, relation to CGI, and false discovery rate. chrl l 31784606 31787983 1.41933931 -0.31644601 159.697521 PAX6 1450 covers exon(s) -109 disjoint chr4 111780296 111782892 1.63173739 -0.17319743 132.277796 PITX2 2340 promoter -39 disjoint chr6 101009118 101012166 1.56292862 0.07999288 121.511837 SDVU 6105 inside intron 0 cover chr4 174692854 174695495 1.69137322 0.12000521 109.12492 HAND2 4902 upstream 280 disjoint chr3 27735081 27737225 1.4863651 -0.28171457 103.880733 EOMES 1563 covers exon(s) 130 disjoint chrl4 94307613 94310653 1.44978345 0.10765894 102.31315 GSC 1362 promoter 0 cover chr2 63126547 63128069 1.7594865 -0.28458065 88.0367223 EHBP1 339911 overlaps 3' 0 overlap chr9 963700 966127 1.41232668 0.00121211 87.4373264 DMRT3 836 promoter 35 disjoint chr6 82515479 82517932 -0.11617841 1.33296722 85.9059159 FAM46A 1214 overlaps exon 0 overlap upstream
chrl l 31778252 31780130 1.50775937 -0.12725076 85.7872915 PAX6 9303 covers exon(s) -260 disjoint chr5 174086712 174088442 1.75529701 0.00109963 85.6376081 MSX2 2532 inside intron -1742 disjoint chr2 66523155 66525137 1.53956949 -0.09867546 85.0156191 MEIS1 7120 covers exon(s) 798 disjoint chr5 122456101 122458523 1.38936079 -0.02772582 82.6647917 PPIC 55778 upstream 52 disjoint chrl4 69416842 69419462 -0.19824968 1.20834882 82.6223597 SMOCl 947 inside intron -562 disjoint chrlO 22661208 22663161 1.47790707 -0.07457995 82.1381419 BMI1 11063 downstream 195 disjoint chr6 137852407 137854382 1.36814374 0.03013524 78.9347235 OLIG3 2841 downstream -510 disjoint chr9 14339184 14341332 1.3243377 -0.09123465 77.7718048 NFffi 35240 upstream 0 cover chr2 156889981 156892146 1.56408799 0.15540625 76.1036644 NR4A2 5299 covers exon(s) 489 disjoint chr20 55266917 55268877 -0.38462956 1.31295385 75.9288397 BMP7 5830 inside intron 3817 disjoint chrlO 13553865 13556897 3.91218779 2.77340962 75.1728488 ClOorfiO 28084 inside intron 0 cover chrl2 113612415 113614212 1.46824729 -0.20251142 74.8083224 TBX3 6064 upstream 179 disjoint chr3 148607478 148609291 1.43068213 -0.14906639 73.7502558 ZIC4 382 promoter 384 disjoint chrl5 34963328 34965118 1.24859878 -0.38523485 73.2583479 MEIS2 212676 downstream 1690 disjoint chr2 10140514 10142176 -0.15386381 1.28455061 68.7801036 CYS1 2526 upstream -2047 disjoint chrl2 52730162 52731585 1.63796456 -0.23413354 67.9276439 HOXC4 33254 inside intron 558 disjoint chr5 142759709 142762066 -0.21656939 0.88384362 67.7592501 NR3C1 1380 overlaps exon 198 disjoint upstream
chr4 111778463 111780067 1.52433275 -0.02281807 66.9492861 PITX2 507 promoter 0 overlap chr5 149847619 149849411 -0.18889687 1.36376714 66.2220883 NDST1 31211 upstream -1388 disjoint chr9 1036495 1039411 1.36546585 0.24212751 65.9277152 DMRT2 2202 promoter -101 disjoint chrl 166462982 166464316 -0.35929034 1.47845303 64.8242749 SFT2D2 1113 inside intron -519 disjoint chr2 176745452 176746662 1.98718118 0.08912374 64.2735217 HOXD3 8402 overlaps 3' 0 overlap chrlO 35965659 35967214 1.42042373 -0.02828301 64.1847895 FZD8 3153 overlaps 3' 1293 disjoint chr4 111758467 111760060 1.61289956 0.1686074 64.1805476 PITX2 3642 overlaps exon 0 cover upstream
chrl 2 113615569 113617118 1.45655962 -0.0416652 63.996903 TBX3 9218 upstream -944 disjoint chr2 144408857 144410536 -0.10667617 1.22862162 63.4659312 GTDC1 395962 downstream 600 disjoint chr20 49847751 49849925 1.04888608 -0.18236327 62.6992872 SALL4 2495 inside intron 794 disjoint chrl3 49600378 49601736 1.55239767 -0.106977 62.687492 KCNRG 112988 downstream 0 overlap chrlO 21827602 21828807 1.40520939 -0.48129466 62.5304957 C10orfl l4 1406 promoter 0 overlap chrl2 79626961 79628584 1.3730142 0.04232383 62.2483215 MYF6 1385 overlaps 3' -114 disjoint chr7 19151550 19153330 1.13026015 -0.0528404 61.9190979 FERD3L 0 overlaps 5' 0 overlap chrl 215376167 215377357 1.65352118 -0.12965591 61.2488985 ESRRG 46569 upstream 15 disjoint chrl5 58474576 58476423 -0.1267126 1.18822035 60.1467502 ANXA2 1053 inside intron 618 disjoint chr9 111119732 111121206 1.59449008 -0.04994457 58.9638981 EPB41L4B 1635 inside intron 17 disjoint chr3 159297572 159299740 1.33681521 0.11610536 58.8402995 SHOX2 3779 overlaps exon 0 cover upstream
chr2 176736313 176737800 1.63327343 0.19509096 58.7718208 H0XD3 0 overlaps 5' 0 overlap chr7 27106893 27108134 1.61198644 0.01775409 58.6008133 H0XA2 784 overlaps exon 1572 disjoint upstream
chr2 66658875 66660266 1.46012019 -0.12209245 57.9542199 MEIS1 142840 downstream -540 disjoint chr6 126108229 126109739 1.22760488 -0.18167589 57.8604421 HEY2 2685 upstream 676 disjoint chr5 115934772 115936152 1.58854413 -0.04002657 57.8094492 SEMA6A 2245 inside intron 144 disjoint chr7 130439092 130440738 -0.04271931 1.3277853 57.4130828 M LN1 222439 upstream 160 disjoint chrl5 94691774 94693280 1.4590623 0.02587501 57.3507874 NR2F2 16825 downstream -1353 disjoint chr3 32835456 32837002 1.42079076 0.02329141 57.2574827 TRIM71 943 inside intron 0 cover chrl 196139120 196141080 1.11899291 0.04977786 56.8551686 Clorf53 721 inside intron -198 disjoint
Chr3 148589527 148590632 1.59584816 -0.30516054 56.4498444 ZIC4 16464 inside intron 566 disjoint chr9 102276375 102277706 1.59031662 -0.02432458 56.0310411 TMEFF1 838 inside intron 0 overlap chrl 5 35173578 35174643 1.60313351 -0.35008018 55.9275189 MEIS2 3151 covers exon(s) 35 disjoint chr2 176666686 176668660 0.9415369 -0.21644756 53.8527549 HOXD13 909 overlaps exon -161 disjoint upstream
chr3 148620314 148621273 1.90219036 -0.15922394 53.257094 ZICl 10444 downstream -299 disjoint chr4 151722401 151723404 1.86044619 -0.29765235 53.0965912 AB21L2 0 overlaps 5' 57 disjoint chr3 148614542 148615993 1.33962917 -0.03015777 52.9759123 ZICl 4672 inside exon -522 disjoint chrl l 31780431 31782210 1.31971017 -0.02747236 52.8408389 PAX6 7223 covers exon(s) 109 disjoint chr3 148587638 148589395 1.2363237 0.19347292 52.7520873 ZIC4 17701 overlaps exon 1803 disjoint upstream
chrlO 22652675 22653622 1.54940518 -0.48360594 52.6684368 BMI1 2530 inside intron 659 disjoint chr4 81403269 81404477 1.71294929 0.14782841 52.6540894 FGF5 2288 promoter 2041 disjoint chr6 10513143 10514243 1.64823552 -0.16251431 52.4938953 TFAP2A 6349 inside intron 0 overlap chrl 212223887 212225199 1.41267876 -0.1036052 52.2142965 PROX1 3283 upstream 150 disjoint chr5 72631433 72632752 1.55907375 0.03752966 51.5934543 TME 174 131604 downstream 0 overlap chr4 54663407 54664534 1.52539942 -0.1795399 51.3548036 GSH2 2453 close to 3' -587 disjoint chrl 7 76339418 76340413 -0.5047575 1.31226294 51.2301116 IAA1303 206199 inside intron -4596 disjoint chrl 7 61731115 61732434 1.00287114 -0.32605409 51.1697293 PRKCA 1728 inside intron -1036 disjoint chr4 54653254 54656517 1.42864271 -0.08533 51.1202836 GSH2 4437 upstream 0 overlap chrl4 36198679 36200022 1.42884466 0.12996355 51.0921342 PAX9 633 promoter -654 disjoint chrlO 8141409 8143320 1.01455344 0.00757763 50.9073342 GATA3 4737 inside intron -635 disjoint chr3 148559843 148560802 1.87070908 0.06016751 50.777823 ZIC4 46294 downstream 0 overlap chrl 196155778 196157454 1.3179303 0.16174518 50.7648828 LHX9 2639 covers exon(s) 0 cover chrl l 44289748 44292120 1.41984069 0.14716226 50.6834069 ALX4 1457 promoter -415 disjoint chr2 45030644 45032479 1.13026345 -0.01747515 50.5191901 SDG 8104 downstream 0 overlap chrS 121673027 121674929 -0.13976622 0.92706584 50.4630188 SNCAIP 789 promoter 420 disjoint chrl 6 85104354 85106590 1.01148338 -0.08518906 50.3432137 FOXF1 2721 overlaps 3' 0 overlap chrl 7 37864755 37865925 -0.31367878 1.08098918 50.2945084 ATP6V0A1 368 inside intron -197 disjoint chr6 10500368 10502013 1.12758579 -0.16262394 50.2912829 TFAP2A 18579 downstream -1284 disjoint chrl 8 55715765 55717622 1.54732796 -0.42193005 50.1197567 PMAIP1 594 promoter 224 disjoint
Figure imgf000139_0001
chr3 4883192 4884119 -0.29537422 1.29522205 40.9744879 ITPR1 373057 downstream 843 disjoint chr4 142274610 142275533 -0.21850947 1.26137732 40.9122333 RNF150 545 promoter -559 disjoint chr4 1 11756724 111757722 1.24225948 -0.12133459 40.630316 PITX2 5980 downstream 955 disjoint chr2 222866029 222867286 1.16157444 0.02924337 40.6244778 PAX3 4657 overlaps 3' 683 disjoint chr22 16230787 16231785 1.20193546 -0.23847212 40.490332 CECR1 160009 upstream -54 disjoint chr6 10525703 10526733 1.42347966 0.02902175 40.3744313 TFAP2A 1049 inside intron 0 overlap chrl3 99446168 99447515 0.9251472 -0.1903809 40.3531723 ZIC2 13849 downstream 0 overlap chr8 21834853 21835957 0.25128115 1.49078591 40.2928191 XP07 1726 inside intron -965 disjoint chr8 102575600 102576505 1.58166876 -0.10776688 40.002449 GRHL2 1439 inside intron 0 overlap chr2 24566107 24566952 2.16296696 0.07633756 39.9675861 NCOA1 93897 upstream 262 disjoint chr7 96492966 96493817 1.47095209 -0.17887215 39.811767 DLX5 888 promoter -831 disjoint chrl3 20185358 20186509 -0.10556272 1.07201553 39.7484546 IL17D 9877 inside intron 7102 disjoint chr7 97865583 97867138 0.24994178 1.2668851 39.620659 BAIAP2L1 1177 inside intron 895 disjoint chrl 219117347 219118497 1.27721602 -0.13242573 39.5360752 HLX1 884 promoter 0 overlap chr7 42233485 42234204 1.44965217 -0.49210691 39.2774323 GLI3 4066 upstream 0 overlap chr7 96489389 96489997 1.94554359 -0.35377365 39.2407958 DLX5 2081 covers exon(s) 0 overlap chr3 159295618 159296706 1.40515825 0.07078055 39.2017106 SHOX2 6813 overlaps 3' -163 disjoint chr5 92950314 92951305 1.48115119 0.08578404 39.0525814 NR2F1 5516 inside intron -61 disjoint chr8 30363430 30364952 0.99255999 -0.10209269 38.9617937 RBPMS 1945 inside intron -1010 disjoint chr6 26333632 26334456 1.85778512 0.11935738 38.8688877 HIST1H3E 271 overlaps 3' 0 overlap chr2 200037949 200039436 0.90792729 -0.09695814 38.8349169 FLJ32063 3427 upstream -23 disjoint chr22 44843075 44844071 -0.37945912 1.10525055 38.8068408 C22or£26 14388 upstream 569 disjoint chrl 215380592 215381312 1.99599543 0.05887783 38.7899086 ESRRG 50994 upstream -2196 disjoint chr2 934438 935538 1.3746914 0.15632669 38.7819133 SNTG2 1016 promoter 148 disjoint chrl l 32869188 32870223 1.18386157 -0.19830937 38.7576608 QSERl 1144 promoter 342 disjoint chrlO 364761 365864 0.04707745 1.33972951 38.712546 DIP2C 359741 covers exon(s) -1602 disjoint chrl8 52963741 52964774 -0.2976927 1.42107702 38.5819941 WDR7 494128 downstream -23549 disjoint chr2 119322687 119323574 1.80658283 0.28369654 38.5786779 EN1 459 promoter 0 cover chrl2 79856029 79856864 1.98216194 0.28982682 38.5145338 LIN7A 205 promoter -384 disjoint chr6 27304933 27306874 1.24493913 0.10758785 38.3829047 PRSS16 16612 upstream 19897 disjoint chr5 115324006 115325354 -0.27226571 0.95491407 38.38115 FLJ90650 815 promoter 152 disjoint chr2 121211702 121212906 1.27471168 0.0947085 38.3371395 GLI2 53420 upstream 0 overlap chr7 27211771 27212642 1.87064212 0.3952644 38.2946966 HOXA13 5522 upstream 0 overlap chrl 7 44006419 44007659 1.12010346 -0.0410507 38.2436146 HOXB3 0 overlaps 5' 1393 disjoint chr7 113510831 113511757 1.2969881 -0.07669011 38.2201065 PPP1R3A 164532 upstream 403 disjoint chrl 3 109230523 109231903 -0.2112348 1.16507154 38.1652952 IRS2 5011 inside intron 564 disjoint chr21 46384349 46386250 1.82628187 0.02049161 38.0669543 FTCD 13658 inside intron 3463 disjoint chr4 174665695 174666480 1.70850822 -0.00015046 37.983599 HAND2 21472 downstream 481 disjoint chr21 26461485 26462918 0.58549596 -0.37912164 37.911977 APP 2084 inside intron 846 disjoint chr9 98422258 98423467 1.02241473 -0.02993963 37.897291 CDC14B 326 promoter -201 disjoint chrl 6 71640295 71641270 1.47201553 -0.09674105 37.8711301 ATBF1 521 promoter -229 disjoint chr5 72633197 72634662 1.76067342 0.33811921 37.8300672 TMEM174 133368 downstream 52 disjoint chrl 4 64239302 64240261 1.44936721 -0.01944425 37.8246656 PLE HG3 684 promoter 368 disjoint chrl 4 93321177 93322351 -0.16152592 1.11140284 37.7861329 PRIMA1 2167 inside intron 1354 disjoint chrlO 21836220 21837096 1.58266657 -0.12422951 37.7480975 FLJ45187 17520 downstream 542 disjoint chrl 7 44004790 44006184 1.04476883 -0.02520951 37.7326138 HOXB3 624 inside intron 2868 disjoint chr7 81911950 81912703 1.77166105 -0.00971925 37.7217206 CACNA2D1 984 promoter -494 disjoint chrl l 6632319 6633032 -0.70472791 1.06582745 37.621127 DCHS1 617 inside intron 40 disjoint chr3 159301979 159303370 1.51755907 0.24683664 37.5949094 SH0X2 149 overlaps exon 553 disjoint downstream
chrl2 128900835 128902152 -0.01856424 1.04089971 37.5706876 TMEM132D 52013 inside intron 3484 disjoint chr5 60660869 60661693 1.8464888 -0.05134927 37.4883351 DKFZP686E2 166821 upstream 569 disjoint
158
chrl 6 49141703 49142618 -0.24317296 1.23062425 37.3877023 NKD1 1962 inside intron -737 disjoint chr5 89888779 89889849 1.50532153 -0.09910689 37.2201052 GPR98 523 promoter 197 disjoint chr3 161424439 161425508 1.69863112 0.54327117 37.0700201 IFT80 174505 downstream 99 disjoint chr4 186552705 186553838 0.07002031 1.25745256 36.8281927 ANKRD37 995 promoter 299 disjoint chrl9 35406528 35407539 1.27056884 -0.15585054 36.7325097 ZNF536 147628 upstream 0 overlap chrl6 17469585 17470725 -0.1451224 1.08062278 36.6902145 XYLT1 1513 inside intron 867941 disjoint chr2 119324479 119325418 1.59649017 0.09521821 36.6440281 EN1 2251 promoter -99 disjoint chr9 70927207 70927993 1.91581456 -0.00890318 36.3972215 FXN 87044 downstream -20 disjoint chr3 170859776 170861041 1.16996466 0.01066232 36.3601067 MDS1 3126 inside intron 1087 disjoint chr8 41287238 41288584 1.29121452 0.17245066 36.3581311 SFRP1 1102 promoter -941 disjoint chrl4 100421536 100422503 -0.20011261 1.1731406 36.2080862 FLJ41170 118894 upstream -1923 disjoint chrl9 6017063 6017881 -0.31960052 1.17213599 36.1982583 RFX2 43672 inside intron -25835 disjoint chrl l 64949547 64950620 -0.27528223 0.97938027 36.1539177 FKSG44 38849 downstream -1913 disjoint chr2 70985864 70986871 1.647413 0.37120001 36.1302393 VAX2 4637 inside intron -100 disjoint chr9 93221086 93222268 -0.12959604 1.09720754 36.1179896 NFIL3 3696 inside intron 960 disjoint chr4 113651832 113652617 1.67447978 -0.01248692 36.066937 NEUROG2 4159 downstream 0 overlap chr8 72916537 72917706 1.24907386 0.14860161 36.0083662 MSC 1578 overlaps exon 0 overlap upstream
chr5 154219106 154220032 -0.13990552 1.31206448 35.9618646 CNOT8 716 inside intron -551 disjoint chrl9 36538829 36539809 1.08996256 -0.3296489 35.9512967 TSHZ3 76815 upstream 0 overlap chrl 162811165 162812119 1.58327994 0.21300667 35.9431306 PBX1 15605 inside intron 45 disjoint chr8 976495 978327 3.5304042 2.196131 35.9429244 ERICH1 305270 upstream 0 cover chr6 134540510 134541574 -0.02928008 1.30769243 35.9333102 SG 2816 upstream -1061 disjoint chrl 219128497 219129717 1.40212372 0.15148187 35.792526 HLX1 9116 downstream -803 disjoint chr5 174090533 174091771 1.29541086 0.26091667 35.7441 MSX2 6353 downstream 0 overlap chr2 96665729 96667046 0.26565799 1.23112831 35.6900575 FLJ10081 763 covers exon(s) 593 disjoint chr4 186369139 186369714 2.05523324 -0.21224619 35.6741435 SNX25 862 inside intron -249 disjoint chr2 86701715 86702720 -0.25063738 1.08495704 35.6273872 RNF103 1768 inside intron 833 disjoint chrlO 90631231 90632305 0.0697541 1.20878597 35.5999355 STA BPL1 1226 inside intron -628 disjoint chr8 848029 849372 -0.1974795 0.83480055 35.5399241 ERICH 1 176804 upstream -7624 disjoint chr7 27109933 27111293 1.43384471 0.15394794 35.5396551 HOXA2 1015 promoter 0 overlap chr7 2305187 2306410 0.23812667 1.29352782 35.5049086 SNX8 14214 inside intron 13745 disjoint chr4 111773533 111774456 1.73451544 0.28304328 35.5046238 PITX2 3500 covers exon(s) 0 overlap chr9 128419394 128420895 1.04836932 0.02382454 35.4981982 LMX1B 2776 inside intron -1467 disjoint chr5 162866105 162867332 -0.06969603 1.07278134 35.4884274 MAT2B 943 inside intron -581 disjoint chr4 174682124 174683053 1.33203868 -0.0258723 35.4786761 HAND2 4899 downstream -1601 disjoint chr2 156894429 156895563 1.28187209 0.11221185 35.4511337 NR4A2 1882 covers exon(s) 0 overlap chr3 148556783 148558297 0.7478876 -0.13741334 35.3838043 ZIC4 48799 downstream 1505 disjoint chrl 3 29319130 29320270 -0.10245666 1.05810038 35.2952603 UBL3 1889 inside intron 1651 disjoint chr9 23812907 23813878 1.48429718 0.17923849 35.2447419 ELAVL2 2184 inside intron -240 disjoint chr5 74196142 74196821 2.05458898 0.14753959 35.0807768 TINP1 97284 downstream 471 disjoint chrl7 44431640 44432871 0.66981024 -0.47929232 35.015976 IGF2BP1 1868 inside intron -599 disjoint chr2 176721629 176722750 1.53891403 0.47229349 34.8048197 HOXD4 1608 promoter 444 disjoint chrl9 40306506 40307186 -0.53195928 1.32791778 34.7231507 FXYD3 7868 overlaps 3' 66 disjoint chr5 146810903 146812189 0.88306483 -0.15953011 34.6738633 DPYSL3 1263 inside intron 564 disjoint chr5 88213262 88214583 -0.29338125 0.65176708 34.5595805 MEF2C 196 overlaps exon 1039 disjoint downstream
chr3 148623908 148624938 1.3437418 0.100801 34.542562 ZIC1 14038 downstream 0 overlap chr2 28471827 28472912 0.12043858 1.18582044 34.4892375 FOSL2 2545 inside intron -1575 disjoint chr9 21994910 21995921 1.47949056 0.0805498 34.3846603 CDKN2B 3390 inside exon 0 overlap chrl5 35183540 35184463 1.20152056 -0.14631163 34.343197 MEIS2 2749 upstream -2000 disjoint chr2 24569028 24570515 -0.13716341 0.92905525 34.3400172 NC0A1 90334 upstream -356 disjoint chr5 78843388 78844211 1.33071045 -0.1097438 34.3305756 H0ME 1 1244 inside intron 892 disjoint chrl5 26067358 26069146 2.70509708 1.86136342 34.2788444 HERC2 171743 inside intron -15789 disjoint chr6 3403641 3404909 1.49812455 0.19760298 34.1499529 C6orf85 13425 upstream -679 disjoint chrl5 34965493 34966106 1.7650159 -0.25789057 34.1334672 MEIS2 211688 downstream 702 disjoint chrl l 75205444 75206334 -0.53342925 0.82994728 34.1059079 UVRAG 1585 inside intron -870 disjoint chrl l 133792794 133793856 0.23041543 1.36750215 34.0923131 B3GAT1 5773 upstream -4665 disjoint chr9 97316427 97317391 1.06946513 -0.24800662 34.0867133 PTCH1 5776 upstream 558 disjoint chr7 4194956 4196375 0.03207979 1.2580873 34.0552685 SDK1 887351 inside intron -58677 disjoint chrl 16147587 16148552 0.04141807 1.33503565 33.6866549 ZBTB17 26548 inside intron -3418 disjoint chrl 24615496 24616770 0.1200371 1.03569209 33.659113 NPAL3 592 inside intron 0 overlap chr22 26528457 26529737 1.06752995 0.00071239 33.5151875 MN1 972 promoter 0 overlap chrl5 94706279 94707046 1.44854863 -0.25676352 33.4364045 NR2F2 31330 downstream -225 disjoint chr4 154075001 154076286 1.26390142 0.11543418 33.4235137 IAA1727 7298 upstream 276 disjoint chrl 6 49747631 49748987 0.87755181 -0.10452081 33.3995863 SALL1 4979 upstream 0 overlap chr8 128877152 128878297 1.52287616 0.34062076 33.3799172 MYC 59655 downstream -1071 disjoint chr7 27117260 27118020 1.42748172 -0.15555828 33.293307 HOXA3 2120 inside intron -317 disjoint chrl 6 52874095 52875381 1.29181571 0.18287109 33.24166 DOG 2497 overlaps 3' 0 inside chrlO 3818610 3819574 1.54084523 0.27721245 33.1926565 KLF6 1156 promoter -484 disjoint chrS 168657986 168659586 0.23033994 1.14168668 33.0803299 SLIT3 967 inside intron 421 disjoint chrl5 75497328 75498542 -0.59563297 0.61415126 32.9997554 HMG20A 1755 promoter 138 disjoint chr9 132580000 132580887 -0.22361474 1.00741636 32.9252847 ABLl 912 inside intron -1278 disjoint chrlO 126418196 126419208 1.38664329 0.16000606 32.8770028 FAM53B 3711 inside intron 2096 disjoint chrlO 62161448 62162561 1.05320368 -0.28838479 32.8555208 CDC2 45680 upstream 230 disjoint chr4 174689601 174690314 1.45353815 -0.19875969 32.8464725 HAND2 1649 promoter -64 disjoint chrl4 103381739 103382992 1.53031091 0.25584893 32.7935231 PPP1R13B 562 inside intron 0 overlap chr5 53851217 53852761 0.0389533 0.9448501 32.6786156 SNAG1 1678 overlaps 3' -154 disjoint chr7 27247454 27248203 1.58428404 0.05347603 32.6746147 EVX1 485 promoter 408 disjoint chr6 2712192 2713113 -0.41704184 1.04323084 32.5792063 WRNIP1 1528 inside intron -418 disjoint chr5 178980948 178981704 -0.3475598 1.16324763 32.5487315 H RPH1 1571 overlaps exon 717 disjoint upstream
chr4 109306264 109306909 2.02400798 0.24900497 32.5454748 LEF1 2117 inside intron 287 disjoint chr4 175371989 175372912 0.96834676 -0.32261502 32.5220816 FBX08 69064 downstream 0 overlap chrl2 8956261 8957380 0.60880715 -0.42041957 32.4850332 PHC1 1202 promoter 833 disjoint chrl 7 59930427 59931450 -0.40570267 0.79101634 32.4489273 DDX5 1418 covers exon(s) 491 disjoint chr22 44841395 44842339 -0.13135148 1.13454524 32.3104988 C22or£26 12708 upstream 2301 disjoint chrl 8 55087868 55089218 0.57792669 -0.39236539 32.2760142 RAX 2386 inside intron -61 disjoint chr8 61996550 61997306 1.43097509 -0.08057243 32.2452884 CHD7 242658 downstream 0 overlap chr2 1 19314742 119315614 1.38620469 0.24927731 32.2191372 EN1 6614 downstream 0 overlap chr3 62336359 62337562 0.96837037 -0.0866244 32.2095891 FEZF2 2299 promoter 85 disjoint chrlO 59943839 59944798 -0.26232877 0.96983078 32.1527099 TFAM 128658 downstream -377 disjoint chr6 32223942 32225082 1.39327528 0.20648229 32.1211558 PRRT1 2615 overlaps 3' 0 overlap chrl5 34958058 34958784 1.6097191 -0.11572199 32.118552 EIS2 219010 downstream 981 disjoint chr4 174674573 174675606 1.36015595 0.1737928 32.0311716 HAND2 12346 downstream 0 overlap chr6 166405574 166406539 0.14761946 1.32789677 32.0207068 LOC441177 84546 downstream -63343 disjoint chr6 84992701 84993627 -0.4905171 0.87036081 31.9426797 KIAA1009 405 inside intron 208 disjoint chr2 174911649 174912673 1.06891008 -0.10635857 31.8852434 FLJ46347 1110 promoter 416 disjoint chr6 27905840 27907508 1.36757055 -0.11945423 31.8701075 HIST1H4K 0 covers 0 cover chr3 148595520 148596592 1.00239274 -0.13363624 31.868717 ZIC4 10504 overlaps exon 0 overlap downstream
chr4 109311333 109312154 1.16744271 -0.21230657 31.7342334 LEF1 2307 promoter 0 overlap chr9 125818589 125819431 1.4693599 -0.08936341 31.6405688 LHX2 4880 inside intron 0 inside chrl7 67623810 67624595 1.24546969 -0.18838781 31.6214881 SOX9 4160 upstream 0 overlap chrl7 7321768 7322832 0.00219398 1.12225576 31.6202315 ZBTB4 5408 inside intron 158 disjoint chrl5 94697217 94698152 1.55827516 0.30691429 31.5464412 NR2F2 22268 downstream 0 overlap chr5 79414629 79415608 -0.23889116 1.25345278 31.4890705 THBS4 47883 overlaps 3' -47385 disjoint chrl2 113621261 113622647 1.57029886 0.29236465 31.4734201 TBX3 14910 upstream 0 overlap chr2 176746750 176747616 1.2282284 -0.09300692 31.4566035 H0XD3 9700 downstream 181 disjoint chr2 45012649 45013684 1.21152155 0.15435829 31.3754671 SDO 8856 upstream 0 cover chr4 4916646 4917608 1.58070059 0.24220086 31.314987 MSX1 4347 downstream 0 overlap chr2 201434189 201435016 -0.52960658 0.91009768 31.3054606 CLK1 2650 covers exon(s) 2121 disjoint chrl2 45053574 45054764 1.57192109 0.48987324 31.3015875 SLC38A2 761 promoter -674 disjoint chrl6 4102137 4102769 -0.54831618 1.28800663 31.2953729 ADCY9 3417 inside intron 2040 disjoint chr20 2436261 2437113 -0.72171411 0.84748261 31.2374995 ZNF343 664 inside intron 77 disjoint chr5 139468695 139469481 1.2265192 -0.26112596 31.2017844 PURA 4410 upstream -839 disjoint chr5 77303311 77304144 1.90071962 0.57305784 31.1507087 AP3B1 322139 downstream 0 overlap chrl 21373594 21374484 -0.25772893 0.97798895 31.1375503 EIF4G3 1442 inside intron 1218 disjoint chr2 156887749 156888636 1.54980072 0.23311805 31.0749309 NR4A2 8809 downstream -2157 disjoint chrl 9 36535214 36535822 1.47510639 -0.23613062 31.0564595 TSHZ3 73200 upstream 0 overlap chr5 88024236 88025538 0.98080132 0.10856911 30.9970478 MEF2C 189241 downstream -2670 disjoint chr6 101020889 101021806 1.42452661 0.17393714 30.9598291 SIM1 2618 upstream 0 overlap chr4 111771548 111772396 1.33322736 -0.02247189 30.9315615 ΡΓΓΧ2 5560 inside intron 132 disjoint chr9 73571566 73572390 1.17670973 -0.18743625 30.8838474 TMEM2 837 inside intron 507 disjoint chrl 7 38976402 38977481 0.90541089 -0.49747042 30.8399514 ETV4 1291 inside intron 649 disjoint chrlO 3814113 3815252 -0.21450609 0.94377888 30.8283701 KLF6 2202 overlaps exon -96 disjoint upstream
chr5 177950491 177951275 -0.05731718 1.35685951 30.7552237 COL23A1 330 promoter -215 disjoint chr5 112286167 112287021 -0.19322008 1.10488823 30.750666 REEP5 238 promoter -136 disjoint chr7 12695285 12696066 1.23748751 -0.11621876 30.7488161 ARL4A 1800 inside exon -1512 disjoint chrl l 116471456 116472295 -0.19558433 1.12449984 30.7341716 IAA0999 1907 inside intron 1764 disjoint chr2 166359924 166360896 1.88802642 0.67427942 30.7267225 GALNT3 24469 upstream -712 disjoint chrl 7 44015119 44015943 1.29395752 0.0163039 30.6859256 HOXB4 4378 upstream -117 disjoint chr4 145788022 145788786 1.1573457 -0.29297677 30.6710418 HHIP 1400 inside intron -1159 disjoint chrl 119335478 119336753 1.55033318 0.49618585 30.5702727 TBX15 1777 promoter 436 disjoint chrl 2 81606332 81607539 -0.1017113 0.91061623 30.4921838 TMTC2 1268 inside intron -555 disjoint chrl 112853626 112854427 1.49340142 0.12807471 30.4795024 WNT2B 238 inside intron 0 overlap chrl 7 39994289 39994900 1.10706819 -0.53456416 30.4621433 FZD2 3839 downstream -1912 disjoint chrlO 116382729 116383478 -0.20676093 1.2164324 30.4440183 ABLIM1 24569 inside intron -912 disjoint chr7 71437052 71438011 0.15033838 1.33919805 30.3041567 CALN1 1884 inside iritron 682 disjoint chr5 50301629 50302450 1.30580141 0.00690888 30.2919627 PARP8 303060 downstream -135 disjoint chrX 39836777 39837829 0.93754239 -0.09889956 30.2600759 BCOR 3770 inside intron -168 disjoint chr2 102605330 102606728 0.07811236 1.03094191 30.2289704 SLC9A2 2733 inside intron -2344 disjoint chr20 54636195 54636861 1.48354972 -0.10019974 30.113068 TFAP2C 903 promoter 0 inside chr8 72920788 72921505 1.72161941 -0.2034737 30.1040566 MSC 1504 promoter -1567 disjoint chr4 78034283 78035197 -0.06399261 1.02457851 30.1014404 ANKRD56 2828 overlaps 3' 1842 disjoint chrl7 44018803 44019767 1.2040642 0.01597175 30.0953723 HOXB5 6334 downstream -3801 disjoint chr6 10531608 10532708 1.01559071 -0.07831345 30.0651228 TFAP2A 3826 upstream -974 disjoint chr7 27137589 27138413 1.56169306 0.34062244 30.0304233 HOXA4 666 promoter -426 disjoint chrlO 101932883 101933734 -0.15068919 1.18788467 29.9719691 SPFH1 1658 covers exon(s) 1827 disjoint chrlO 94440853 94442083 1.32053878 0.29066857 29.9507237 HHEX 1174 inside intron 0 cover chr2 176693206 176694129 1.22433803 0.10536124 29.9394078 HOXD10 3469 downstream 541 disjoint chr 34951093 34951668 1.60207854 -0.29110865 29.8420398 NBEA 536638 inside intron 0 overlap chr2 174906633 174907454 1.32670521 0.0498608 29.8417426 FLJ46347 3085 overlaps 3' 255 disjoint chr3 171555291 171556112 1.41597249 0.08472152 29.8290805 SKIL 2097 promoter 1365 disjoint chr4 115740315 115741028 1.01606737 -0.43520355 29.8281692 UGT8 21943 upstream 0 overlap chrl6 56718330 56719007 -0.38592419 1.1012187 29.820245 C16orf80 1789 inside intron 1248 disjoint chr4 30333743 30334462 1.8242152 0.41459039 29.8077558 PCDH7 2609 inside exon 0 overlap chr2 66507575 66508719 1.18991148 0.17719711 29.7060266 MEIS1 7316 upstream 0 overlap chr4 124541477 124542573 -0.00577835 1.0846253 29.5881974 SPRY1 1345 overlaps exon -2029 disjoint upstream
chrlO 124218089 124218979 0.06066256 1.27337721 29.5720366 HTRA1 7043 inside intron -5859 disjoint chr8 22355564 22356594 -0.1443314 0.83979129 29.5297431 PPP3CC 1024 inside intron -477 disjoint chr4 174659289 174660227 1.43921915 0.30342524 29.5293354 HAND2 27725 downstream -271 disjoint chrl4 51849417 51850354 -0.22788891 1.02669463 29.4617456 PTGER2 508 promoter 83 disjoint chr5 11955022 11955804 0.24408633 1.6879937 29.3342179 CTNND2 1305 inside intron 746 disjoint chr8 75396686 75397561 -0.35371547 0.94986888 29.331202 JPH1 570 promoter -30 disjoint chr4 147776235 147777305 -0.20629266 0.78786792 29.3111203 POU4F2 2189 promoter 376 disjoint chrl6 55197586 55199613 0.05954606 1.00991896 29.252795 T2A 398 promoter 17 disjoint chr6 10517456 10518103 1.51533716 -0.16150717 29.2414682 TFAP2A 2489 inside intron 0 overlap chrl3 107320627 107321592 -0.148237 0.9131692 29.2301315 LIG4 343538 downstream -1563 disjoint chrl8 58343146 58343986 1.09442494 -0.10885958 29.2288103 ZCCHC2 13907 upstream -57 disjoint chrl8 51240890 51241963 -0.27356358 0.90295461 29.1934577 TCF4 164477 inside intron 166053 disjoint chrl4 23089148 23089933 0.83342524 -0.48937294 29.1814826 THTPA 5137 upstream 0 Overlap chr22 44839222 44840220 -0.09885737 1.12781438 29.1779315 C22orf26 10535 upstream -2530 disjoint chr6 13817340 13818286 -0.3049493 1.0686901 29.1771702 RANBP9 1488 inside intron 672 disjoint chrl 212236443 212237156 -0.18205789 1.34789428 29.1601055 PROX1 7961 inside exon -7083 disjoint chr3 140144937 140145900 1.30665196 0.14364718 29.1569311 FOXL2 2590 overlaps 3' 505 disjoint chrX 48659812 48660525 1.29617504 -0.15621339 29.1438506 PIM2 702 covers exon(s) 182 disjoint chrH 28311428 28312865 -0.42701798 0.32350434 29.1076724 FOXG1B 5391 downstream 289 disjoint chr2 239360152 239361049 0.06554668 1.13609496 29.1068788 FLJ43879 151852 downstream 58796 disjoint chr7 96474667 96475276 1.61392213 -0.0984248 29.1016084 DLX6 1442 covers exon(s) -982 disjoint chrl 48229737 48231027 0.28542423 1.20385504 28.9727948 SLC5A9 229963 upstream 1372 disjoint chr5 59223568 59224281 1.57361215 0.12639027 28.9386111 PDE4D 305537 upstream 522 disjoint chrlO 101757470 101758877 -0.13331038 0.78222123 28.930842 CPN1 72706 downstream 56074 disjoint chr20 47329939 47331033 0.65181139 -0.42520196 28.8637451 ZNFX1 1931 promoter -1333 disjoint chrl 7 9490197 9491338 1.38812956 -0.16790417 28.8413274 WDR16 69514 downstream 0 overlap W
144
chrl l 19755778 19756387 1.55851369 -0.13719627 28.8270693 NAV2 64291 inside intron -253 disjoint chr7 27207517 27208493 1.31410174 0.30738106 28.7871572 H0XA13 1268 promoter -681 disjoint chr20 49852370 49853047 1.37281441 -0.14089684 28.7605138 SALL4 0 overlaps 5' 0 overlap chr4 189190243 189190845 1.83206693 0.08422237 28.719619 ZFP42 36325 downstream -36373 disjoint chr4 184255050 184255817 1.57299005 0.21025773 28.7133732 FLJ30277 1528 overlaps 3' 7 disjoint chr9 118489930 118490889 -0.11823234 1.19618256 28.6814376 TRIM32 501 inside intron -342 disjoint chr9 14301857 14302969 0.70356425 -0.24715867 28.6361919 NHB 975 inside intron 0 overlap chr8 1303571 1304710 0.09018922 1.33372356 28.6012898 DLGAP2 132265 upstream 3929 disjoint chr4 151720773 151721384 1.75866626 0.05546162 28.6009836 LRBA 434714 inside intron -24 disjoint chrl 232809915 232810670 -0.01378924 1.20793109 28.5629284 IRF2BP2 1223 overlaps exon 229 disjoint upstream
chrl8 13860374 13861613 -0.15471482 0.88938193 28.5402565 MC2R 43921 downstream -1348 disjoint chr2 172661776 172662573 1.48986118 -0.01097495 28.5119293 DLX1 3323 inside exon -370 disjoint chr5 95095627 95096529 -0.2603568 0.94531634 28.494653 RH0BTB3 3022 inside intron -2059 disjoint chr2 104841052 104842142 1.03467316 -0.09616738 28.4727988 POU3F3 2652 downstream -1132 disjoint chr6 30525723 30526766 0.2191081 1.38091679 28.456712 HLA-E 38483 upstream 57 disjoint chr9 137149847 137151262 3.49294953 2.48785036 28.4521477 0LFM1 42856 overlaps exon 165 disjoint upstream
chr2 78860830 78861951 -0.10414956 1.18448524 28.4442023 REG3G 244382 upstream 211749 disjoint chr6 101013331 101014120 1.46613019 -0.16799937 28.4269809 SMI 4151 inside intron 0 overlap chr2 66662713 66663534 1.24812055 0.07099196 28.423241 MEIS1 146678 downstream 0 overlap chrl 8 2838632 2839527 -0.28642777 0.78648999 28.3871687 EMELIN2 1605 inside intron -457 disjoint chrl2 119419615 119420682 -0.0969587 1.19907016 28.3679071 DYNLL1 1374 overlaps 3' -519 disjoint chrlO 32258888 32259842 -0.2779115 0.94857419 28.3624995 ARHGAP12 1113 promoter -490 disjoint chrl2 6532030 6532840 0.09121805 1.37364728 28.3254088 HOM-TES- 2649 inside intron 1846 disjoint
103
chrl 7 75364793 75365758 0.91464388 -0.1575456 28.3177611 CBX2 829 promoter 215 disjoint chr6 159511609 159512565 -0.10874887 0.97492059 28.2878813 FNDC1 1193 inside intron -302 disjoint chrl4 72427053 72428070 1.44155 -0.04782591 28.2663641 DPF3 2523 inside intron 472 disjoint chrl 7 73467672 73468565 0.8702718 -0.2860774 28.2527427 FLJ45079 75909 upstream -125 disjoint chr8 49995255 49996308 -0.03213769 1.05488782 28.2193578 SNAI2 232 overlaps two 2232 disjoint exons
chr7 126677193 126678150 0.00297763 1.14183517 28.217734 GRM8 6648 upstream 386 disjoint chr3 74745150 74746070 -0.10073697 0.95421382 28.1788486 CNTN3 92118 upstream 123 disjoint chrl 7 56885838 56886500 1.32324386 -0.24104829 28.1749597 TBX4 2088 promoter 5 disjoint chr2 3163123 3164346 3.86869618 2.54956668 28.1422821 TSSC1 196258 downstream 0 Overlap chrlO 132997840 132999071 -0.12733143 0.81803697 28.1186272 TCERG1L 902 inside intron 112 disjoint chr8 102572779 102573531 1.28011299 -0.20759629 28.0332612 GRHL2 630 promoter 123 disjoint chrl l 2255385 2256365 0.06717805 1.02832001 28.0167705 ASCL2 6628 upstream -5877 disjoint chrl l 19693101 19694024 0.23950959 1.23555052 28.0083893 NAV2 1614 inside intron -1205 disjoint chrl 9 36537647 36538597 1.1063984 0.02045547 27.9611349 TSHZ3 75633 upstream 1189 disjoint chrl 6 86080459 86082018 0.01281927 1.33725645 27.9386741 ZCCHC14 942 inside intron -11330 disjoint chrlS 34960305 34961023 1.16555273 -0.39048929 27.8754822 MEIS2 216771 downstream 0 overlap chr4 85635369 85636426 1.02937779 -0.10900502 27.858292 NKX6-1 1984 covers exon(s) 257 disjoint chrl2 41267894 41268951 -0.17946324 0.76710704 27.8571045 PRIC LEl 793 inside intron 148 disjoint chrl 2 121944796 121945947 0.1689921 1.03908987 27.8472141 VPS37B 717 inside intron 339 disjoint chr7 148025157 148026045 0.07074408 1.25565214 27.8337364 CUL1 820 promoter 318 disjoint chrl l 27448314 27449522 0.88795481 0.01403554 27.8144277 LGR4 1346 inside intron 694 disjoint chrl 2 107646995 107647921 -0.31275178 0.97979694 27.759497 COR01C 1502 inside intron 432 disjoint chr7 113515113 113515766 1.4896401 -0.11651567 27.7065279 PPP1R3A 168814 upstream -82 disjoint
Figure imgf000146_0001
chr6 109807698 109808865 -0.26241015 0.65443319 26.3619234 CD 164 1474 inside intron 726 disjoint chrl 219123936 219124843 1.48969437 0.33750044 26.2877945 HLX1 4555 overlaps exon 0 cover upstream
chrlO 118913541 118914388 1.41041729 -0.15348479 26.2699725 VAX1 25740 upstream -31 disjoint chr7 36161680 36162639 0.22680506 1.2279921 26.2373217 IAA1706 2320 inside intron -1721 disjoint ehr2 85967711 85968427 -0.0798242 1.20858195 26.2148753 ST3GAL5 1240 inside intron 674 disjoint chr6 134255598 134256634 1.08822615 0.15452221 26.1989913 TCF21 3629 overlaps exon 0 cover upstream
chr8 72628601 72629809 0.88502361 -0.07796532 26.1655377 EYA1 191581 upstream 1305 disjoint chr2 222864985 222865521 1.74112795 -0.06533189 26.0728496 PAX3 6422 inside intron -587 disjoint chr6 10506685 10507413 1.49938272 0.20234178 26.0600215 TFAP2A 13179 overlaps exon 0 overlap upstream
chr5 72775112 72775927 1.1109464 -0.08857776 26.0353651 FOXD1 4180 downstream 0 overlap chrl3 99437170 99437920 1.24440148 -0.02013515 26.0092672 ZIC2 4851 downstream 1415 disjoint chrl4 53483487 53484502 1.17390526 0.01967794 25.9865845 BMP4 6517 downstream 0 overlap chrl 9 61711291 61712169 -0.11419798 1.09443412 25.92337 ZNF471 268 inside intron 0 overlap chrl2 130735145 130737664 3.3591384 2.38547496 25.8968084 SFRS8 23923 upstream 0 cover chr5 113723142 113724132 0.87370472 -0.25904727 25.8840742 CNN2 1782 promoter 283 disjoint chr3 170348640 170349630 1.00621053 -0.12932427 25,862865 MDS1 514537 overlaps 3' 272 disjoint chrl l 95164242 95165091 1.99867644 0.88372663 25.8541643 CEP57 953 inside intron -551 disjoint chr7 6112135 6112709 -0.38534987 1.19275801 25.8469246 USP42 1034 inside intron -290 disjoint chr4 175375772 175376384 1.73369581 0.20447242 25.8313745 FBX08 65592 downstream -3701 disjoint chrX 147391034 147391819 1.0687907 -0.07055485 25.8254049 AFF2 1204 inside intron -59 disjoint chr7 27135137 27136101 1.45007107 0.36026912 25.8213509 HOXA4 822 overlaps exon 0 overlap upstream
chr5 87476895 87477930 1.2118908 0.33832881 25.812755 TMEM161B 122490 downstream -3634 disjoint chr3 198959742 198960636 -0.00700548 1.14414767 25.8028177 FYTTDl 443 promoter 20 disjoint chr5 87990657 87991382 1.40850902 0.17300754 25.7994468 MEF2C 223397 downstream 12 disjoint chrl 6 78193900 78194718 -0.25593462 0.86733562 25.7980389 MAF 1789 promoter -862 disjoint chr5 45732504 45733256 0.11040816 1.40923399 25.7931255 HCN1 528 promoter -237 disjoint chr4 108964323 108964958 0.98319248 -0.4743061 25.7718278 MGC26963 68920 upstream 320 disjoint chrl 50660007 50660873 1.2174487 0.0435451 25.7687751 FAF1 537650 downstream 0 inside chr6 108548193 108548908 1.47408626 0.09759428 25.7283657 NR2E1 45046 upstream -292 disjoint chr2 70165546 70166652 1.41092777 0.1045809 25.6860654 PCBP1 1552 promoter 52 disjoint chr3 159299933 159300739 1.43296518 0.24548384 25.674262 SHOX2 2780 covers exon(s) -1147 disjoint chr9 122874175 122876453 -0.37312858 1.59402016 25.6672718 CEP110 13941 upstream 70 disjoint chr22 36528885 36529746 0.81769602 -0.38807705 25.5883615 H1F0 1313 promoter 872 disjoint chr22 27800650 27801523 -0.35112604 1.0448013 25.5637594 KREME 1 1545 inside intron -417 disjoint chr8 50054480 50055544 -0.1734672 0.81628702 25.5298172 SNAI2 57940 upstream -1053 disjoint chrl l 34333957 34334781 1.05220869 0.0049844 25.4782847 ABTB2 596 inside intron 24 disjoint chrl l 128066074 128066955 1.08257595 -0.02991025 25.3779829 FLU 2243 promoter -327 disjoint chrl 5 21438872 21440130 0.33588788 1.30722533 25.3204129 NDN 43412 downstream 42522 disjoint chrl 2 127867656 127868372 -0.07960169 1.2397468 25.3105049 SLC15A4 6121 inside intron 5528 disjoint chr5 140583315 140584035 -0.35797668 0.86076066 25.304806 PCDHB14 54 inside exon 602 disjoint chr6 28662992 28664084 1.18841813 0.20029869 25.2712602 ZNF452 0 overlaps 5' 0 overlap chr8 120290515 120291193 1.14411599 -0.238542 25.2684404 MAL2 725 inside intron -112 disjoint chrl2 113371287 113372202 1.13482331 -0.06612081 25.2585806 TBX5 40658 upstream -325 disjoint chrl 9 18819486 18820238 -0.09023011 1.18331329 25.2453469 UPF1 15743 covers exon(s) 6397 disjoint chrlO 126835482 126836144 1.18494332 -0.30192912 25.2377473 CTBP2 2869 inside intron 1070 disjoint chr6 99396335 99397025 1.31555369 -0.14484088 25.2038231 POU3F2 7035 downstream 0 overlap chr6 134216952 134217632 1.26868288 0.03314754 25.1451367 TCF21 34337 upstream -15910 disjoint chr7 150694651 150695437 0.06135343 1.20438269 25.1372393 NUB1 24861 covers exon(s) 13958 disjoint chrlO 16600895 16601659 1.85044386 0.45306194 25.1111838 C1QL3 2350 inside intron 0 overlap chrl l 65839391 65840101 -0.01748703 1.27535409 25.0586207 CD248 989 inside exon 47 disjoint chr3 3818317 3819102 1.28040494 0.00356545 25.0263117 LRRN1 1768 inside intron -455 disjoint chr7 96484859 96485401 1.62496264 0.10592459 25.0088066 DLX5 6677 downstream -324 disjoint chr7 27122100 27122887 1.50271126 0.20549452 24.9980801 H0XA3 2851 inside intron -149 disjoint chrlO 71835256 71836508 0.49347727 1.25443213 24.8655545 EIF4EBP2 1329 inside intron -677 disjoint chrl 39954442 39955401 -0.06554778 0.95843745 24.8375167 ZNF599 547 covers exon(s) 87 disjoint chrl l 82120036 82120821 1.09590189 -0.04454799 24.8367039 MGC33846 1732 overlaps 3' 262 disjoint chr20 33824082 33825008 1.29990721 0.29832904 24.8362174 PHF20 746 inside intron -418 disjoint chrl8 54680123 54681067 0.53607942 -0.49150852 24.8343443 ZNF532 0 overlaps 5' 308 disjoint chrH 28316729 28317720 -0.20159156 0.78000623 24.7563876 F0XG1B 10692 downstream 0 cover chr7 27147387 27148447 1.93844788 1.03561473 24.7263695 HOXA5 1364 overlaps 3' 691 disjoint chrl3 40135524 40136459 1.20275856 -0.12247444 24.7156239 FOX01A 2274 inside intron 41 disjoint chrl9 7420990 7422147 3.83412763 2.75139686 24.7097736 ARHGEF18 69125 overlaps exon -9804 disjoint upstream
chrl6 83877307 83877974 -0.09566556 1.16751429 24.6951009 FAM92B 173693 upstream 101 disjoint chr6 26152486 26153633 -0.08242374 1.23088597 24.6457558 HIST1H3C 0 overlaps 5' 0 overlap chrl7 35473832 35474651 -0.24125587 1.04278392 24.6187759 THRA 1244 inside intron -426 disjoint chrl7 56884781 56885461 1.13423668 -0.09680232 24.5924833 TBX4 3127 upstream 0 overlap chr3 24847250 24848266 -0.1072094 0.8417926 24.5730156 THRB 335934 upstream -877 disjoint chrl 119349858 119350709 1.63505916 0.44995063 24.5494468 TBX15 16157 upstream 0 overlap chr20 39678199 39678937 -0.37587439 0.94811008 24.548589 CHD6 1609 inside intron 822 disjoint chr6 35418986 35420016 -0.07322038 1.07250577 24.5423456 PPARD 674 inside intron -322 disjoint chrl2 48509197 48509838 2.07062095 0.6464251 24.5306817 LOC144233 13303 downstream -321 disjoint chr9 108661175 108662045 1.13839143 0.14871071 24.5237093 ZNF462 3153 upstream 200 disjoint chr7 28184340 28185374 -0.12412296 0.8371291 24.5154292 JAZF1 1587 inside intron 586 disjoint chrl l 16585844 16586847 1.02384463 -0.44952859 24.5090861 Cllorf58 129922 upstream -88 disjoint chr6 1339533 1340315 1.74208329 0.53780433 24.5067107 FOXF2 4466 overlaps exon -364 disjoint upstream
chrl4 93323807 93324448 1.42426846 0.03223338 24.5035444 PRIMA 1 70 overlaps exon 0 inside upstream
chrlO 118882059 118882947 1.03659241 0.00683984 24.4917959 VAX1 4854 inside intron 0 cover chr4 174678609 174679632 1.20739138 0.20572004 24.4846723 HAND2 8320 downstream 308 disjoint chr2 171282517 171283477 -0.26839011 0.61143766 24.4717982 SP5 2411 overlaps 3' -367 disjoint chr2 36439294 36440302 -0.15598475 0.7931276 24.4480855 CRMl 2394 inside intron -808 disjoint chr3 32837350 32838062 1.09066808 -0.14529529 24.4389173 TRIM71 2837 inside intron 116 disjoint chr5 168656558 168657286 0.01696529 126752313 24.421 SLIT3 3267 inside intron 2721 disjoint chr4 47182675 47183428 -0.34008555 0.98097874 24.3983065 ATP10D 509 inside intron -22099 disjoint chrl 2 24608272 24608885 1.08028562 -0.16179493 24.3702424 SOX5 1626 promoter -762 disjoint chrl 2 52727755 52728611 1.16590089 0.22705203 24.3420487 HOXC4 30847 inside intron 0 overlap chr7 152249022 152249675 0.09636782 1.42756915 24.3115771 ACTR3B 161239 downstream 3174 disjoint chr6 27172792 27173682 1.33925284 0.23435676 24.2829112 HIST1H2BJ 34871 downstream 0 overlap chr2 222142288 222142896 1.3489894 -0.15914983 24.2318876 EPHA4 2357 inside intron 1382 disjoint chr4 40447434 40448379 1.22561698 0.01998598 24.2252354 NSUN7 736 overlaps exon 0 cover downstream
chr3 5000611 5001537 0.55803875 1.58665001 24.1951698 BHLHB2 4404 inside exon -644 disjoint chr5 172601571 172602261 1.71924831 0.19319279 24.1720592 KX2-5 6704 upstream 1174 disjoint chr5 179429372 179430191 1.76441601 0.48093627 24.1178052 RNF130 1523 inside intron 706 disjoint chrl9 35556383 35557303 0.866923 -0.08821 122 24.0897737 ZNF536 1216 inside intron 220 disjoint chrl2 38783248 3878431 1 2.05594245 1.2878131 23.9412071 SLC2A13 1616 inside intron 918 disjoint chrl S 10445475 10446224 -0.32566934 0.84532421 23.9121972 APCDD1 851 inside intron -207 disjoint chr5 140836720 140837604 0.27705047 1.35776479 23.9015979 PCDMGC3 968 inside exon 0 overlap chrl 183970738 183971496 -0.26906426 0.76442421 23.8970359 HMC 1 433 overlaps exon -453 disjoint downstream
chr4 174684373 174684948 1.15794226 -0.3007372 23.8679406 HAND2 3004 inside exon 0 overlap chrl4 102412496 102413932 3.45867807 2.21970898 23.8385767 TRAF3 98928 overlaps exon 29658 disjoint downstream
chr4 146318686 146319549 1.28136076 0.23454808 23.8285789 OTUD4 3341 upstream 655 disjoint chrl 6 53922438 53923433 1.15262074 0.23109472 23.8213848 IRX6 6467 downstream 0 overlap chr7 2065896 2066729 4.73409005 3.15356736 23.7977604 MAD1L1 172379 inside intron 0 overlap chr5 87999017 87999854 1.00889101 0.00585534 23.7511994 MEF2C 214925 downstream 4537 disjoint chrl 239868224 239868838 1.27823566 -0.09775906 23.7473263 0PN3 1485 inside intron 745 disjoint chr8 77755277 77755809 1.74608295 -0.24886061 23.74622 ZFHX4 23025 upstream 1001 disjoint chr 19119425 19120085 1.13168879 -0.3122875 23.7275242 ADFP 1853 promoter -1545 disjoint chr5 153834344 153835424 0.91649149 -0.0680259 23.7086856 HAND1 2592 overlaps 3' 0 overlap chr6 25017557 25018237 -0.07777314 1.06633242 23.6583686 C6orf32 31996 upstream 368 disjoint chrl4 67356202 67357571 -0.07986229 0.71368151 23.6176787 RAD51L1 0 overlaps 5' -144567 disjoint chrl 3 92675166 92675982 1.58787486 0.55720158 23.6144729 GPC6 1 113 promoter 1264 disjoint chr3 32838581 32839186 1.08024954 -0.40001541 23.6082246 TPJM71 4068 inside intron -162 disjoint chr8 4841891 4842802 0.35561733 1.36783673 23.5934502 CSMD1 2156 promoter -1848 disjoint chr3 182924358 182925245 1.02683614 0.12706335 23.5653775 SOX2 11943 downstream 1855 disjoint chrl2 103222055 103222670 -0.18310627 1.18657357 23.5496731 EID3 377 inside exon 0 overlap chrlO 93381857 93382664 -0.19946418 0.99763038 23.4859381 PPP1R3C 173 inside intron 0 overlap chrl 177812214 177813166 -0.09947563 0.8216126 23.4774172 NPHS2 524 promoter -284 disjoint chr6 74462958 74463933 -0.08313317 0.95966327 23.4769372 CD109 724 overlaps exon -216 disjoint upstream
chrl 7 78634924 78635571 -0.03917123 1.3151442 23.3594199 ETRNL 4069 inside intron 344 disjoint chr7 27169657 27170448 -0.00150461 0.96758684 23.3384608 HOXA9 1225 overlaps exon 0 overlap upstream
chrl 4 102744495 102745371 -0.08638888 0.97119929 23.3303348 TNFAIP2 82079 downstream -399 disjoint chrl 7 39992624 39993398 1.09543418 -0.02947563 23.3280657 FZD2 2174 close to 3' -247 disjoint chr2 60637613 60638356 1.04020067 -0.15752936 23.2394687 BCL11A 3477 upstream -1330 disjoint chr6 107544512 107545588 0.5903851 -0.22704599 23.2119459 PDSS2 341859 downstream -509 disjoint chrl 6 85168280 85168919 1.39358483 -0.03315958 23.1997553 FOXL1 696 promoter -314 disjoint chr2 96563766 96564515 0.02491383 1.04824304 23.166698 ARID5A 1675 promoter 1525 disjoint chr9 1039721 1040152 2.11523432 0.1620762 23.130133 DMRT2 1461 promoter 0 overlap chr21 42054855 42055743 0.96125225 -0.0321769 23.0820552 RIPK4 4574 inside intron 3606 disjoint chrl 219126157 219126837 1.40807433 0.20633725 23.0574835 HLX1 6776 downstream 636 disjoint chrl 143641476 143642289 0.05211254 1.192505 23.0533153 PDE4DIP 1099 overlaps exon 407 disjoint downstream
chr7 97749938 97750585 0.04630254 1.33461524 23.0465281 BRD 1016 inside intron -384 disjoint chr20 9437281 9438216 0.90468302 -0.05244645 23.0290301 C20orfl03 5054 upstream -1392 disjoint chrlO 6170285 6170752 -0.77397063 0.99688154 23.0210782 RBM17 260 promoter 40 disjoint chr3 140143062 140143970 1.4668865 0.44361631 22.9928874 FOXL2 4520 downstream -1268 disjoint chrl 29378733 29379500 -0.26164864 1.19193134 22.9898127 SFRS4 1447 inside intron 1063 disjoint chrl2 1575131 1575883 -0.12629263 1.04413328 22.9651708 FBXL14 1540 promoter -638 disjoint chrS 141469499 141470179 -0.82956723 0.36170271 22.9541618 NDFIP1 992 inside intron -396 disjoint chr6 26124877 26125737 0.3965813 1.3793323 22.9326349 HISTIH1A 281 overlaps 3' 2913 disjoint W
149
chr2 151048780 151049891 -0.0676973 1.08852115 22.9228011 RND3 2534 inside intron 97 disjoint chrl8 11136919 11137715 1.34330706 0.21678232 22.8855567 FAM38B 449106 upstream 592 disjoint chr3 6880498 6881421 0.22416551 1.08465261 22.8792713 G M7 2572 inside intron -857 disjoint chr4 95899233 95899871 1.53155488 0.19634013 22.8591024 BMPR1B 1083 inside intron -401 disjoint chr4 100795177 100796208 0.55615963 1.34833199 22.8471119 MTTP 80174 downstream -1500 disjoint chr2 45010860 45011860 0.76334104 -0.14027562 22.8086547 SDC3 10680 upstream -307 disjoint chr22 38247619 38249135 0.25331399 1.22266682 22.7150623 ATF4 1105 overlaps 3' -480 disjoint chr7 157233158 157235470 2.99513728 2.10684768 22.6881142 PTPRN2 837708 inside intron 7838 disjoint chr2 201690193 201691141 -0.15273416 1.17436391 22.6788301 CFLAR 1059 inside intron -259 disjoint chr5 54553881 54554666 1.53433031 0.4587471 22.6776608 U G2 10598 downstream 145 disjoint chr9 78826548 78827555 0.80603274 -0.20521117 22.6517826 F0XB2 2158 close to 3' 79 disjoint chrl l 90437553 90438668 -0.08005338 0.65210764 22.6313572 CH0RDC1 841700 upstream -841547 disjoint chrl4 53981103 53981711 0.23496441 1.55246517 22.6145398 C H 3206 upstream -3116 disjoint chr3 23827674 23828323 1.49317683 0.13002745 22.6106188 UBE2E1 5232 covers exon(s) -162 disjoint chrl4 90952183 90953001 1.37127797 0.34787726 22.6093494 SMEK1 93395 downstream 113 disjoint chrl 144219299 144219949 -0.10920709 1.55429554 22.6024913 RBM8A 305 covers exon(s) -11 disjoint chrX 39835042 39835829 0.92403865 -0.16055151 22.5856545 BCOR 5770 inside intron 14 disjoint chr4 54669426 54670070 1.44940969 0.11365857 22.4906569 GSH2 8472 downstream 74 disjoint chr2 42572847 42573284 1.64334308 -0.15635129 22.4810004 CNG3 1456 inside intron 4 disjoint chr4 6694320 6695260 0.03612658 1.01566741 22.4743632 MRFAP1 975 overlaps exon -97 disjoint upstream
chrl 2 12402050 12403119 -0.1831019 0.80952558 22.4607541 LOH12CR1 729 inside intron -355 disjoint chr3 64404402 64405308 -0.04793095 1.02433877 22.4218171 ADAMTS9 243096 downstream 314 disjoint chr8 75388529 75389297 0.03866629 0.99991905 22.418141 JPH1 6819 inside intron 599 disjoint chr9 114860800 114861865 0.50982698 1.47678811 22.4032308 ZFP37 1984 promoter 27 disjoint chr5 95323855 95324674 1.30092664 0.26432364 22.3917445 ELL2 325 promoter -661 disjoint chrl 146292385 146293277 1.12066072 0.0596632 22.375353 NBPF1 1111359 inside intron 0 cover chr2 54049034 54049780 -0.28633945 0.75105548 22.3727867 PSME4 1573 inside intron 1500 disjoint chr5 122454674 122455482 1.30677964 0.25076144 22.3611275 PPIC 54351 upstream 0 overlap chr8 58292007 58295418 2.55570627 1.77102503 22.3479546 IMP AD 1 223051 upstream -4279 disjoint chrl 35792750 35793801 0.83660264 -0.14797634 22.308423 KIAA0319L 1789 inside intron 1466 disjoint chrl6 71648030 71648761 1.11257616 -0.09628156 22.3007209 ATBF1 8256 upstream 254 disjoint chrl4 60177727 60178371 1.26783311 0.05331248 22.2867913 SKI 7561 downstream 336 disjoint chr4 36920157 36921234 0.09464083 0.89315164 22.2842448 C4orfl9 341015 upstream 411 disjoint chr6 30051168 30052109 1.18221895 -0.01481494 22.2670465 HCG9 298 overlaps exon 272 disjoint downstream
chr4 174657366 174658022 1.42433385 0.17464334 22.2585816 HAND2 29930 downstream 0 overlap chr7 92075312 92075912 1.66818899 0.0442636 22.2570664 CDK6 225235 inside exon -17503 disjoint chrl l 117362786 117363640 -0.17916244 0.88765024 22.232379 IL10RA 468 inside intron -278 disjoint chrl 7 45397294 45397975 1-26994221 0.01543023 22.2205547 DLX4 3587 upstream 0 inside chr 83495614 83496507 1.85433353 0.70814701 22.2178889 TLE1 2199 promoter -793 disjoint chr6 34966145 34966804 -0.09515893 1.11981381 22.1787515 ANKS1A 1127 inside intron -503 disjoint chr2 66527517 66527921 1.87271113 -0.1434143 22.1773798 MEISl 11482 inside intron -377 disjoint chr4 46087336 46088088 -0.11102176 0.90985696 22.1772233 GABRA2 635 promoter -7 disjoint chr20 30815278 30816260 1.20304899 0.00880318 22.1388602 D MT3B 1427 inside intron -354 disjoint chrl 8 53864270 53865127 1.29330935 0.14214415 22.1205852 NEDD4L 1493 inside intron -740 disjoint chrl 146256458 146257659 1.31879095 0.319784 22.0228398 NBPF1 1146977 inside intron 0 overlap chr6 155678139 155679237 -0.22855375 0.74990661 22.0120564 TFB1M 830 promoter -565 disjoint
Figure imgf000151_0001
chr2 111590167 111590951 -0.04080191 1.03371463 21.3600786 FLJ44006 1935 promoter 726 disjoint chr6 150501932 150502848 0.03193614 0.84488288 21.3578538 PPP1R14C 3077 upstream 2616 disjoint chr4 111760401 111761156 1.13824627 0.02936232 21.3484007 ΡΓΓΧ2 2546 inside intron 355 disjoint chrl 9980285 9980965 -0.08758754 1.16051453 21.3454041 COL5A3 1181 inside intron 785 disjoint chr2 54535446 54536322 1.08903188 -0.03246616 21.3082373 SPTBN1 635 promoter 81 disjoint chr3 149898740 149899246 -0.11805828 1.39094379 21.307304 AGTR1 386 inside intron -121 disjoint chr2 156893008 156893780 1.45419659 0.2496602 21.296793 NR4A2 3665 covers exon(s) 23 disjoint chrl l 2654235 2655125 -0.36484809 0.42004676 21.2961531 CNQ1 214976 inside intron 21861 disjoint chrl l 120828635 120829482 1.32155632 0.39966222 21.2887351 SORLl 506 inside intron -123 disjoint chrl5 41906690 41907769 0.15868931 1.11056238 21.2631819 WDR76 191 overlaps exon -121 disjoint upstream
chrl5 65601633 65602211 -0.40586291 0.85620321 21.2585307 MAP2K5 19863 upstream -398 disjoint chr2 222872773 222873345 1.16349998 -0.18988298 21.2502464 FLJ32447 1664 inside intron -617 disjoint chrl5 58075144 58075884 1.00868379 -0.10982866 21.2014719 FOXB1 7828 upstream -189 disjoint chr3 197842965 197843675 -0.46192794 0.53836282 21.1877369 LRRC33 7377 upstream 0 overlap chrl 219125209 219125859 1.5346886 0.31193253 21.1826494 HLX1 5828 downstream -829 disjoint chr4 108174041 108174754 0.12640882 1.16774705 21.1820477 DKK2 2147 inside intron 1250 disjoint chr3 73753124 73753996 0.3460489 1.17493695 21.1772674 PDZRN3 2765 inside intron 1921 disjoint chr4 183303562 183304401 0.99098101 0.04010819 21.1756493 DCTD 771222 downstream -198 disjoint chrl 113736096 113736776 -0.11333366 0.98308229 21.1521148 AGI3 918 inside intron -503 disjoint chrl 8 27517582 27518154 1.05741784 -0.23407775 21.1501605 B4GALT6 471 inside intron 547 disjoint chrl 180290918 180291661 0.2796497 1.29252606 21.1471184 ZNF648 5808 inside exon 566 disjoint chr5 108090358 108090969 -0.13290516 1.08565264 21.0917783 FER 20452 upstream 530 disjoint chrl 2 113320439 113321443 1.17890018 0.21787522 21.0391622 TBX5 4642 covers exon(s) 1252 disjoint chrl 91074507 91075158 1.0067301 -0.24126477 21.0184268 ZNF644 184459 downstream -28 disjoint chrl5 65142928 65144214 1.09556018 0.19451767 21.0169204 SMAD3 1034 promoter 179 disjoint chr6 158323583 158324605 0.32185692 1.17918048 21.0155919 SYNJ2 677 inside intron -151 disjoint chr2 191819858 191820727 -0.24142767 0.69136232 21.0041679 MY01B 1484 inside intron -673 disjoint chr6 31894184 31894759 0.37256174 1.63584956 21.0031416 HSPA1A 2869 downstream -1015 disjoint chr22 44838017 44838987 0.48092612 1.43742287 21.0024774 C22orf26 9330 upstream -1325 disjoint chrl 90060385 90060996 1.93068599 0.76963126 20.9567576 LRRC8D 285 inside intron -575 disjoint chrl l 20581723 20582436 0.07649568 0.98202198 20.9515254 SLC6A5 4202 overlaps exon -1748 disjoint upstream
chr6 1337367 1338080 0.90474756 -0.13948429 20.9499525 FOXF2 2300 inside intron 0 overlap chrlO 80872778 80873673 0.22766148 1.08428375 20.929173 C10orf56 1712 inside intron 785 disjoint chrl2 28015483 28016172 1.10397108 -0.15753488 20.9143598 PTHLH 10 overlaps exon -443 disjoint downstream
chrl9 3315044 3316233 1.35026421 0.29134293 20.912436 NFIC 4429 inside intron 1510 disjoint chr5 131588689 131589510 0.30127246 1.18039859 20.9080834 P4HA2 1323 inside intron 1483 disjoint chr2 118697311 118698219 0.88530756 -0.03815957 20.8954682 INSIG2 134792 downstream 20 disjoint chrl4 60188120 60188729 0.90182423 -0.30407648 20.8776067 SKI 2188 promoter -1815 disjoint chrlO 118018016 118018829 -0.5083349 0.50628456 20.8652747 GFRA1 2954 inside intron 1893 disjoint chrlO 104669665 104670459 0.77527699 -0.2020923 20.8641666 CNNM2 1562 overlaps exon -363 disjoint downstream
chr5 43080648 43081358 1.32666084 0.21708381 20.8618919 LOC389289 4551 upstream -1414 disjoint chr6 34468801 34469546 -0.0602856 1.25743283 20.838668 NUDT3 383 promoter -21 disjoint chrl 168896553 168897161 1.41376343 0.18887288 20.8231393 PRRX1 2775 upstream 0 overlap chr7 25866943 25867761 1.58011652 0.37347007 20.8204436 NFE2L3 290623 upstream 885 disjoint chr4 141437002 141437853 0.42826366 1.36598175 20.8158184 SCOC 39113 inside intron -42985 disjoint chr2 28471161 28471700 -0.12084794 1.29905966 20.7885446 FOSL2 1879 inside intron -909 disjoint chrl7 45219790 45220365 1.22588483 -0.29763106 20.7755635 MYST2 704 promoter 608 disjoint chr7 35266150 35267284 1.01066671 0.0118048 20.7723745 TBX20 6384 upstream 391 disjoint chrl l 2265610 2266506 0.44847265 1.31255174 20.7486771 TSPAN32 13312 upstream -16102 disjoint chrl 226338241 226339098 0.27067283 1.19200199 20.7396654 ARF1 768 inside intron -117 disjoint chr3 129686675 129687266 1.47485943 -0.01438809 20.7381889 GATA2 7451 overlaps exon 916 disjoint downstream
chr6 125725535 125726178 1.56503334 0.2255769 20.7323825 HDDC2 60555 upstream 65 disjoint chrl 6 49535316 49535858 -0.03666437 1.38065577 20.7318051 CYLD 201787 downstream -102493 disjoint chr2 45724631 45725239 -0.00805642 1.21174518 20.7314564 PR CE 7307 upstream -76 disjoint chr6 6887752 6888619 0.14057621 1.2139548 20.7134919 RREB1 164643 upstream 107876 disjoint chr6 117690421 117691191 0.2528623 1.28480784 20.6815376 VGLL2 2222 promoter 86 disjoint chrl4 73779743 73780608 -0.08315577 0.82563256 20.6780669 CHX10 3816 inside intron -1798 disjoint chr8 98726770 98727534 -0.53754188 0.48529805 20.6485663 MTDH 1188 inside intron -364 disjoint chrl2 128952367 128952909 -0.24942533 1.12120462 20.6381941 TMEM132D 1256 inside intron 653 disjoint chrl 8 23017295 23018152 -0.04403091 0.76053616 20.6375867 CHST9 1126 inside intron 797 disjoint chrl2 102849401 102850397 -0.23983245 0.56634063 20.6323783 HSP90B1 1083 covers exon(s) -460 disjoint chr2 36320900 36321588 0.20770748 1.27286243 20.608309 CRIM1 115312 upstream 114313 disjoint chrl 232815150 232815892 0.16601061 1.26636958 20.5938754 IRF2BP2 3257 upstream -1503 disjoint chr8 58218751 58219656 0.18077524 1.03542469 20.5483719 IMPAD1 149795 upstream 0 overlap chr5 1033549 1034266 0.21265492 1.2034516 20.5182227 NKD2 27901 upstream -21377 disjoint chr8 19214228 19215016 -0.04370567 0.95204822 20.51305 SH2D4A 470 promoter 263 disjoint chr8 65456272 65456844 -0.27420221 1.02401119 20.500065 BHLHB5 198523 upstream -2772 disjoint chr7 27196095 27196866 1.16292778 0.14259094 20.4909606 H0XA11 4736 upstream -527 disjoint chr2 119310344 119311219 1.28591657 0.16057641 20.4347601 EN1 11009 downstream -29 disjoint chr7 30292600 30293355 1.94762727 0.5232879 20.4095675 ZNRF2 2153 inside intron -434 disjoint chr20 48781985 48782595 1.07863841 -0.10490402 20.3631747 PARD6B 498 inside intron 0 overlap chr2 63137881 63138644 1.14362086 -0.18365834 20.3538533 0TX1 6413 downstream -230 disjoint chrl3 76797045 76798008 0.02599005 0.81324792 20.3523873 MYCBP2 1169 inside intron 497 disjoint chr6 169167938 169168881 0.17353413 1.07300564 20.3415479 THBS2 227180 downstream -492 disjoint chrl5 34959195 34959740 1.35146398 -0.0858676 20.335635 MEIS2 218054 downstream 25 disjoint chr20 32566628 32567344 1.19563755 0.04060563 20.3243399 DYNLRB1 520 promoter 429 disjoint chr2 30225745 30226318 1.32587702 0.15765745 20.2971334 YPEL5 2414 inside intron -1320 disjoint chrl 2 116984791 116985795 1.01578476 -0.1035447 20.2846295 WSB2 1458 promoter -935 disjoint chrl 9 13836245 13836739 -0.288411 1.26360117 20.2813255 C19orf57 41169 downstream 0 overlap chrl l 43859535 43860200 0.00413066 1.34574775 20.2230854 ALKBH3 563 inside intron -431 disjoint chrS 72915829 72916485 1.77781555 0.35524602 20.2061757 MSC 2799 overlaps 3' 0 overlap chr6 10498774 10499488 1.09935524 0.12940321 20.1967072 TFAP2A 21104 downstream 0 cover chr2 9059761 9060264 1.66064724 0.19302742 20.1824312 MBOAT2 1062 inside intron 314 disjoint chr8 30360172 30360915 1.43781321 -0.1234341 20.1791338 RBPMS 570 promoter 43 disjoint chrl3 111753432 111754597 -0.04591371 0.72955303 20.1747079 SOX1 15316 upstream 1208 disjoint chrl 87574097 87574806 -0.30748002 0.97817862 20.1679107 LM04 7359 inside intron -257 disjoint chrl 9 47107539 47108186 -0.10950493 0.97216638 20.1522378 ARHGEFl 27254 downstream 646 disjoint chrl2 113610091 1 13610595 1.23124803 -0.20844935 20.1446972 TBX3 3740 upstream -556 disjoint chr9 967676 968395 1.37921927 0.14472293 20.1249983 DMRT3 713 inside intron 0 overlap chrlO 29007322 29008317 0.94213078 -0.03307043 20.1142145 BAMBI 893 inside intron -50 disjoint chrl l 114881407 114882099 1.34273174 0.18581657 20.1121462 IGSF4 1083 promoter -316 disjoint chrl 28031065 28031811 0.14640634 1.11477903 20.0989352 PPP1R8 1186 inside intron -690 disjoint chr3 150329148 150329864 -0.1791095 0.82322744 20.0851666 HPS3 196 promoter 21 disjoint chr4 111767049 111767621 1.49254703 0.34658376 20.0737646 ΡΓΓΧ2 10335 inside intron 1707 disjoint chrl 238841146 238841926 -0.26204596 0.57265881 20.04443 GREM2 158 overlaps exon -117803 disjoint downstream
chr7 137793949 137794752 1.16516227 -0.00985503 20.0367984 TRIM24 866 promoter 455 disjoint chr6 26151847 26152386 -0.2407045 1.08360495 20.0106651 HIST1H2BB 0 overlaps 5' 0 overlap chrl 40716094 40716633 -0.55497244 0.75033417 19.9922106 ZNF642 206 overlaps exon -120 disjoint downstream
chrl 6 23756839 23758051 0.24801637 1.11289981 19.9848659 PRKCB1 2017 inside intron -1236 disjoint chr2 139252241 139253103 0.81921501 -0.0704156 19.9665534 NXPH2 1177 inside intron 1059 disjoint chr9 20614264 20614909 0.86475669 -0.16525658 19.9608637 MLLT3 1815 promoter -2402 disjoint chr3 170867640 170868332 0.83735758 -0.12887168 19.9211925 MDS1 3473 upstream 627 disjoint chr22 29696207 29696866 1.81017429 0.45033463 19.9047729 M0RC2 2021 promoter -632 disjoint chr8 1494643 1495250 0.41947829 1.58733939 19.8995937 DLGAP2 57668 inside intron 2007 disjoint chrl4 34941401 34942046 0.11256118 1.1815291 19.8992162 NFKBIA 1648 covers exon(s) 752 disjoint chr8 82187172 82188417 1.76444837 0.76920327 19.8896729 PAG1 315 promoter -134 disjoint chr5 140481179 140481928 0.38246556 1.08182228 19.8777594 PCDHB4 0 overlaps 5' 1146 disjoint chr5 172596636 172597435 1.33892874 0.29374196 19.8663901 KX2-5 1769 promoter 0 overlap chr2 85216522 85217091 2.01238866 0.64032235 19.8191459 TCF7L1 2278 inside intron -418 disjoint chrl 90958190 90958966 0.95809213 -0.08692866 19.8172726 BARHL2 2809 upstream -25 disjoint chr6 10995350 10996149 1.28187114 0.09337038 19.8154802 N0145 301 overlaps exon 0 overlap downstream
chr2 176654337 176655147 1.08461009 0.19086681 19.7978121 H0XD13 10630 upstream 0 inside chr5 72562323 72563030 1.4987613 0.1904653 19.7848796 TMEM174 62494 downstream -70 disjoint chrl l 20578568 20579285 -0.09794374 0.83952484 19.7708676 SLC6A5 1047 overlaps exon 11 disjoint upstream
chr9 127546747 127547581 0.29684214 1.24042641 19.7350531 PBX3 1905 promoter 561 disjoint chrl l 62065255 62066293 0.04068567 1.11396105 19.7148367 AHNAK 4614 inside intron 3565 disjoint chrl 8 18967728 18968370 1.10131973 0.02447991 19.7048715 CABLES 1 21416 upstream 596 disjoint chr3 99025229 99025942 0.22810018 1.36306567 19.7005744 ARL6 58945 downstream -909 disjoint chrl 3132557 3133280 0.21006738 1.22096546 19.6993419 PRDM16 156954 inside intron 4425 disjoint chr6 2915350 2915817 0.00674503 1.36767145 19.6982562 SERPINB6 1271 inside intron 268 disjoint chr3 20055205 20056012 0.27152919 1.14105225 19.6896128 PCAF 515 promoter 450 disjoint chrl 9 3788351 3789199 3.37988774 2.291449 19.6591932 MATK 35542 upstream 0 overlap chr5 140536798 140538583 0.26417393 1.27897861 19.6390877 PCDHB8 0 overlaps 5' 532 disjoint chr7 96468682 96469317 1.10858815 -0.10334747 19.6223227 DLX6 3908 upstream 2 disjoint chr9 1033900 1034675 1.18204459 0.0059199 19.6056057 D RT2 6938 upstream 866 disjoint chrlO 112250170 112250919 0.11454947 1.07277778 19.5888347 DUSP5 2556 inside intron -1496 disjoint chr6 170325288 170329875 0.41095254 1.42637131 19.5868159 DLL1 111746 downstream 119 disjoint chrl 7 73888931 73889542 -0.00230325 1.16197579 19.5788067 PGS1 2602 inside intron -2135 disjoint chrl l 62123730 62124381 -0.08207743 0.98588873 19.5683114 TA2 1497 covers exon(s) 649 disjoint chrl 152848289 152849088 1.59935967 0.03332913 19.5644582 ADAR 17972 inside intron -868 disjoint chr2 45251269 45252067 1.47834696 0.63389804 19.5248281 SK2 161244 upstream 0 overlap chrl 2 105054564 105055300 -0.21320263 0.80956121 19.5247786 NTJAK.1 2640 inside intron 936 disjoint chrlO 121568878 121569456 1.09899294 -0.10810397 19.5200501 INPP5F 93280 inside intron -503 disjoint chr2 200040337 200040912 1.35021285 0.16970777 19.5191667 FLJ32063 1951 promoter 1020 disjoint chrl 215379014 215379652 1.04333977 -0.13685664 19.5065191 ESRRG 49416 upstream -618 disjoint chr20 6462584 6463175 -0.17654626 1.04277246 19.5031403 BMP2 233569 upstream 232877 disjoint chr21 37004998 37005573 1.07002295 -0.25694946 19.4836106 SM2 11138 inside intron -1295 disjoint chr8 8782868 8784013 -0.27575785 0.78883683 19.4609665 MFHAS1 4527 inside intron 2049 disjoint chrl l 87882297 87883052 1.48483894 0.4781377 19.4540666 GRM5 537785 overlaps exon -87 disjoint upstream
chr2 120019890 120020363 -0.23899867 1.25658172 19.442545 MGC33657 1374 covers exon(s) -965 disjoint chrl3 44782546 44783223 0.11652972 1.07695178 19.4397457 TPT1 30073 downstream 531 disjoint chr6 44147359 44147862 -0.11434842 1.28576208 19.4385456 MRPL14 55306 downstream 1130 disjoint chr5 92930972 92931733 1.16465651 0.25631026 19.4249583 NR2F1 13065 upstream 262 disjoint chrl6 52882066 52882578 1.1163736 -0.38002026 19.4201993 IRX3 4188 upstream 0 overlap chr6 1560799 1561626 1.27314557 0.3309289 19.4179463 FOXC1 5120 downstream 0 overlap chr7 27171652 27172158 -0.06725918 1.31347528 19.4092635 H0XA9 0 overlaps 5' 0 inside chrl 94483667 94484242 1.73129837 0.52612483 19.3740688 ARHGAP29 7891 upstream 1252 disjoint chr2 63133925 63134541 1.41725753 0.13276328 19.3733982 0TX1 2457 inside intron 0 overlap chrl 7 14142042 14142612 1.14923425 0.02580382 19.3694632 HS3ST3B1 2618 upstream 0 overlap chrlO 102980622 102981161 1.27754856 0.04101123 19.3575219 LBX1 1916 promoter -569 disjoint chrl 3 1 12917250 112918278 2.63874569 1.79675913 19.328628 CUL4A 5319 inside intron 0 cover chr3 194116370 194117147 1.11163985 0.09209138 19.3084431 C3orf59 1496 inside intron 0 overlap chrl2 118592417 118593127 0.14972159 1.08367304 19.3008292 PR AB1 2274 inside intron -1802 disjoint chrlO 100986851 100987462 1.38303834 0.21564522 19.2884329 HPSE2 1243 promoter -2673 disjoint chr6 26138174 26138716 1.7707152 0.39597688 19.2745168 HIST1H3B 1550 close to 3' 1143 disjoint chr6 26162285 26163001 -0.10839906 0.88010919 19.2524953 HIST1H1C 1676 close to 3' 1145 disjoint chrl 2 52681969 52682772 1.28542668 0.38700701 19.2521928 H0XC9 1826 overlaps exon -1054 disjoint upstream
chrl 2 45510421 45511068 1.29054192 0.22500936 19.2418273 SLC38A4 4420 upstream 111 disjoint chr20 56699039 56699617 -0.11233636 1.09096169 19.2408813 NPEPL1 1650 promoter 1316 disjoint chrl 6221722 6222315 1.25712975 0.0500916 19.2328187 ICMT 3092 upstream 1967 disjoint chr5 140508969 140509580 -0.15123845 0.96084612 19.2281031 PCDHB6 442 promoter 1761 disjoint chr6 101024531 101025091 1.63725372 0.35335814 19.209085 SMI 6260 upstream -287 disjoint chrl 6 603898 604971 4.06738385 2.78039964 19.1975304 RAB40C 23719 inside intron 0 cover chrl 6 68155189 68156082 1.26664432 0.2764112 19.1903175 NFAT5 415 promoter 856 disjoint ehrl2 127319752 127320481 0.02565156 0.99469925 19.1566667 SLC15A4 554012 downstream -648 disjoint chrlO 102750639 102751142 -0.18768004 1.17434536 19.1556537 LZTS2 3685 inside intron -851 disjoint chr5 16986168 16987007 -0.19665955 0.92125514 19.1544743 YO10 2131 inside intron 1548 disjoint chrl l 31800168 31800710 1.28993796 0.18775775 19.1333649 PAX6 10714 upstream -1589 disjoint chrlO 15800144 15800896 0.09879357 1.10666227 19.1306589 ITGA8 879 overlaps exon 533 disjoint downstream
chr9 101627155 101627832 1.25375402 0.07861791 19.119472 N 4A3 3198 overlaps exon 0 overlap upstream
chrl 6 48746440 48747336 -0.1732433 0.5566583 19.0881656 PAPD5 872 inside intron -88405 disjoint chr3 62330365 62331099 0.91118533 -0.10977465 19.080657 FEZF2 2961 overlaps 3' 0 overlap chrlO 69318244 69318888 -0.19935737 0.97219612 19.0792984 SIRT1 3812 covers exon(s) -3060 disjoint chr7 153213687 153214225 -0.08637869 1.31414203 19.0737415 DPP6 1126 promoter 25 disjoint chrl4 60191248 60192143 0.95850211 0.19798588 19.0612964 SKI 5316 upstream 1223 disjoint chr7 115639913 115640451 -0.31251243 1.01967809 19.0491695 TES 2097 inside intron -1649 disjoint chr9 126389454 126389990 0.12916957 1.34956893 19.0401974 NR6A1 183406 inside intron -81974 disjoint chrH 85063691 85064618 -0.18230423 0.6981942 19.0366098 FLRT2 1622 promoter 1629 disjoint chrl 4 56346196 56346887 0.6902795 -0.42345955 19.0227215 OTX2 49 covers exon(s) 0 overlap chr5 140509668 140510276 0.44787492 1.47485925 19.0105148 PCDHB6 0 overlaps 5' 1065 disjoint chrlO 5775013 5775480 1.76278154 0.33223573 18.9966542 ASB13 26467 upstream -7310 disjoint chr5 72767341 72768021 1.2047977 0.26860482 18.9929382 FOXD1 12086 downstream 0 cover
Chr2 8549124 8549558 0.18550233 1.67925152 18.9595031 C2orf46 163125 upstream -34100 disjoint chr7 121738145 121738789 0.97307144 -0.23384451 18.9260827 FEZF1 6311 upstream 0 overlap chrl7 20912278 26912748 -0.20103167 1.12024734 18.8863819 RAB11FIP4 169511 downstream -788 disjoint chr7 77264405 77265049 -0.31171718 1.05777416 18.872619 TMEM60 633 inside intron 218 disjoint chrl2 11696150 11696860 -0.02340327 1.03071124 18.8708327 ETV6 2096 inside intron -1900 disjoint chr7 1093299 1094207 -0.11138593 1.2579961 18.8421727 GPR30 331 overlaps exon 0 overlap downstream
chrX 106903532 106904425 1.42938565 0.47015573 18.8353622 TSC22D3 1247 inside intron 837 disjoint chrll 19323945 19324554 -0.65119321 0.98002353 18.8020271 E2F8 104863 upstream 0 inside chr7 1234209 1235054 0.78153863 -0.07153107 18.7820921 ZFAND2A 67886 upstream 637 disjoint chrl7 44039063 44039727 1.82270731 0.65952637 18.778275 H0XB7 3654 overlaps 3' 516 disjoint chrl 89872251 89872760 1.54247109 0.16352033 18.7134416 LRRC8C 902 inside intron -371 disjoint ohrl4 68512205 68513145 0.09744607 1.20690674 18.7122972 ACTN1 2563 inside intron 1247 disjoint chrl 201562103 201562813 1.50649739 0.15628575 18.7031211 FMOD 24098 downstream 87 disjoint chrl l 78825260 78825904 1.45881404 0.31479205 18.6927191 NARS2 861894 upstream 102 disjoint chrl 2 119247686 119248288 -0.0415549 1.05239918 18.6890072 PLA2G1B 1686 covers exon(s) -7631 disjoint chrlO 17313123 17313758 -0.14567605 0.94089997 18.6809476 VM 1820 inside intron -500 disjoint chr20 32046602 32047496 -0.41704605 0.69717358 18.6633427 ALY 1210 inside intron -439 disjoint chr9 137248560 137249273 0.52394579 1.49287247 18.66053 OLFM1 141569 downstream 26598 disjoint chr7 103757983 103758699 0.14238453 1.22273721 18.6488686 LHFPL3 1644 inside intron -788 disjoint chr2 236747440 236748146 0.90183098 -0.17554663 18.641331 GBX2 6050 upstream -307 disjoint chrl 9 35631503 35632248 -0.23689204 0.73559008 18.6399692 ZNF536 76336 inside intron 1445 disjoint chr3 151961283 151962110 0.16906991 1.10282084 18.6306007 SIAH2 1842 inside intron 311 disjoint chrl6 85161749 85162390 1.49418152 0.2853934 18.6246975 FOXC2 3307 downstream -1599 disjoint chrl 231008516 231009268 1.94225491 0.98345929 18.6204517 Clorf57 143724 upstream -186 disjoint chrl3 49604462 49605238 1.30004043 0.21885495 18.594162 KCNRG 117072 downstream 348 disjoint chrl 7 7998969 7999780 -0.32461341 0.82411319 18.5702111 PERI 2543 upstream 501 disjoint chrl 3 1 11773879 111774508 1.12430477 -0.13675676 18.5598878 SOX1 3966 overlaps 3' 0 overlap chr8 68140365 68141397 0.16572026 1.09781505 18.5218127 CSPP1 1209 inside intron -363 disjoint chr4 104337475 104338191 0.00909808 0.97228719 18.5005406 CE PE 823 inside intron 577 disjoint chr7 27100651 27101328 1.37439843 0.29615889 18.499301 HOXA1 821 overlaps exon 0 overlap upstream
chrl 7 44032842 44033520 1.27252997 0.20169409 18.4930817 HOXB6 3812 inside intron -2254 disjoint chrl 7 61617469 61618144 -0.30215487 0.98075868 18.4905839 CCDC46 290 inside intron 30 disjoint chrl 177981694 177983154 0.28377246 1.16124321 18.4892139 Clorf76 2774 inside intron -1120 disjoint chrl2 2939778 2940389 0.82591614 -0.26073643 18.4876575 TEAD4 556 inside intron -73 disjoint chr5 55324268 55325130 -0.06459368 0.94159471 18.4705073 IL6ST 1389 inside intron 962 disjoint chrlS 39006493 39007137 1.08062164 -0.03086822 18.4289985 DLL4 1701 promoter 0 inside chr2 176687338 176687869 1.22209038 -0.0696151 18.4278924 HOXD10 1868 promoter 1142 disjoint chr7 35262485 35263416 0.62173946 -0.253553 18.4207537 TBX20 2719 upstream 30 disjoint chr8 819298 819807 0.10004196 1.36038214 18.416107 ERICH1 148073 upstream 2437 disjoint chr7 19149528 19149998 1.53212143 0.14177118 18.3975832 FERD3L 1570 close to 3' 748 disjoint ctel7 75393616 75394368 0.56938857 -0.29408273 18.387176 CBX8 8132 upstream -553 disjoint chr21 45715393 45716091 0.19227678 1.19170654 18.3830927 COL18A1 15542 inside intron 0 overlap chr3 15114306 15115153 -0.16464645 0.85661228 18.3722939 ZFYVE20 505 covers exon(s) 0 overlap chrl2 33485110 33485757 0.0005992 1.11433473 18.3642788 SYT10 1090 promoter -793 disjoint chr4 175374024 175374877 1.09332645 0.13175392 18.3611752 FBX08 67099 downstream -1953 disjoint chrl4 90351302 90351916 -0.34763196 0.8001708 18.3589418 TTC7B 597 inside intron 64 disjoint chr6 89848692 89849408 -0.18415758 0.73369983 18.3571482 PNRC1 1477 inside intron -192 disjoint chr8 60191716 60192528 0.46292422 -0.3563557 18.3518258 TOX 1792 inside intron 160 disjoint chrl2 27375621 27376401 -0.43918123 0.81786157 18.3265443 ARNTL2 853 promoter 549 disjoint chr5 139471261 139471764 1.37960064 0.13154725 18.3015049 PURA 2127 promoter 1143 disjoint chr7 24S80732 24581379 1.64740012 0.46757472 18.2897249 MPP6 1123 inside intron 181687 disjoint chr6 7055642 7056348 1.60096145 0.58460661 18.2885872 RREB1 2380 inside intron -789 disjoint chrl l 119549214 119549966 0.22712454 1.10363925 18.2807281 TRIM29 35142 upstream -3719 disjoint chr2 177063954 177064669 0.10297839 1.07768762 18.279453 MTX2 221572 downstream -183 disjoint chrl l 97374S4 9738134 0.15717148 1.13595939 18.2348327 SWAP70 95251 downstream -408 disjoint chr9 90983474 90984001 1.25055353 -0.18552238 18.2343582 SHC3 0 overlaps 5' -43 disjoint chr22 19604237 19605207 -0.07395104 0.98521295 18.2278844 CR L 2524 inside intron -1621 disjoint chr5 54636958 54638553 -0.19792721 0.9004286 18.2114633 DHX29 724 inside intron 413 disjoint chr!8 74254285 74254962 0.32727649 1.32215199 18.2086193 SALL3 586300 upstream -1766 disjoint chrl8 55086187 55086834 1.15376293 0.11783333 18.1896905 RAX 4770 overlaps 3' 0 inside chrlO 11906088 11906824 0.02805389 1.15358423 18.1778734 C10orf47 686 inside intron -98 disjoint chr9 137314960 137315720 0.29177613 1.27220282 18.1764897 0LFM1 207969 downstream 17585 disjoint chr6 97480039 97480719 0.03461978 1.1259237 18.1724522 KIAA1900 714 inside intron -657 disjoint chrl7 73547890 73548569 -0.141666 0.99220698 18.1656889 TNRC6C 8019 upstream 100 disjoint chr2 64098322 64098861 -0.10663651 1.1556052 18.1580494 VPS54 856 inside intron 577 disjoint chr3 198667022 198667720 1.43167867 0.43778576 18.125583 BDH1 99534 downstream 78 disjoint chr3 159294253 159294723 1.50633129 0.12476034 18.1252589 SHOX2 8796 downstream 21 disjoint chr4 122906077 122908186 1.80499355 0.48908662 18.1193095 TMEM155 288 promoter -62 disjoint chr2 9262646 9263431 0.8521147 0.12242238 18.1108325 DDEF2 913 promoter 403 disjoint chr9 23809885 23810499 1.14215603 0.03074951 18.0946384 ELAVL2 5563 inside intron 192 disjoint chr4 52597757 52598327 -0.13171753 1.16899847 18.0929082 SGCB 875 inside intron 884 disjoint chr7 1232244 1232786 1.35955922 0.12694119 18.0909883 ZFAND2A 65921 upstream -339 disjoint chrl 23943792 23944370 -0.0950175 1.03154222 18.0847884 TCEB3 1244 inside intron -590 disjoint chrl 219134753 219135458 1.84942351 0.48680938 18.0742459 HLX1 15372 downstream 0 overlap chrl 6 25612323 25613003 -0.13278412 0.86039161 18.0712324 HS3ST4 1476 inside intron -191 disjoint chrl 158638182 158638754 -0.45934955 0.67905128 18.0609143 VANGL2 1192 inside intron -900 disjoint chrl 7 15101696 15102337 -0.07686657 0.91490398 18.0603644 PMP22 2480 inside intron 2318 disjoint chrl3 44051361 44052004 1.02144263 -0.1487586 18.0546551 TSC22D1 2661 upstream -1073 disjoint chrl2 24945846 24946281 1.76952925 0.24216696 18.0409146 BCAT1 47217 covers exon(s) 585 disjoint chr7 1216501 1217144 0.20662871 1.37045055 18.038233 ZFAND2A 50178 upstream 208 disjoint chrl5 94687276 94687851 1.15755297 -0.01299696 18.0358953 NR2F2 12327 downstream 568 disjoint chr7 45925262 45926044 0.16608239 1.01835004 18.0285492 IGFBP3 1351 inside intron 618 disjoint chr2 66664183 66664725 1.25462733 0.07587999 18.0202278 MEIS1 148148 downstream -1275 disjoint chrl3 87125902 87126654 1.69468727 0.8219844 18.0170935 SLITRKS 3032 inside exon 741 disjoint chrlO 134775790 134776794 3.09758199 2.04165678 17.9917993 GPR123 41368 inside intron 0 overlap chr20 20128127 20128624 -0.50645029 1.1852803 17.9884679 C20or£26 146932 covers exon(s) -146656 disjoint chrl 7 69718287 69719011 1.45263562 0.46290849 17.9463751 RPL38 6898 downstream 1058 disjoint chr6 119439367 119440128 0.27387871 0.98229766 17.925382 C6orf60 1382 inside intron 662 disjoint chr7 48096643 48097110 1.68303498 0.3095766 17.9232545 UPP1 1373 inside intron -157 disjoint
Chrl 2 121922122 121922727 -0.55879862 0.47763454 17.9207588 VPS37B 23937 inside intron -4251 disjoint chrl 9 51166887 51167534 -0.13146606 0.88718448 17.9125282 NOVA2 962 inside intron -18544 disjoint chr3 162573450 162574127 1.42147011 0.51351657 17.9072174 C3orf57 886 promoter -110 disjoint chr3 148559072 148559680 0.83828146 -0.01130411 17.8964975 ZIC4 47416 downstream 122 disjoint chr7 42234490 42234996 1.29561817 -0.03469214 17.8928011 GLI3 5071 upstream -142 disjoint chrll 31774904 31775445 1.11562241 -0.05971261 17.8896073 PAX6 13988 inside intron 1191 disjoint
Figure imgf000158_0001
chrl l 58099384 58099854 -0.25459261 1.04371163 17.4569487 LPXN 55 overlaps exon 2395 disjoint downstream
chrl2 65747458 65748036 1.27158977 0.14748028 17.4492098 CAND1 201379 upstream 901 disjoint chrl 198273646 198274194 1.3742411 0.12492916 17.4334141 NR5A2 10254 inside intron 821 disjoint chr2 45020685 45021299 1.32211335 0.20179065 1 .4315996 srsa 1241 promoter -614 disjoint chr2 200028254 200028655 1.56096003 -0.04909916 17.4289131 SATB2 4790 inside intron 92 disjoint chr8 37676574 37676969 1.39874967 -0.18531081 17.4246653 ZNF703 4116 downstream 116 disjoint chr20 41250006 41250642 -0.136621 1.06881973 17.4019082 PTPRT 1328 inside intron 247 disjoint chrl 3 113302171 113303268 3.23975812 2.21678825 17.3904877 TFDP1 15115 inside intron 4924 disjoint chr4 3764377 3765314 0.12399659 1.08455619 17.3791 ADRA2C 26284 downstream -20517 disjoint chrl 1 17951727 117952558 1.39588991 0.41061523 17.3761598 FAM46C 1601 inside intron -534 disjoint chrl 3 111906864 111907337 -0.47430995 0.94354416 17.3740372 S0X1 136951 downstream -9642 disjoint chr3 71917794 71918525 -0.11035465 0.84575417 17.3660901 PROK2 893 promoter -395 disjoint chr4 151719534 151720262 0.96551524 0.11358988 17.3658113 LRBA 435836 inside intron 0 overlap chr3 99793753 99794364 -0.03807193 1.02715626 17.3446535 CPOX 766 inside intron 232 disjoint chrl5 70764621 70765482 1.14669897 0.28262356 17.3371011 BBS4 105 promoter 0 overlap chr2 164301967 164302647 0.88243344 -0.07893316 17.3103707 FIGN 1209 promoter -210 disjoint chrl 16926283 16927097 2.50409205 1.39329711 17.2932178 NBPF1 113715 upstream -1805 disjoint chr6 4717814 4718584 0.28661755 -0.544295 17.2820009 CDYL 66423 inside intron 1546 disjoint chr5 77182009 77182691 1.56008868 0.66689106 17.2558974 TBCA 74069 upstream 63 disjoint chrl 3 36292300 36292839 -0.34649754 0.78668533 17.2508096 RFXAP 962 inside intron -208 disjoint chrl 7 50331672 50332319 0.99879614 0.17788081 17.2497177 TOM1L1 883 promoter 546 disjoint chr21 27258928 27259536 -0.02473415 1.05173892 17.2113704 ADAMTS5 1166 overlaps exon 191 disjoint downstream
chr3 19252377 19252988 0.12693637 1.1424637 17.2000179 KCNH8 87357 inside intron -87273 disjoint chr7 156426290 156427555 2.9400058 1.91651135 17.1829178 NOM1 7622 upstream 0 cover chr2 171383527 171384189 1.03960666 0.06044015 17.1648525 GAD1 2082 inside intron 0 overlap chrl l 22602519 22603064 1.49891319 0.33533133 17.0674416 FANCF 898 inside exon 218 disjoint chrlO 119483733 119484269 1.22721672 -0.01479647 17.0653998 E X2 191788 downstream 214 disjoint chr2 2919355 2920356 3.57728198 2.51158837 17.0418324 TSSC1 440248 downstream 122023 disjoint chr3 148625260 148625835 0.99993482 -0.2311697 17.0376726 ZIC1 15390 downstream -182 disjoint chrl 9 4862677 4863228 0.13629716 1.41259984 17.0160762 UHRF1 1112 inside intron -1421 disjoint chrl l 2127603 2128280 0.11234503 1.03588944 17.0064645 1NS-IGF2 10734 inside intron 5135 disjoint chrl 2 64408533 64409204 1.16211567 -0.16431415 17.0057755 HMGA2 95302 upstream 0 overlap chr7 128653176 128653865 1.86753721 0.91338744 16.99736 IAA0828 1077 inside intron -285 disjoint chrlO 52505571 52506251 0.12679527 0.95529515 16.9952917 PR G1 1273 inside intron -813 disjoint chr4 77352764 77353372 -0.35104879 0.74224567 16.9706815 SCARB2 686 inside intron 218 disjoint chrl 7 18030293 18030820 -0.08560593 1.12418857 16.9683872 ALKBH5 2280 inside intron -1208 disjoint chr9 87326338 87327062 0.16518935 1.24256544 16.9664606 AGTPBP1 219646 downstream 367 disjoint chrX 35846752 35847522 -0.03894755 0.96425734 16.9502161 CXorf22 256 promoter -292514 disjoint chrl 51967085 51967519 1.19374259 -0.34081735 16.9389412 OSBPL9 111734 inside intron 97 disjoint chrlO 134527007 134527738 0.34409508 1.39110926 16.9360137 C10orf92 5782 upstream -4413 disjoint chr4 85724168 85724873 1.25363218 0.19391751 16.9322111 CDS1 1088 inside intron -251 disjoint chr4 85642984 85643697 1.05214066 0.22046077 16.9294854 X6-1 4574 upstream -770 disjoint chr7 156883755 156884402 0.40476042 1.33122088 16.9243812 DNAJB6 61284 inside intron 1279 disjoint chrl5 94695276 94695675 1.86381117 0.28089008 16.9152504 NR2F2 20327 downstream 635 disjoint chrl 3 99440135 99440880 1.11704663 0.06927961 16.8912626 ZIC2 7816 downstream 0 overlap chrl3 111907602 111908309 -0.18768409 0.697343 16.8811072 SOX1 137689 downstream -10380 disjoint chrlO 30386453 30387066 -0.20505706 0.75280201 16.8768321 PAPDl 291187 downstream 539 disjoint chrl2 121002738 121003494 0.02834155 0.85729625 16.8551313 LXIP 1596 inside intron -1148 disjoint chrl 14792081 14793409 1.55743316 0.64166012 16.8281746 KIAA1026 4390 upstream 3788 disjoint chrl9 1306996 1307571 -0.0328935 1.01451729 16.8191259 MUM1 987 covers exon(s) -646 disjoint chr8 142078891 142079289 -0.65511729 0.83630986 16.8100899 PT 2 1224 inside intron 333 disjoint chr3 11733134 11733924 -0.00473178 1.05647296 16.7974217 VGLL4 3112 inside intron 1714 disjoint chrlO 26265273 26266337 0.00845979 1.06341159 16.7881371 MY03A 2072 inside intron -1245 disjoint chr6 43349758 43350471 1.71680292 0.84356691 16.7760097 TTBK1 30559 inside intron 1100 disjoint chrl 9 53707177 53707611 -0.05027077 1.34610484 16.7518571 PSCD2 42754 downstream -425 disjoint chr6 45500432 45501154 1.49975471 0.37165229 16.749929 RUNX2 2541 inside intron -808 disjoint chr20 19142104 19142803 -0.0559725 0.98232585 16.7498668 SLC24A3 815 inside intron -202 disjoint chr6 100166992 100167705 1.02964773 0.18766854 16.7358381 PRDM13 5622 overlaps exon 0 overlap upstream
chrlO 43388604 43389251 0.10799706 1.05859337 16.717593 ZNF239 4692 upstream 114 disjoint chr3 50102247 50102993 0.03912459 0.71703107 16.7127891 RBM5 876 covers exon(s) -39 disjoint chr20 21641271 21641950 1.2121523 0.32326052 16.6764474 PAX1 6908 inside intron 522 disjoint chr3 119197273 119197956 -0.23391193 0.91662967 16.6737448 IGSF11 1038409 downstream 831 disjoint chr3 124227118 124227762 1.32250828 0.35151467 16.6594864 SEMA5B 1503 inside intron 108 disjoint chr7 27146249 27146856 1.53800141 0.62111067 16.6535433 HOXA5 2955 downstream -213 disjoint chr2 115135470 115135943 -0.12630228 1.18111481 16.6406119 DPP10 219102 inside intron 255 disjoint chr2 45092581 45093192 1.62913169 0.56203806 16.6311549 SK2 2556 upstream 684 disjoint chr9 134030583 134031260 0.33076066 1.26379448 16.6291103 NTNG2 694 promoter -784 disjoint chr5 135442454 135442825 1.68150567 0.07450993 16.6248511 TGFBI 49858 downstream 143 disjoint chr2 237837984 237838451 -0.0424488 1.20635073 16.6243442 COL6A3 149107 downstream 106763 disjoint chr6 167233855 167234625 2.92567554 2.15169738 16.622216 RNASET2 55441 downstream 0 inside chr5 78569426 78570171 1.08095229 0.22503029 16.5991142 JMY 384 inside intron -175 disjoint chrl 57861340 57861987 0.23061471 1.17416617 16.5903756 DAB1 626811 inside intron -198115 disjoint chrl 7 52176041 52176550 3.45888 2.23988439 16.5871113 DGKE 90001 upstream 36141 disjoint chr9 134807820 134808500 -0.09864879 0.80416582 16.5842269 TSC1 1340 inside intron 847 disjoint chr7 96493839 96494485 0.93778393 -0.05380358 16.5799902 DLX5 1761 promoter -1704 disjoint chr5 140599653 140600195 0.25224087 1.33315321 16.578955 PCDHB15 5135 upstream 853 disjoint chr2 121214436 121214852 1.47550021 -0.11422037 16.5659771 GLI2 51474 upstream 846 disjoint chr5 134940673 134941421 0.10092833 0.87263574 16.5557141 CXCL14 1446 inside intron 656 disjoint chr2 19425419 19426224 -0.04885818 0.90705597 16.5539671 OSR1 3567 upstream 6 disjoint chrl 163589845 163590560 1.17667018 0.16927827 16.5453058 L X1A 1080 inside intron 0 cover chrlO 131648902 131649581 0.60313627 -0.28889738 16.5431524 EBF3 2499 inside intron -125 disjoint chrl2 113608896 113609435 1.3740394 0.22349222 16.5421895 TBX3 2545 upstream 0 overlap chr2 119308380 119309048 1.46452983 0.35115389 16.5266526 EN1 13180 downstream 24 disjoint chrl 6 56719170 56719745 -0.26402964 0.83430968 16.5099231 C16orf80 1051 inside intron 510 disjoint chr9 97305770 97306805 1.56291332 0.40966509 16.5076012 PTCH1 3846 inside intron 1491 disjoint chr9 99782433 99783116 0.03659336 0.95350193 16.4992291 A P32B 2347 promoter 1687 disjoint chr4 122904295 122904939 1.9846218 0.99851752 16.4453386 TMEM155 850 covers exon(s) 371 disjoint chrl7 15100854 15101429 0.08923001 1.1814171 16.4367926 PMP22 3388 inside intron 3226 disjoint chrl 8 43709051 43709652 0.87294247 -0.27387549 16.425536 SMAD2 1271 inside intron 830 disjoint chr6 99398564 99398998 1.30623445 -0.05673241 16.4157018 POU3F2 9264 downstream -106 disjoint chr9 14336209 14336818 1.08837539 0.08725498 16.40996 NFIB 32265 upstream 0 overlap chrlO 102484267 102484734 0.83982766 -0.47209015 16.4004606 PAX2 10587 upstream 372 disjoint chr5 76543169 76543711 -0.13526666 0.95037549 16.3933441 PDE8B 708 inside intron -224 disjoint chrl4 76568046 76568774 -0.10600267 0.73842953 16.3868228 C14orf4 3260 upstream 133 disjoint chr3 2110700 2117305 0.30772097 1.34867234 16.3830457 CNTN4 0 overlaps 5' 0 overlap chr22 30480831 30481406 0.03810627 1.1342867 16.3747808 DEPDC5 763 covers exon(s) -767 disjoint chr6 149907573 149908079 -0.03381547 1.28852131 16.3697215 PPIL4 784 inside intron 645 disjoint chrl2 83831138 83831606 1.36425122 0.11659085 16.3671309 SLC6A15 434 promoter -178 disjoint chrl4 32471198 32471806 1.19305653 0.23369158 16.3412365 PAS3 6403 upstream 39 disjoint chr8 10956856 10957398 0.29522482 1.36878143 16.3363201 XKR6 138886 inside intron -2349 disjoint chrl7 44152491 44153087 0.91929564 -0.25639374 16.3220476 PRAC 1793 close to 3' -200 disjoint chrll 41284550 41285451 -0.21693135 0.79831306 16.3179225 LRRC4C 1012311 upstream 2004564 disjoint chrl2 113607592 113608096 1.23103301 0.0165774 16.3137676 TBX3 1241 promoter -264 disjoint chr7 27250542 27250940 1.32656654 -0.18385851 16.3061695 EVX1 1854 inside intron 224 disjoint chr6 28662257 28662940 0.74019511 -0.04253 16.2970965 Z F452 150 inside exon 0 overlap chrl6 47403698 47404228 -0.15003977 1.17505171 16.2832569 N4BP1 202078 upstream -933 disjoint chr5 38295561 38296064 0.06130047 1.23657622 16.2695803 EGFLAM 1272 inside intron -668 disjoint chr3 57555614 57556294 0.09004329 0.95877973 16.2661622 ARF4 1823 inside intron 1766 disjoint chr2 216007098 216007806 -0.14809146 0.73013028 16.2576721 FN1 1229 covers exon(s) 706 disjoint chr2 171384421 171384891 1.3628117 0.01686023 16.2547894 GAD1 2976 inside intron 0 overlap chr20 48161089 48161736 0.28315916 1.2234686 16.2532283 UBE2V1 1380 inside intron 939 disjoint chr4 155881308 155881742 2.0190963 0.77619318 16.2502146 LRAT 2870 upstream 0 overlap chr5 172129158 172129730 0.17550569 1.20391928 16.2484243 DUSP1 1078 covers exon(s) 358 disjoint chrl l 133163769 133164361 0.15439536 1.15144796 16.2429927 SPATA19 56240 downstream 43901 disjoint chr2 100089158 100089913 1.31724488 0.47995511 16.2373761 AFF3 35555 inside intron -1985 disjoint chrl3 21139917 21140624 1.37153652 0.36316229 16.2243264 FGF9 3250 upstream 635 disjoint chrl 181077587 181078519 0.3297363 1.18231674 16.2221761 DHX9 2514 covers exon(s) -1842 disjoint chrl 26103419 26104102 -0.2092486 0.76091745 16.1944318 STMN1 1128 covers exon(s) 435 disjoint chr4 120766952 120767494 1.62889226 0.48430934 16.1908015 PDE5A 395 inside intron 157 disjoint chr6 137153592 137154342 0.00475499 0.82048072 16.1844054 MAP3K.5 1006 inside intron 27 disjoint chr7 65308839 65309495 0.20588885 1.08853737 16.1839304 TPST1 1091 inside intron -459 disjoint chr7 153217364 153218009 0.16854819 1.04431983 16.1661657 DPP6 2013 inside intron -765 disjoint chr6 15799159 15799596 -0.1769499 1.16834426 16.1435299 DTNBP1 27910 upstream -27768 disjoint chrl 9 50836033 50836713 1.01571488 0.1288572 16.1281416 EML2 1525 promoter 0 overlap chrl 196149733 196150164 1.36420771 0.03233229 16.1268481 LHX9 1476 inside intron -1473 disjoint chrl5 37662541 37663083 0.05439221 1.10985768 16.1062768 THBS1 1970 inside intron -1682 disjoint chrl 8 40516342 40517029 0.49558036 -0.35129648 16.09066 SETBP1 18437 upstream -1549 disjoint chr6 78233216 78233791 1.0151286 0.15089709 16.0448509 HTR1B 3378 upstream -2409 disjoint chrlO 22805568 22806247 1.20580209 0.35085064 16.0368779 SPAG6 131164 downstream 0 inside chrlO 94816975 94817707 0.05208662 0.90816856 16.0365772 CYP26C1 5965 inside intron 385 disjoint chr2 60628979 60629773 0.74618769 -0.08076518 16.0286542 BCL11A 4363 inside intron 327 disjoint chr2 38455970 38456775 0.03891276 0.89179852 16.0284402 ARL6IP2 1143 inside intron 298 disjoint chrl l 33715257 33716268 0.16273065 1.13585295 16.0180968 CD59 658 promoter -559 disjoint chrlO 112248679 112249428 0.94544775 0.20740287 16.0061409 DUSP5 1065 inside intron -5 disjoint chrl 6081024 6081461 0.12169019 1.45452638 15.9940343 KCNAB2 72058 overlaps exon -26452 disjoint upstream
chrX 129080186 129080942 0.15652951 1.15459822 15.9740223 ELF4 8040 upstream 1223 disjoint chr2 127860261 127860875 -0.05804252 1.00160689 15.9710742 PROC 31611 upstream 712 disjoint chr3 110613361 110613900 -0.22098499 0.94230077 15.9648449 DPPA4 74279 upstream -293585 disjoint chr20 52224494 52225081 1.25850015 0.0259679 15.9638395 CYP24A1 564 promoter -101 disjoint chrS 140751810 140752400 -0.00860812 1.02517026 15.9615665 PCDHGA8 144 inside exon 169 disjoint W 201
161
chr8 486388 487032 0.84991896 0.00266399 15.9554624 C8orf42 1058 promoter -305 disjoint chr6 109885141 109885746 0.14982364 1.22636891 15.9479094 MICALl 1259 promoter -803 disjoint chr5 153840229 153840858 0.87533712 -0.26263164 15.9253313 HAND1 2213 promoter -923 disjoint chr2 170733957 176734580 1.53599483 0.64221886 15.9142809 H0XD3 2470 promoter -19 disjoint chr8 8784090 8784972 -0.18367504 0.71530561 15.9138475 MFHAS1 3568 inside intron 1090 disjoint chrX 38550826 38551614 0.83952061 -0.01743022 15.9030611 MIDIIPI 2810 downstream -1118 disjoint chrl9 12974786 12975256 0.41706969 1.57134653 15.8999473 NFK 7203 inside intron -215 disjoint chr9 125816630 125817146 1.23820844 -0.08192351 15.8929119 LHX2 2921 inside intron 0 inside chrl 237618062 237618650 0.08634774 1.12581314 15.8892061 CHR 3 240345 upstream -100 disjoint chrl5 91249072 91249614 -0.21517468 0.9047448 15.8803428 CHD2 4650 inside intron -245 disjoint chr3 162305963 162306466 0.06479086 1.18015279 15.8776573 B3GALNT1 110 promoter -12 disjoint chrlO 3488437 3491156 2.83145779 1.95872336 15.8759988 PITRM1 283435 upstream 0 cover chrl l 94522724 94523415 1.22736875 0.21949075 15.8549499 SESN3 80478 downstream 0 cover chr4 79692581 79693218 1.29752104 0.29686447 15.846967 ANXA3 816 inside intron -380 disjoint chr2 222996427 222997108 1.22232271 0.30216689 15.816104 SGPP2 457 promoter 58 disjoint chrl 62434659 62436658 1.46306228 0.22262924 15.7980696 L1TD1 1536 covers exon(s) -1125 disjoint chr20 39092154 39092757 -0.37039568 0.5637023 15.7920252 TOPI 1279 inside intron -328 disjoint chrl 7 34081606 34082112 1.03498474 -0.09099019 15.7871236 MLLT6 33288 upstream 1106 disjoint chr5 10407931 10408704 0.18201776 1.27362013 15.7729418 6-Mar 1104 inside intron -419 disjoint chrl l 1977077 1977685 1.90121596 0.94342413 15.7567144 RPL23 51964 downstream -638 disjoint chr3 135609001 135609555 1.07219874 0.07758504 15.7566712 AMOTL2 32906 upstream -443 disjoint chr8 31618265 31618827 -0.06282078 1.09960953 15.737894 NRG1 1456 inside intron -377 disjoint chr9 21983247 21983714 1.39549668 -0.04737357 15.7263146 CDKN2A 775 inside intron 387 disjoint chr21 27257980 27258660 0.02451806 0.86518133 15.718512 ADAMTS5 2042 inside intron 1067 disjoint chr3 173949737 173950333 0.00134387 0.89649946 15.7032942 ECT2 4658 upstream 730 disjoint chr8 79880148 79881043 0.18971515 1.0644247 15.6769407 IL7 0 overlaps 5' -190 disjoint chrl 5 40655660 40656341 -0.34375849 0.40620021 15.6513114 CEP27 27316 downstream -114 disjoint chr5 150059389 150060191 -0.03799233 0.82274183 15.6503007 RBM22 625 inside intron 133 disjoint chr6 4719230 4719946 0.56307892 -0.32818733 15.6424268 CDYL 67839 inside intron 184 disjoint chrl l 75600030 75600503 1.66357677 0.46034894 15.6419617 WNT11 4809 upstream -6 disjoint chrlO 125029804 125030403 0.06509384 1.07788258 15.6322897 BUB3 125945 downstream -125088 disjoint chrX 114047584 114048264 0.97601429 0.14624816 15.6305202 HTR2C 322778 inside exon 281898 disjoint chr6 160032326 160032869 -0.11008492 1.00826703 15.628175 SOD2 1473 inside intron 678 disjoint chrl 7 8868799 8869432 0.57226875 -0.33385482 15.6197457 NTN1 3216 inside intron -1154 disjoint chr3 120702307 120702846 0.01900725 1.0362506 15.6189784 C3orfl 2250 overlaps exon -1864 disjoint downstream
chrl 4 68326846 68327361 -0.28457723 0.7957405 15.6171789 ZFP36L1 2176 overlaps exon -57 disjoint upstream
chrl 47466118 47466876 0.95632283 0.01352992 15.6017797 TALI 1153 inside intron -1804 disjoint chrl 7 5614070 5614799 -0.47487606 0.9144511 15.5936072 NALP1 185518 upstream -268744 disjoint chrl 7 70660138 70660729 1.07432545 0.07260763 15.5919191 HN1 1639 inside intron 696 disjoint chr3 165201691 165202224 0.24859832 1.4654294 15.5877523 SI 1076751 downstream 2517 disjoint chr2 205119425 205120105 -0.02652207 0.93653152 15.5801167 PARD3B 665 inside intron -270 disjoint chr2 218423333 218423914 0.09888264 1.28928094 15.5751583 TNS1 93091 inside intron -93590 disjoint chr2 119328149 119328551 1.55189485 0.08570025 15.568085 EN1 5921 upstream 0 overlap chrl 33667998 33668465 1.11887303 -0.18490705 15.5627186 ZNF31 42380 upstream 124 disjoint chrl 9 45664098 45664538 0.1496423 1.36511947 15.5622654 SPTBN4 427 promoter 0 inside chrl6 11979197 11979912 -0.14414603 0.93583387 15.5598396 RUNDC2A 1095 inside intron -826 disjoint chr6 85531345 85531882 1.42467785 0.39298506 15.5490458 KIAA1009 537313 upstream -494 disjoint chr3 154036624 154037268 1.71831673 0.89068229 15.5323477 P2RY1 1199 inside exon -225 disjoint chrl 163593036 163593588 1.66782105 0.32040774 15.5159301 L X1A 1396 promoter -84 disjoint chr9 137868452 137870614 2.47662964 1.55335306 15.5145233 CAMSAP1 43949 inside intron -17532 disjoint chr21 45319928 45320365 -0.15502169 1.14480849 15.5111023 ADARB1 986 inside intron -28 disjoint chr3 48318678 48319271 1.73040617 0.69748767 15.510915 NME6 827 promoter -416 disjoint chr2 71359018 71359598 0.70106457 -0.31551299 15.5077363 ZNF638 52798 upstream -1277 disjoint chr6 18388143 18388688 0.19318712 1.16815444 15.5026777 DEK 15366 upstream -2102 disjoint chrl9 6483203 6484082 1.44855721 0.24577945 15.4922292 TNFSF9 1167 covers exon(s) -651 disjoint chrl 3 47964670 47965227 -0.08247389 1.04317395 15.4758266 RCBTB2 40089 inside intron 39185 disjoint chr20 34633653 34634413 1.08577522 0.21151206 15.4434189 TGIF2 1023 promoter 324 disjoint chr3 16528474 16529006 0.0748073 1.21779369 15.434896 RFTN1 1219 inside intron 325 disjoint chr7 43117784 43118473 -0.16527936 0.64837477 15.4241014 HECW1 249 promoter 72 disjoint chr7 157648642 157649490 3.36500917 2.38331103 15.4107256 PTPRN2 423688 inside intron 182 disjoint chr4 13093535 13094146 1.0320419 -0.0309163 15.4028361 RAB28 725 inside intron 474 disjoint chrl 7 74901227 74901850 2.604647 1.70993853 15.389229 LOC146713 29715 inside intron 69990 disjoint chr4 42093034 42093769 1.3522262 0.44989689 15.3836987 ATP8A1 259877 downstream 140 disjoint chrlO 90739545 90740065 -0.17125406 0.88798291 15.3717103 FAS 202 promoter 208 disjoint chr3 16902131 16902706 -0.27889232 0.67040117 15.3710448 PLCL2 46879 upstream -278 disjoint chr2 176660107 176660959 1.51015656 0.45473479 15.3481258 HOXD13 4818 upstream 0 overlap chr5 92948803 92949511 1.20891514 0.32114677 15.3361968 R2F1 4005 overlaps exon 0 overlap upstream
chr7 4690285 4690787 0.08902499 1.13692749 15.3316278 FOXK1 1830 inside intron -980 disjoint chr6 39869213 39869858 0.22892915 1.07925869 15.3213107 DAAM2 443 inside intron -809 disjoint chrl2 54722828 54723370 0.23985119 1.44126518 15.3096594 RPS26 876 inside intron -155 disjoint chrX 133505756 133506363 0.88334515 0.14201217 15.2966647 PLAC1 113815 downstream 0 overlap chr2 234327018 234327764 0.12368212 1.46267371 15.2905552 UGT1A3 24507 inside intron 570 disjoint chr8 134654816 134655742 -0.13230715 0.83280283 15.2872305 ST3GAL1 1473 promoter -759 disjoint chr6 33050442 33051032 -0.27298623 0.75642866 15.2862042 BRD2 6028 overlaps exon -1510 disjoint downstream
chrl 3 49598457 49599030 1.15950904 0.09131337 15.2857251 KCNRG 111067 downstream 0 inside chr7 27173819 27174511 0.10011545 0.88385961 15.2832056 HOXA9 2146 promoter -832 disjoint chr22 24129361 24130027 -0.15022157 0.94820338 15.2813576 LRP5L 40838 upstream 527 disjoint chr6 7488826 7489329 1.16963066 0.10705188 15.259984 DSP 1958 inside intron -355 disjoint chrl 4 89917469 89918260 0.02019087 0.78768982 15.2481162 CALM1 14865 upstream 487 disjoint chrlO 127573396 127574007 -0.2562742 0.59364582 15.2413475 FANK1 1093 promoter 232 disjoint chrl 8 27991860 27992507 -0.06284316 0.82607195 15.2398848 RNF138 65216 downstream -64548 disjoint chr8 96214207 96214695 1.22818216 0.07295315 15.2298181 PLE HF2 518 promoter 241 disjoint chr4 2212082 2212762 -0.07131901 0.93232199 15.2232643 C4orfl5 895 overlaps exon 287 disjoint upstream
chr3 182927978 182928699 0.73336808 0.03818485 15.2132711 SOX2 15563 downstream -287 disjoint chr9 114859007 114859513 -0.24058711 0.83285154 15.206051 ZFP37 191 promoter 0 overlap chrl5 29945555 29946269 0.25350061 1.05706601 15.2055422 CHRNA7 163748 upstream 163187 disjoint chr7 43763958 43764389 1.13355121 -0.33407244 15.1984807 BLVRA 407 promoter 0 overlap chr4 174688587 174689126 1.50412475 0.53191571 15.1781913 HAND2 635 promoter 0 inside chr3 130643696 130644230 -0.2187776 0.95113433 15.1777721 IFT122 2039 inside intron -1532 disjoint chr8 109162323 109163058 0.53799187 -0.24901329 15.1525524 RSP02 1683 inside intron 603 disjoint chrl 7 44033539 44034009 1.21181648 0.04085728 15.1491492 HOXB6 3323 inside intron -2951 disjoint chrl3 113847285 113847790 0.10844277 1.18017272 15.1358211 RASA3 68406 inside intron 6378 disjoint chr6 5938918 5939635 1.41196139 0.24822565 15.1285646 NRN1 12996 downstream 273 disjoint chrl l 131287511 131288119 0.48553372 1.39543076 15.1193482 HNT 1590 inside intron -769 disjoint chrX 24929483 24930042 0.90579382 -0.21232287 15.0777112 ARX 13732 downstream 116 disjoint chrX 44619916 44620693 -0.08062643 0.74957845 15.0660125 UTX 2192 inside intron -1706 disjoint chr4 77726782 77727391 1.07556406 0.19275771 15.0630301 SHR00M3 151506 inside intron -419 disjoint chr5 180160958 180161829 0.02896216 1.04390402 15.0602423 MGAT1 824 inside intron 152 disjoint chr6 1330471 1331046 1.38653838 0.41769292 15.0589066 FOXF2 4021 upstream -261 disjoint chrl7 7423530 7424250 0.23242287 1.13986751 15.0489795 CD68 1 overlaps two 2759 disjoint exons
chrl4 55115260 55115838 0.06026981 1.09635989 15.0477114 KTN1 954 promoter 549 disjoint chr3 188943023 188943515 1.6105657 0.50409136 15.0425538 BCL6 2653 inside intron 1150 disjoint chrl 184914668 184915177 0.17700789 1.23620617 15.0401466 PTGS2 1001 covers exon(s) 756 disjoint chrl2 52061585 52062272 -0.21970938 0.74744373 15.030235 SP1 1340 covers exon(s) -715 disjoint chrl 6 51136372 51136986 0.58749123 -0.30327507 15.0205933 CHD9 509459 upstream 151 disjoint chr2 119316209 119316834 1.25976134 0.07594425 15.0033101 EN1 5394 overlaps 3' 0 inside chr5 272792 273379 0.16420467 1.28203203 15.002376 SDHA 1346 inside intron -664 disjoint chr2 85967189 85967587 0.14323346 1.45652032 14.9984594 ST3GAL5 2080 inside intron 1514 disjoint chr8 25956047 25956586 1.20403189 0.17528988 14.9878538 EBF2 1722 inside intron 0 overlap chrl7 56835938 56836405 1.52106919 0.36206017 14.9798024 TBX2 3900 inside intron 0 inside chrl2 116111051 116111593 0.00178355 1.07866908 14.9781513 FBX021 1089 covers exon(s) 440 disjoint chr5 174088646 174089334 1.37831861 0.2676953 14.9693435 MSX2 4466 overlaps exon 1952 disjoint upstream
chrl 7 59562019 59562417 -0.00605795 1.35406711 14.9613757 ERN1 812 promoter -237 disjoint chr7 1250641 1251271 1.17704215 0.30379746 14.9561085 ZFAND2A 84318 upstream -75 disjoint chrl9 61846925 61847539 0.19413085 1.31178241 14.9411916 BC37295_3 28518 downstream -98 disjoint chr8 1495563 1496163 0.25939647 1.25509851 14.9403119 DLGAP2 58588 inside intron 1094 disjoint chr2 3269868 3270569 2.95812916 1.99693539 14.9318716 TSSC1 90035 inside intron 0 cover chr6 41451541 41451972 1.41840069 0.18767382 14.9191225 NCR2 40037 downstream -1020 disjoint chr6 159158161 159158736 1.16943265 0.25943418 14.9060605 VIL2 510 inside intron 333 disjoint chr6 108594796 108595332 1.28929348 0.14531136 14.9056317 NR2E1 842 inside intron 0 inside chrl 7 2257236 2257670 0.08425606 1.29314623 14.900485 LOC284009 7809 overlaps exon -5084 disjoint upstream
chrlO 7750378 7751004 0.51575602 1.3772801 1 14.8726075 ΓΓΙΗ5 1439 promoter -88422 disjoint chr3 69143940 69144515 0.31387709 1.28018569 14.8672442 C3orf64 948 overlaps exon 331 disjoint downstream
chr8 77753586 77754056 1.16799634 0.06268418 14.8578659 ZFHX4 24778 upstream -658 disjoint chr5 92939282 92939719 1.42323858 0.14309602 14.8347937 NR2F1 5079 upstream 807 disjoint chrlS 38590110 38590580 0.25898912 1.39054729 14.8341578 D4ST1 39606 downstream 292 disjoint chrl 19407903 19408340 -0.14921575 1.10347652 14.8222862 ZUBR1 992 inside intron 398 disjoint chrll 62230779 62231249 1.12015035 0.03604029 14.8130811 BSCL2 145 overlaps exon -47 disjoint downstream
chrlO 89566854 89567396 0.95203757 -0.01412011 14.7966739 ATADl 500 inside intron 65 disjoint chr20 55270504 55271113 1.63012465 0.65127094 14.782835 BMP7 3594 inside intron 1581 disjoint chr8 59487113 59487586 1.22556781 0.08843297 14.7827529 LOC137886 737 inside intron -379 disjoint chrlO 100982707 100983375 0.77060782 -0.12166188 14.773218 HPSE2 2233 inside intron -30 disjoint chr2 166357389 166358051 1.02929915 0.17613492 14.7665626 GALNT3 21934 upstream 104 disjoint chrX 74059751 74060274 0.09036788 1.08689763 14.7424542 KIAA2022 1434 inside intron 303 disjoint chrl 3 49467777 49468284 1.48294642 0.31805828 14.7397856 TRIM13 859 promoter 92 disjoint chrl 38948167 38948733 0.16918702 1.34842473 14.7372533 RRAGC 149193 downstream -640 disjoint chrl 94778820 94779428 1.42305064 0.49721769 14.7319979 F3 474 inside intron 0 overlap chrlO 22808050 22808878 0.11559681 1.08268694 14.7285476 PEP5K2A 234611 downstream -994 disjoint chr6 151604598 151605101 1.69479601 0.48142731 14.7281008 AKAP12 1397 inside intron -355 disjoint chrl 163868421 163869068 0.08850546 0.90988764 14.7073566 MGST3 1348 inside intron -1223 disjoint chr6 170448654 170449211 1.10005631 0.16523535 14.7010678 DLL1 7033 upstream -250 disjoint chrS 140192233 140192784 -0.15327213 0.91030852 14.6957777 PCDHA6 4400 inside intron 1468 disjoint chrl l 16590932 16591574 -0.66794216 0.19778932 14.6894198 Cllorf58 125195 upstream 0 overlap chrl 4 32476022 32476589 0.92972708 -0.09989186 14.6890829 NPAS3 1620 promoter -2192 disjoint chrl7 44016139 44016538 0.8788997 -0.49410978 14.6814719 H0XB4 5398 upstream -1137 disjoint chrl l 67838046 67838729 -0.18035318 0.83285031 14.6794927 LRP5 1336 inside intron -539 disjoint chrl 2 113588606 113589204 1.55342092 0.08733789 14.6608302 TBX3 17147 downstream 27 disjoint chr21 29594577 29595155 1.59559991 0.5933129 14.6421488 BACH1 970 inside intron -920 disjoint chr5 126654685 126655332 0.62294264 -0.18723638 14.6346149 MEGF10 172 inside intron 0 overlap chrl 3 36147921 36148525 0.5101653 1.4281088 14.6280116 LOC400120 1873 inside intron -1458 disjoint chr3 87121374 87122024 -0.13456457 0.76390796 14.6091657 VGLL3 922 inside intron 273 disjoint chr7 112514377 112514883 -0.63677499 0.39890255 14.5995301 GPR85 131 overlaps exon -146924 disjoint downstream
chrl 7 6859295 6859972 0.06620085 0.8593832 14.5886562 C17orf49 448 covers exon(s) -32 disjoint chrll 125733920 125734803 0.12385162 1.24439347 14.5763201 ST3GAL4 2615 inside intron -2637 disjoint chrl 3 23050160 23050851 0.61891944 1.58584558 14.5760977 TNFRSF19 7438 inside intron 48 disjoint chr4 75936247 75936936 0.45554409 1.24062466 14.5747766 BTC 1916 inside intron 1189 disjoint chrlO 9488815 9489495 2.93836283 1.96294354 14.5698227 LOC389936 0 overlaps 5' 0 overlap chrlO 6663566 6664277 1.80616017 0.96291777 14.5633303 PRKCQ 1323 promoter -918 disjoint chr5 140532399 140532942 0.40293902 1.59647579 14.5616044 PCDHB7 0 overlaps 5' 923 disjoint chrl 7 43981372 43981966 0.99635171 0.10277391 14.5562416 HOXB3 24842 inside exon 820 disjoint chr6 10533168 10533892 0.72060268 -0.14825716 14.5513173 C6orf218 8867 downstream 294 disjoint chrlS 75564642 75565109 3.08828525 1.88094281 14.5443242 CTDP1 23854 inside intron 203 disjoint chrl 160258963 160259575 0.33743982 1.1923404 14.5333098 0LFML2B 692 inside intron 71 disjoint chr4 111765040 111765336 1.44683013 -0.37676903 14.5331127 ΡΓΓΧ2 12620 inside intron -1127 disjoint chr6 1332823 1333224 1.4158113 -0.04227072 14.5320205 F0XF2 1843 promoter 914 disjoint chr2 227367237 227367674 -0.12555522 1.08503184 14.5270447 IRS1 5044 inside intron -2346 disjoint chr2 171722770 171723428 1.5564813 0.46225822 14.5236826 TLK1 1777 inside intron 1356 disjoint chrl 159858162 159858824 1.79843645 0.22954563 14.4870304 FCGR3B 8700 downstream -9161 disjoint chr9 21980085 21980586 1.08102176 0.00397032 14.4849572 CD N2A 3903 inside intron 0 overlap chr9 97314495 97315106 0.92112052 -0.12694094 14.4739423 PTCH1 3844 upstream -766 disjoint chr4 184956851 184957318 1.40957102 0.31420887 14.4683377 FLJ12716 139412 downstream -103 disjoint chrl 7 75538954 75539565 1.14405711 0.34571805 14.4654278 TBC1D16 84676 overlaps exon 0 overlap upstream
chr6 106541125 106541454 1.56416904 -0.02743105 14.4592883 PRDM1 99433 upstream 0 overlap chrl 8 32663682 32664218 -0.53652008 0.51233619 14.4580987 IAA1328 605 inside intron -395 disjoint chr6 5946679 5947080 1.23269185 -0.12195532 14.4477304 NKNl 5551 inside intron 390 disjoint chr2 172652770 172653201 2.0832286 0.84680603 14.4470547 MAPID 79721 covers exon(s) 33 disjoint chrl 166623303 166623740 1.8789112 0.64865579 14.4421322 TBX19 106402 downstream -160840 disjoint chrl 8 75182870 75183376 0.51456616 1.65191168 14.4247198 ATP9B 252486 inside intron 5075 disjoint chr3 132096816 132097406 -0.25258768 0.70780189 14.4176996 ATP2C1 693 inside intron -644 disjoint chr6 106547514 106547987 1.21416814 -0.00891337 14.4170668 PRD 1 92900 upstream 692 disjoint chr6 52966527 52967066 -0.19298742 0.72041426 14.4108844 GSTA4 1032 covers exon(s) 458 disjoint chr7 5534797 5535210 0.00118977 1.56929879 14.409663 ACTB 1536 overlaps exon 378 disjoint upstream
chr3 99024776 99025177 -0.02556711 1.2840218 14.405478 ARL6 58492 downstream -456 disjoint chr6 43153795 43154235 -0.22917309 0.98845544 14.4000814 PTK7 1789 inside intron -760 disjoint chrl 3477977 3478672 -0.0671802 0.98617368 14.3932305 MEGF6 39246 inside intron 11090 disjoint chrl2 52695079 52696194 1.21848407 0.15616774 14.3899356 H0XC6 714 promoter -699 disjoint chr9 120068972 126069580 0.34137017 1.12288438 14.3776543 NEK6 8903 inside intron -8410 disjoint chrl 7 7997518 7998230 0.10096016 1.28084985 14.3760416 PERI 1092 promoter -958 disjoint chr8 59732920 59733492 -0.08544364 0.87172862 14.3742405 NSMAF 1447 inside intron 665 disjoint chrl 75375556 75375954 1.10126545 -0.07317025 14.3635842 LHX8 8850 inside intron -90 disjoint chrl 3 99442200 99442775 1.06996272 0.07634375 14.3622004 ZIC2 9881 downstream -1105 disjoint chrl 37711731 37712165 -0.07209291 1.35448221 14.3465539 ZC3H12A 574 promoter 145 disjoint chrl 2 56444482 56445054 1.45978261 0.5412353 14.3161105 CYP27B1 2188 covers exon(s) 68 disjoint chrl 8 75505471 75505980 0.09880096 1.0633494 14.3026397 CTDP1 34808 upstream 5043 disjoint chrlO 131646447 131646914 1.09070338 0.00089325 14.288387 EBF3 5166 inside intron 0 overlap chrl5 58082031 58082708 0.77486084 -0.17689792 14.2763813 FOXBl 1004 promoter 719 disjoint chr7 55608265 55608795 1.09658226 -0.08125449 14.2761214 ECOP 572 promoter -172 disjoint chrl4 22378458 22378853 0.08131778 1.31001477 14.2671745 MMP14 2826 inside intron -1605 disjoint chr2 204698 205290 -0.18363155 1.26599814 14.2540744 SH3YL1 41050 downstream -453 disjoint chr7 130002632 130003219 0.30569376 1.27077993 14.2531287 COPG2 918 covers exon(s) 391 disjoint chrl l 118714652 118715125 1.09167817 0.08580493 14.2501532 C1QTNF5 1665 overlaps 3' 375 disjoint chr4 174490521 174491048 -0.2629735 0.825788 14.2350547 HMGB2 1118 covers exon(s) 210 disjoint chr20 34527518 34528495 0.10975114 1.0067848 14.2348457 DLGAP4 3963 inside intron -4106 disjoint chr3 158288208 158288678 0.26862439 1.40743536 14.2341254 FLJ16641 261419 downstream 701 disjoint chrl 6 3448933 3449445 -0.18897752 0.82188695 14.2304031 FLJ14154 855 inside intron -326 disjoint chrl 2 117297576 117298011 0.51266503 1.71578437 14.2265717 SUDS3 729 promoter 386 disjoint chr3 37782345 37782743 -0.12993719 1.1631129 14.2235509 ITGA9 313529 inside intron 94199 disjoint chrl l 82548134 82548736 -0.45158501 0.37176332 14.223405 PCF11 2274 inside intron -1926 disjoint chrl 150428544 150429288 -0.16100838 0.85255943 14.2204747 HRNR 34004 downstream 0 overlap chrl5 83327069 83327695 -0.07842864 0.89503403 14.213333 PDE8A 861 inside intron -200 disjoint chr6 41624004 41624402 1.4090515 0.09340512 14.209812 FOXP4 1863 inside intron 0 overlap chrfi 36105198 36105839 0.00078769 0.98396294 14.2079436 MAP 14 1648 inside intron -848 disjoint chr6 19262997 19263500 0.21433018 1.25127676 14.1984428 ID4 682095 upstream 536389 disjoint chr6 74461558 74462286 0.04882154 0.87798062 14.1786198 CD 109 0 overlaps 5' 35 disjoint chr5 140515609 140516220 0.51341774 1.33658912 14.1778036 PCDHB6 5587 downstream 860 disjoint chr7 153219780 153220325 0.50084381 1.32110297 14.1769107 DPP6 4429 inside intron -3181 disjoint chrl5 94667845 94668406 1.12544109 0.11828806 14.1768977 NR2F2 6543 upstream -54 disjoint chrX 136458620 136459045 1.14328907 -0.1448955 14.1700302 ZIC3 16966 upstream -651 disjoint chr2 200042650 200043226 1.10466191 0.17910953 14.1545085 FLJ32063 0 overlaps 5' -233 disjoint chr3 10834846 10835283 0.02099917 1.27630153 14.1436159 SLC6A11 1930 inside intron -1399 disjoint chr5 74379632 74380736 0.53404304 1.31726101 14.1425763 GCNT4 17153 upstream 3261 disjoint chrl 5 50879888 50880723 0.35135503 1.1473205 14.1399721 ONECUT1 10388 upstream 2583 disjoint chr7 96486208 96486868 1.23067655 0.23237174 14.1385409 DLX5 5210 downstream 1289 disjoint chr20 2678623 2679061 1.03118601 0.00628079 14.1369079 CPXM1 50220 downstream 0 overlap chr8 59629721 59630194 -0.38634798 0.69302732 14.1288729 SDCBP 1440 inside intron -1064 disjoint chr2 45088315 45088833 1.28236369 0.22592406 14.1280649 SK2 1192 inside intron 182 disjoint chr2 219143372 219143914 -0.19612089 0.87124698 14.1236183 RQCD1 1451 inside intron -1173 disjoint chr 78817055 78817489 1.2686906 0.12813852 14.1227398 FOXB2 6901 upstream 1241 disjoint chr8 41283744 41284250 1.15493278 0.12372641 14.1144311 SFRP1 1886 inside intron 759 disjoint chr3 140144130 140144636 1.24777537 0.30687303 14.090494 FOXL2 3854 downstream 1769 disjoint chr!6 9094795 9095357 -0.4409471 0.45767548 14.0889877 C16orf72 1758 inside intron -605 disjoint chr4 78038618 78039022 1.23636262 -0.03997042 14.0814485 AN RD56 593 promoter 0 overlap chr8 50988252 50988689 -0.38275682 0.99020807 14.07391 SNTG1 1103 inside intron -2839 disjoint chr4 187746876 187747451 2.67808135 1.83069872 14.0679168 FAT 134529 overlaps exon -33038 disjoint upstream
chr5 140541968 140542435 0.15846178 1.13101708 14.0673705 PCDHB16 805 inside exon 1259 disjoint chrl2 127868394 127868872 -0.03009144 1.06379053 14.0631312 SLC15A4 5621 inside intron 5028 disjoint chrl 232108536 232109147 0.33620648 1.27171027 14.0455492 SLC35F3 1235 inside intron -456 disjoint chrlO 20141815 20142426 0.05842982 0.92627189 14.0440054 PLXDC2 2951 upstream 2031 disjoint chr7 15690564 15691328 -0.06166634 0.77220421 14.0417344 ME0X2 1504 inside intron 735975 disjoint chrl 6 86554404 86555046 0.10376339 1.36447599 14.0368121 BANP 11866 inside intron -5307 disjoint chr3 33732720 33733306 0.36024338 1.19071473 14.0308186 CLASP2 1545 inside intron 904 disjoint chr2 128358378 128358848 0.36762913 1.38579236 14.0293958 MGC4268 55 overlaps exon 409 disjoint downstream
chr2 139255208 139255770 0.99515966 -0.05671432 14.0168278 NXPH2 928 promoter -88 disjoint chr6 139390213 139390803 1.11155927 0.19952739 14.0142361 REPS1 39123 upstream 845 disjoint chrl5 58478751 58479287 -0.59752192 0.44153573 14.0100694 ANXA2 1275 promoter -529 disjoint chr8 48336847 48337481 -0.55210797 0.54879598 13.9997842 CEBPD 475841 downstream -218 disjoint chr8 49630356 49630856 0.05137777 1.16892623 13.9988957 EFCAB1 179487 downstream 380 disjoint chr8 17316713 17317213 0.01114134 1.08549247 13.9914253 MTMR7 1507 promoter -1222 disjoint chrl l 62450278 62450820 1.36164697 0.31493062 13.9876461 CHRM1 4691 upstream 0 inside chrX 150615199 150615600 -0.02100149 1.18604275 13.9788938 PRRG3 1834 promoter -465 disjoint chr7 23478112 23478626 0.89655404 -0.16917967 13.9724055 IGF2BP3 1593 promoter 1433 disjoint chrl 5 34659667 34660101 2.10075892 0.93695777 13.9656138 C15orf41 14285 upstream -478 disjoint chr3 135688312 135688969 0.08275541 0.85388206 13.9588351 CEP63 576 inside intron -186 disjoint chrl5 33159611 33160323 0.24500778 1.11911322 13.9554784 ZNF770 91866 upstream 12040 disjoint chr4 75243436 75244011 1.32112983 0.43252361 13.946476 THFD2L 35582 inside intron -535 disjoint chrl l 46217676 46218317 -0.09451761 1.17321824 13.9450943 CREB3L1 37486 upstream -155 disjoint chr3 126255030 126255536 -0.01436124 0,99711965 13.944718 SLC12A8 158736 downstream 1397 disjoint chrl 9 61968565 61969101 0.37482443 1.39497864 13.9293733 ZIM2 74785 downstream 0 overlap chrl2 113601689 113602372 0.31171612 -0.40387965 13.9164527 TBX3 3979 covers exon(s) 2785 disjoint chr20 5936044 5936586 -0.65988714 0.26080697 13.903459 CRLS1 1166 inside intron -747 disjoint chrl l 16589266 16589778 1.26468204 0.24212438 13.8987809 Cllorf58 126991 upstream 0 overlap chr4 81336365 81336841 1.24063877 0.20384119 13.8645689 PR0M8 11903 covers exon(s) 320 disjoint chrl l 59191281 59192066 -0.28363014 0.62442815 13.8461192 FLJ36874 8288 upstream 711 disjoint chrl 7 77091298 77092041 0.14999763 1.04961256 13.8446085 ACTG1 2380 overlaps 3' 789 disjoint chrl 8 44727478 44727953 0.04606601 1.00834601 13.8430027 SMAD7 3125 inside intron 976 disjoint chr5 172595901 172596545 1.33573623 0.48876129 13.8260642 NKX2-5 1034 promoter 0 overlap chr2 40531084 40531569 -0.11347157 1.06261263 13.8226306 SLC8A1 20137 upstream 412 disjoint chr3 157877379 157878020 -0.28433082 0.4980531 13.8202877 TIPARP 2307 inside intron -1081 disjoint chr20 21637335 21637817 1.46613839 0.30539009 13.8197016 PAX1 2972 overlaps exon 0 overlap downstream
chrl l 31782580 31782945 1.10190013 -0.23662348 13.8188127 PAX6 6488 inside intron 0 inside chr6 27755547 27756240 1.13397798 0.16548022 13.8140645 HIST1H2BL 127447 downstream 0 cover chrl2 56523029 56523635 0.1909465 1.0978757 13.8108104 CTDSP2 3378 inside intron 1472 disjoint chrlO 118881250 118881870 0.92836145 0.04348301 13.8095704 VAX1 5931 overlaps exon 281 disjoint upstream
chr8 61725955 61726578 1.36220892 0.31724099 13.8026996 CHD7 27314 upstream 180 disjoint chr2 176676298 176676828 1.08742622 0.03365106 13.8026669 HOXD12 3523 downstream 635 disjoint chr4 124645758 124646333 1.24818237 0.12471014 13.7850157 SPRY1 105626 downstream 0 overlap chr7 2620602 2621033 0.13793306 1.28651061 13.7829306 IQCE 55445 downstream -8311 disjoint chrl 27687629 27688343 -0.28137217 0.52768466 13.7719423 WASF2 912 inside intron 586 disjoint chr5 67519569 67520334 1.12544465 0.10176417 13.7499701 PK3R1 37883 upstream 26294 disjoint chr8 37675489 37675991 1.04703411 -0.04160633 13.7423184 ZNF703 3031 overlaps 3' -409 disjoint chrlO 101277595 101278182 0.94433606 -0.06148723 13.7407839 NKX2-3 4517 upstream 0 overlap chrl 2 119452023 119452457 -0.03157269 1.2540314 13.7360272 C0Q5 677 promoter -602 disjoint chr3 129850776 129851282 0.04113387 1.07507684 13.7319651 RPN1 1126 inside intron 334 disjoint chr7 147131374 147131988 0.28434045 1.11611759 13.7269312 CNTNAP2 1686989 inside intron 535439 disjoint chrl 6 71654154 71654447 1.39848142 -0.31725334 13.7258781 ATBF1 14380 upstream 0 overlap chr 78980419 78980964 -0.32053805 0.6241795 13.724046 VPS13A 1216 promoter 926 disjoint chrl 7 6862839 6863309 -0.10649443 0.99636249 13.7194565 C17orf49 3992 downstream 2815 disjoint chr3 148598090 148598773 1.1991542 0.42053583 13.7160781 ZIC4 8323 inside intron 0 overlap chrl 8 70302981 70303379 0.04203922 1.2116719 13.6987037 CNDP2 11197 upstream 10536 disjoint chrl 1659491 15 165949618 1.31402313 0.28416439 13.6961521 RCSD1 83162 downstream 483 disjoint chrl 48222102 48222538 1.67413153 0.45879945 13.6958407 SLC5A9 238452 upstream 0 overlap chr5 50297681 50298264 1.46211245 0.09266645 13.69446 PARP8 299112 downstream 2578 disjoint chrl l 128060697 128061268 1.09149167 -0.09043424 13.6888214 FLU 7930 upstream 4045 disjoint chrl 4 60194376 60194843 1.0580969 -0.01715473 13.6636895 SKI 8444 upstream -10 disjoint chr20 48034929 48035504 0.13405123 1.04347594 13.6609958 SNAI1 1996 inside intron -1865 disjoint chr2 45029939 45030379 1.45173406 0.31073558 13.6608405 SK3 7399 downstream 0 overlap chr8 104453384 104454037 0.49343714 1.39497966 13.6484116 CTHRC1 423 inside intron -99 disjoint chr8 73078887 73079787 1.21619897 0.33891127 13.6429315 TRPA1 70585 downstream 72 disjoint chr7 112368104 112368571 2.44240022 1.39542121 13.6107271 FLJ31818 937 promoter -651 disjoint chrll 124213530 124214000 1.51913991 0.36337335 13.6062229 R0B03 26491 upstream 432 disjoint chr7 145445333 145446004 -0.00078136 0.98686851 13.6042018 CNTNAP2 948 inside intron -316 disjoint chrl 2 105053392 105053982 -0.07376999 0.78262062 13.6032647 NUA 1 3958 inside intron 2254 disjoint chrlS 74418545 74418987 1.85999041 -0.08248086 13.5972989 ISL2 2344 inside intron 330 disjoint chr7 100025647 100026150 1.45904861 0.39233133 13.5752046 FBX024 3756 covers exon(s) -3086 disjoint chr4 189154018 189154425 1.65409633 0.25780685 13.5702384 ZFP42 100 inside intron -148 disjoint chrl l 108800533 108801124 1.93293921 0.6767786 13.5608908 LOC399947 2449 inside exon -340 disjoint chr21 36989389 36989946 0.85903383 -0.0089668 13.5589609 SIM2 3914 upstream 117 disjoint chrl 46730652 46731260 0.94073304 -0.01649718 13.5504069 DMBX1 13994 upstream -944 disjoint chrl l 31801293 31801793 1.30508125 0.37499699 13.5491777 PAX6 11839 upstream 1915 disjoint chrl 90964473 90964942 0.96159362 -0.11112558 13.5480139 BARHL2 9092 upstream 0 inside chr3 109290804 109291350 -0.21941808 0.72993982 13.5479389 CD47 1274 inside intron 712 disjoint chrl4 37121496 37122119 0.94298902 0.03211526 13.5268301 F0XA1 12120 downstream 277 disjoint chr5 134854511 134854984 1.340828 0.30085745 13.5196172 NEUROG1 44553 downstream -116 disjoint chrl5 34968519 34969149 0.69945433 -0.08324752 13.5147038 MEIS2 208645 downstream -1445 disjoint chr5 74198499 74198969 1.10610625 0.06198893 13.5094365 TINP1 99641 downstream -27 disjoint chrl 4093845 4094418 0.17356579 0.99653239 13.506309 Clorfl74 287137 upstream -742 disjoint chr3 18459643 18460116 1.46004094 0.48923299 13.5046078 SATB1 19300 upstream 0 overlap chrl 7 44011410 44011913 0.87754218 -0.03871438 13.5018203 HOXB4 669 promoter -807 disjoint chrl 219133275 219134032 1.26470262 0.29376049 13.4924087 HLX1 13894 downstream 38 disjoint chr5 122451258 122451767 1.17233872 0.23913206 13.4865625 PPIC 50935 upstream 469 disjoint chrl 4 32479314 32479745 1.16367748 0.00191672 13.4823123 NPAS3 1041 inside intron -5484 disjoint chrl 2 1624419 1625141 0.23255835 1.22766995 13.4774637 WNT5B 15747 inside intron 117 disjoint chr4 40013694 40014167 0.22145234 1.29211237 13.4693092 CHRNA9 18058 upstream 120411 disjoint chrl6 85353384 85353785 0.23687102 1.38693724 13.4658045 F0XL1 183769 downstream 73578 disjoint chrlO 105602506 105603576 0.34716847 1.0854439 13.4622469 SH3PXD2A 1577 inside intron 925 disjoint chr7 157086267 157086878 0.12195806 1.01240705 13.4353482 PTPRN2 986300 inside intron -6184 disjoint chr2 74582297 74582836 1.32898752 0.4582268 13.4299955 LBX2 1 114 inside intron 71 disjoint chrl 191045571 191046022 -0.26503541 0.89104288 13.4196399 RGS2 778 covers exon(s) -750 disjoint chrlO 45192522 45193163 -0.17258732 0.84518061 13.4131545 AL0X5 2888 inside intron -2360 disjoint chrl 7 71643064 71643520 1.08638109 -0.08759278 13.4053454 F0XJ1 4640 downstream 1714 disjoint chr6 32836105 32836602 -0.05498666 0.98303541 13.4039936 HLA-DQA2 18965 downstream 718 disjoint chr20 24922307 24922648 -0.23831391 1.24637359 13.4013717 C20orf3 883 promoter -607 disjoint chrl 117007880 117008317 -0.00709621 1.08644597 13.3937403 IGSF3 3519 inside intron 3030 disjoint chr2 937228 937849 1.48253614 0.74337032 13.3921102 SNTG2 674 inside intron 0 overlap chr3 180650127 180650633 -0.36365526 0.60889639 13.3889856 GNB4 1431 inside intron 793 disjoint chrl 7 75376786 75377666 0.96251466 0.19638702 13.3853146 CBX2 10199 downstream 293 disjoint chrX 74063036 74063503 -0.01039038 1.09386567 13.3768045 KIAA2022 1328 promoter -1135 disjoint chr21 43399018 43399386 -0.38722064 0.93871217 13.3658725 U2AF1 1370 inside intron 846 disjoint chr3 199004617 199005178 0.19022238 1.13265796 13.3643583 LRCH3 2076 inside intron -1441 disjoint chr3 173011320 173011852 -0.28952179 1.1094347 13.3541285 PLD1 72755 upstream -171 disjoint chr6 75851057 75851562 1.82753494 0.87310471 13.3515805 COL12A1 120780 inside exon 38 disjoint chr5 41960433 41960936 0.04930597 0.98904007 13.3511059 FBX04 176 promoter 110 disjoint chr6 17388388 17388723 1.52110384 0.08549555 13.3475388 RBM24 2187 promoter 0 overlap chrl3 92676073 92676615 0.70016877 -0.28083078 13.3398376 GPC6 480 promoter 631 disjoint chr9 1031965 1032501 1.29667547 0.17781032 13.3396382 DMRT2 9112 upstream 0 overlap chrl5 64577394 64578002 0.02900647 0.8505561 13.337828 SNAPC5 195 promoter -92 disjoint chrl 9 47479025 47479561 -0.7358634 0.17706509 13.3301687 CIC 1095 promoter -1643 disjoint chr4 46085341 46086026 -0.1706983 0.82874315 13.329309 GABRA2 675 covers exon(s) 634 disjoint chrl4 34940788 34941385 0.33212236 1.17033259 13.3280149 NF BIA 2309 overlaps two 1413 disjoint exons
chr8 131437615 131438288 0.35138675 1.15197995 13.3231703 DDEF1 45110 inside intron 981 disjoint chr2 222143527 222144289 -0.32869695 1.14199377 13.3190557 EPHA4 964 inside intron 0 overlap chr3 184455412 184455879 1.3464769 0.39814062 13.3184918 B3GNT5 1687 inside intron -86 disjoint chr9 95970545 95970910 -0.41009835 0.86977011 13.2938617 PTPDC1 83979 downstream -1263 disjoint chr7 970970 971401 0.41692146 1.52474667 13.2842693 COX19 10359 overlaps 3' 2284 disjoint chr20 54632900 54633442 0.89119131 -0.12942642 13.2680305 TFAP2C 4322 upstream 244 disjoint chr7 27120790 27121507 1.20369132 0.37543399 13.2501807 HOXA3 4231 inside intron 17 disjoint chrl 7688485 7689021 0.37275898 1.14354201 13.2453094 CAMTA1 920515 inside intron -42 disjoint chrl5 69195770 69196333 1.37535373 0.14022655 13.2441101 THSD4 24508 upstream -218 disjoint chrlO 65058323 65058937 -0.27697067 0.63170011 13.2429463 REEP3 107195 downstream 944 disjoint chrl3 49605920 49606390 1.54799725 0.55064784 13.2377689 KCNRG 118530 downstream 0 overlap chr20 21439773 21440348 0.98421396 -0.0773936 13.2368272 N X2-2 2315 inside exon 0 inside chrl2 12309029 12309502 0.08605166 1.09967565 13.2347691 LRP6 1510 inside intron 1444 disjoint chrl 6 3868656 3869348 0.08508723 0.82522001 13.232528 CREBBP 1363 inside intron 136 disjoint chr6 124164652 124165296 0.27608715 1.04448277 13.2274019 TCBA1 1471 promoter 580 disjoint chr7 27168580 27169143 -0.35540386 0.51855669 13.2271453 HOXA9 2530 overlaps 3' -1095 disjoint chr2 65518130 65518582 1.54173492 -0.07748892 13.2220223 FLJ16124 782 inside intron -747 disjoint chr2 171275883 171276414 1.25393049 0.26701757 13.2151676 LOC440925 2908 downstream 154 disjoint chr6 114395681 114396340 1.22694863 0.47231098 13.2108312 HDAC2 2706 inside intron 1764 disjoint chr6 10499651 10500223 1.15361177 0.24183178 13.20856 TFAP2A 20369 downstream -567 disjoint chrl 5 72252473 72253093 -0.18022665 1.15132523 13.2056003 ISLR 46 promoter 1573 disjoint W 201
169
chr2 216655441 216655944 1.37688749 0.48047548 13.2015696 TME 169 555 inside intron -462 disjoint chrl 160798805 160799308 -0.08432918 0.91377188 13.1901173 UAP1 859 inside intron -328 disjoint chr2 201100053 201100454 -0.54568764 0.60261034 13.1860105 SGOL2 867 inside intron -591 disjoint chrl l 17052561 17053256 -0.26378345 1.0845344 13.1733342 RPS13 2539 overlaps two 2159 disjoint exons
chr20 50156049 50156749 1.22096739 0.293302 13.1724017 ZFP64 85181 inside intron -730 disjoint chr5 66336576 66337220 0.81359734 0.08392192 13.1722767 LOC375449 408613 downstream -737 disjoint chrl 36625214 36626043 0.11955891 1.10377077 13.1690871 STK40 1143 promoter -754 disjoint chr2 120233007 120233357 0.9856377 -0.4603832 13.1562836 PTPN4 319 promoter 179 disjoint chr5 50296152 50296517 1.2761158 0.02949335 13.1485789 PARP8 297583 downstream 4325 disjoint chr2 211048605 211049051 -0.1551726 1.04103474 13.1461749 LANCL1 624 inside intron 375 disjoint chrl2 52655707 52656180 0.89821827 -0.10137742 13.1452165 H0XC11 2531 inside exon -337 disjoint chrX 132378320 132378793 0.72892318 -0.24660732 13.134725 GPC4 1450 promoter -370 disjoint chr9 136275775 136276179 0.33967338 1.51150401 13.1335936 RXRA 82051 upstream 80704 disjoint chr4 109310412 109310990 0.81823055 -0.03140747 13.1317868 LEF1 1386 promoter -556 disjoint chrl2 108544171 108544698 -0.02373149 0.98026338 13.1285969 MVK 48172 downstream -48189 disjoint chr5 77176882 77177336 1.56210489 0.45575081 13.126199 TBCA 68942 upstream -212 disjoint chr6 10518506 10518940 1.26188524 0.12718186 13.1183304 TFAP2A 1652 overlaps exon 0 overlap upstream
chr7 31341062 31341670 0.30081097 1.140024 13.0989209 NEUROD6 5392 downstream 700 disjoint chr2 176748865 176749335 0.81165516 -0.20298357 13.0976195 HOXD3 11815 downstream -668 disjoint chrlO 116382204 116382707 -0.21133972 0.71330692 13.0927624 ABLIM1 25340 inside intron -387 disjoint chrl 3 21140853 21141359 0.97782451 -0.005568 13.0810497 FGF9 2515 upstream 0 overlap chr3 158358839 158359426 -0.07770354 0.72699375 13.0517254 CCNL1 1749 overlaps exon 440 disjoint downstream
chrl 6 30596705 30597566 1.06026734 0.08908104 13.0511148 FBS1 12578 downstream -18049 disjoint chr8 102574006 102574620 1.11597252 0.04037331 13.0463219 GRHL2 0 overlaps 5' 0 overlap chrl 182621283 182621981 1.09931176 0.12661556 13.0417553 Clorf21 791 promoter 57 disjoint chrl5 46722744 46723391 -0.53647504 0.19198763 13.0403565 FBN1 1818 inside intron 711 disjoint chr7 157064591 157064986 0.08689137 1.2722443 13.0388822 PTPRN2 1008192 inside intron -2436 disjoint chr2 200033986 200034541 0.8934441 -0.12674405 13.0319511 SATB2 541 promoter 0 inside chrl 5 27210438 27210908 0.35626036 1.37529978 13.0318162 APBA2 209294 downstream -14917 disjoint chr7 26159352 26159819 0.82986098 -0.27053773 13.024168 NFE2L3 968 inside intron -70 disjoint chr7 139985650 139986184 -0.08665382 1.05694689 13.0198042 DEHND2A 860 inside intron 282 disjoint chrl l 67912991 67913704 2.66305089 1.79542641 13.0143671 LRP5 76281 inside intron 931 disjoint chr 10604767 10605210 -0.04325022 1.00281943 13.0105311 PTPR 2259 promoter -1434 disjoint chr6 31742369 31742806 -0.23383884 0.84607572 13.0022396 CSN 2B 734 covers exon(s) -297 disjoint chr6 110786509 110787072 -0.26765761 0.67696518 12.9904825 DDO 56373 downstream 0 overlap chr2 60636764 60637370 0.82606589 0.00575724 12.9806962 BCL11A 2628 upstream -481 disjoint chrl 33572519 33572920 0.17890323 1.3584094 12.9745679 PHC2 15165 inside intron 14450 disjoint chr6 133602937 133603511 1.61227374 0.31594672 12.9472219 EYA4 676 promoter 268 disjoint chrl5 52058072 52058671 -0.03381315 0.81291103 12.9371148 WDR72 218922 upstream -218776 disjoint chr3 129254858 129255460 0.03426842 0.9300091 12.9340669 SEC61A1 957 inside intron -547 disjoint chr5 88003562 88004032 0.66216974 -0.3473137 12.9265778 MEF2C 210747 downstream 359 disjoint chrll 128063753 128064504 1.37196301 0.27850443 12.9254598 FLU 4694 upstream 809 disjoint chr9 90981608 90982153 0.90680193 0.09152038 12.9234403 SHC3 1348 inside intron 329 disjoint chrlO 76833874 76834305 1.45700263 0.35485301 12.9132813 Z F503 2444 promoter 0 inside chrl 7 56834764 56835463 1.11805633 -0.05539524 12.9079672 TBX2 2726 covers exon(s) 0 inside chr9 85782300 85782818 -0.1511635 0.94767902 12.9019784 HNRPK 2083 covers exon(s) 1328 disjoint W
170
chr2 104851131 104851460 1.62054798 0.2862376 12.8848322 POU3F3 12731 downstream -273 disjoint chrl 221053963 221054364 0.27997433 1.44066185 12.883593 FLJ43505 76783 downstream 503 disjoint chr8 75425944 75426276 1.04436639 -0.38682293 12.8807038 GDAP1 737 covers exon(s) -345 disjoint chr6 1557371 1557966 0.88765319 0.06395249 12.871152 FOXC1 1692 close to 3' 0 inside chr6 3693931 3694510 0.24966374 1.05134019 12.8677269 C6orfl45 2424 inside intron 1277 disjoint chr20 31748839 31749277 0.50588464 1.57785806 12.8636811 PXMP4 22519 downstream -10673 disjoint chrl 9 9908504 9909001 0.65910403 -0.14831061 12,8349268 OLFM2 435 promoter -26 disjoint chr5 124015666 124016168 -0.44321005 0.53411724 12.8318638 ZNF608 92535 inside intron -19 disjoint chrl 231496796 231497197 1.62196352 0.3661809 12.8236808 IAA1804 32939 upstream 575 disjoint chr5 140546933 140547856 0.14328981 1.21124897 12.8173191 PCDHB9 0 overlaps 5' 544 disjoint chr2 151826820 151827312 0.15722315 1.12123098 12.8149621 C2orf38 198 promoter -95 disjoint chrl 39345439 39345987 0.47820813 -0.43396857 12.8146938 MACF1 25735 inside intron -993 disjoint chr2 191219954 191220554 -0.0338851 0.80742222 12.8125657 NAB1 1538 promoter 637 disjoint chr5 82807572 82808144 0.49393093 -0.33400157 12.8032486 CSPG2 4234 inside intron -1217 disjoint chr20 28136104 28136990 1.94032968 0.61286885 12.8016755 MGC72104 88549 upstream 11581 disjoint chr6 108992028 108992432 -0.10291028 1.07601116 12.7900788 FOX03A 3267 inside intron -1931 disjoint chrlO 24021645 24022253 0.03563192 0.9063141 12.781023 C10orf67 347868 upstream 135 disjoint chrl 110011366 110011905 0.12332072 1.00575326 12.7740675 GSTM2 308 promoter 199 disjoint chr8 10502847 10503524 0.41752849 1.23472358 12.76919 RP1L1 46502 inside exon 3681 disjoint chrl2 106691796 106692374 0.14495418 1.03004376 12.7683019 ASCL4 0 overlaps 5' 742 disjoint chr4 139231054 139231699 0.26994862 1.05971242 12.7638126 SLC7A11 151253 downstream 469485 disjoint chrl 145014367 145015062 0.2288692 1.16007936 12.7604187 PRKAB2 95690 downstream 1412 disjoint chr4 146624607 146625078 -0.1788705 0.80257286 12.7587637 SMAD1 1201 inside intron -1174 disjoint chr8 61756101 61756427 1.3023412 -0.09093132 12.7583186 CHD7 2209 inside intron -367 disjoint chr5 3654692 3655200 1.51029281 0.65152835 12.7562019 IRX1 5525 downstream 0 inside chrlO 51236054 51236713 -0.4756377 0.33243519 12.7533701 MSMB 16496 downstream -400 disjoint chr7 91409036 91409750 -0.30744181 0.59838406 12.7507626 AKAP9 909 inside intron -752 disjoint chrl 9 6227534 6228121 0.26594942 1.10320207 12.746213 MLLT1 2837 inside intron 2362 disjoint chrl 8 75430555 75431073 2.50031924 1.64793671 12.74413 NFATC1 169242 downstream 5996 disjoint chrl 6 50228510 50228947 0.88673927 -0.11845795 12.7415557 SALL1 485858 upstream -480749 disjoint chrl l 44299304 44299699 1.17360949 0.0156287 12.7377887 ALX4 11013 upstream -971 disjoint chrl5 97378972 97379526 2.40312488 1.51851654 12.7289979 IGF1R 368685 downstream -2279 disjoint chr2 236753450 236753921 -0.13431292 0.86634095 12.7257717 GBX2 12060 upstream -248 disjoint chr4 29887716 29888201 0.37894421 1.3477266 12.7249872 PCDH7 442933 upstream 439750 disjoint chrl 5 88444675 88445234 0.03299922 0.96257634 12.7183589 IDH2 1477 inside intron 768 disjoint chrl 7 71579129 71579569 -0.34066461 0.70034128 12.7105678 SRP68 632 inside intron 200 disjoint chrX 136472396 136472902 0.63421689 -0.30843252 12.7045756 ZIC3 3109 upstream 2290 disjoint chr5 133891913 133892524 0.12298875 0.91349841 12.7042277 PHF15 2217 inside intron -586 disjoint chr7 154977288 154977830 1.41204002 0.42950243 12.7023004 EN2 35113 downstream -171 disjoint chrlO 102097772 102098179 1.5283056 -0.07639296 12.6964189 SCD 1011 covers exon(s) -60 disjoint chr2 172571984 172572493 -0.11200454 0.82587619 12.6960664 MAPID 556 promoter 366 disjoint chr5 76960708 76961272 0.60692148 -0.23300898 12.6894657 OTP 9005 inside exon 0 overlap chr4 54670279 54670647 1.55632134 0.28755295 12.6876839 GSH2 9325 downstream 0 inside chr7 90065095 90065598 0.17457065 1.06586398 12.6873466 PFT 1 111049 upstream -795 disjoint chrl 69808338 69808765 1.36605903 0.09766279 12.6839624 LRRC7 189680 upstream -1255 disjoint chr9 126946727 126947227 0.25123949 1.21891999 12.6812806 C9orfl26 1132 promoter -959 disjoint chrl3 29938878 29939417 0.0760753 0.95218944 12.6802604 HMGB1 866 promoter -20741 disjoint chr8 116730095 116730515 -0.13000833 1.04633208 12.6775439 TRPS1 19886 inside intron -174 disjoint chr3 6881512 6882120 0.25116506 0.96042012 12.6755481 GRM7 3586 inside intron -1871 disjoint chrX 51168566 51169123 -0.06386913 0.80182428 12.6721246 LOC340602 2060 close to 3' -915 disjoint chr8 145907010 145907533 0.19629983 1.02592614 12.6701802 ZNF34 68935 downstream 1768 disjoint chr2 176729388 176729927 1.19181933 0.40926071 12.6671063 H0XD4 5030 downstream 2820 disjoint chrlO 28076052 28076519 0.71851824 -0,25530609 12.6597162 MKX 1300 promoter -835 disjoint chrl6 840575 841120 3.21969538 2.39114617 12.6483595 TMEM112 119864 downstream 0 overlap chr6 168583475 168583981 0.01479996 0.9946113 12.6339137 S 0C2 898 promoter 306 disjoint chrl3 111680535 111681309 0.34937475 1.25813583 12.6331917 S0X1 88604 upstream -1738 disjoint chr2 127692150 127692515 1.30638766 0.01759161 12.6330843 FLJ 16008 12338 upstream 344 disjoint chrlO 719492 720013 0.35530929 1.24910255 12.6237308 DIP2C 5592 inside intron 4694 disjoint chrl 9277029 9277430 0.05146081 1.18926765 12.6188746 SPSB1 1459 inside intron -29426 disjoint chr6 41545386 41545926 1.24999378 0.20027623 12.6137766 FOXP4 76215 upstream 114 disjoint chr2 173001813 173002349 0.9399069 -0.03135012 12.6076779 ITGA6 1198 inside intron -384 disjoint chr20 20817973 20818374 0.38690612 1.49323698 12.6051755 C20orf74 176851 upstream 130391 disjoint chr8 35214825 35215353 -0.09685057 0.82691954 12.59908 UNC5D 306098 upstream -1172 disjoint chrl l 18611177 18611740 -0.12027537 0.76529565 12.5907711 SPTY2D1 855 inside intron 647 disjoint chr4 151724611 151724943 1.34062353 0.01541569 12.5900306 MAB21L2 1859 inside exon -76 disjoint chr2 121213030 121213397 1.44692509 0.17518047 12.5768263 GLI2 52929 upstream -1326 disjoint chr7 92298188 92298766 2.18569875 1.21860778 12.5721826 CDK6 2381 inside intron 1371 disjoint chrl 26817697 26818356 0.90600153 0.13108968 12.5709807 RPS6KA1 72768 downstream 1075 disjoint chr7 27105351 27105714 1.34106608 0.07917164 12.559033 HOXA2 3204 downstream -2090 disjoint chr6 131423847 131424286 0.10562995 1.16527671 12.5578486 EPB41L2 1728 inside intron 838 disjoint chrl 198483082 198483552 0.31002361 1.20176833 12.5565775 NR5A2 219690 downstream 54347 disjoint chrl 65546704 65547261 1.39037723 0.28002106 12.5562631 DNAJC6 43687 inside intron 345 disjoint chrl 8 22488143 22488754 -0.46943831 0.34354775 12.5551229 KCTD1 13838 upstream 833 disjoint chr8 37762735 37763166 0.13711908 1.18240481 12.5434288 PROSC 23903 downstream 10040 disjoint chrl 13949243 13949856 -0.27849531 0.82235759 12,5424231 PRD 2 781 inside intron -198 disjoint chrl3 38162916 38163419 0.37564172 1.42287205 12.5423478 FREM2 3435 inside exon -2617 disjoint chr5 14505146 14505613 0.13054225 1.11459023 12.5406466 TRIO 308318 inside intron 8517 disjoint chr8 38209270 38209719 -0.18101131 0.95965211 12.5391184 DDHD2 1007 overlaps exon -157 disjoint upstream
chr2 202216916 202218144 -0.01609106 0.83054181 12.5390998 MPP4 53517 overlaps 3' -401 disjoint chrl 5 38055026 38055891 0.14405777 0.81768917 12.5352021 EIF2A 4 41388 inside intron 0 overlap chrl4 23083610 23084116 1.06466551 0.24554789 12.5252573 THTPA 10954 upstream 5726 disjoint chr6 132312221 132312717 0.18342383 1.10008225 12.5067928 CTGF 1493 overlaps exon 332 disjoint upstream
chr7 27130658 27131032 1.82598938 0.54251405 12.5033728 HOXA3 2131 inside intron -35 disjoint chr8 17315656 17316126 1.37840435 0.36422928 12.4993069 MTMR7 450 promoter -165 disjoint chrl l 14337552 14338084 -0.10404626 0.89261492 12.4991845 RRAS2 264 promoter -239 disjoint chrl 4 20224280 20224891 0.26424397 1.00752761 12.4980246 ANG 1672 inside intron -1700 disjoint chr4 165525100 165525750 0.55515488 1.24455466 12.495227 ANP32C 186788 upstream -473 disjoint chr8 25962461 25963036 0.86129132 -0.22917603 12.4813454 EBF2 4153 upstream -702 disjoint chr20 61030336 61030838 0.61887669 -0.25799943 12.480582 DIDOl 8880 inside intron 40 disjoint chrl l 124176494 124177089 -0.34816776 1.03786665 12.4743097 Cllorf61 986 promoter -765 disjoint chrl 91260739 91261305 0.17781636 1.07478584 12.460145 ZNF644 481 promoter -344 disjoint chr22 24288959 24289791 -0.28573619 0.65213988 12.4600508 ADRBK2 1154 promoter 1168 disjoint chrl l 89594091 89594597 2.11949571 1.32649311 12.4537789 CHORDCl 1256 inside intron 793 disjoint chr4 174678081 174678518 0.83429052 -0.1727224 12.4489573 HAND2 9434 downstream -1257 disjoint chr8 58066860 58067511 -0.1313531 0.78138476 12.4343446 IMPAD1 1445 inside intron 743 disjoint chrl2 99636349 99636924 0.23437549 1.01377899 12.4197268 TME 16D 75791 upstream -596 disjoint chr21 37365811 37366603 0.01541095 1.21365617 12.4180426 PIGP 369 overlaps exon 127 disjoint downstream
chr20 35473818 35474643 0.10947641 1.10542446 12.4101675 SRC 65848 downstream -5201 disjoint chrl l 118373150 118373842 -0.0182723 1.03013632 12.4069653 CCDC84 219 promoter 9 disjoint chr3 109425020 109425490 -0.32424577 0.67185717 12.4043935 IFT57 1083 promoter -830 disjoint chrl8 45273072 45273510 1.5655086 0.54172838 12.3960339 RPL17 169 promoter -126 disjoint chr5 75736582 75737196 0.61472911 1.31483432 12.3940216 IQGAP2 1678 inside intron -666 disjoint chrl7 37862282 37862922 0.04852388 0.79204133 12.3883606 ATP6V0A1 1465 promoter 1350 disjoint ohrl5 71765246 71765824 0.18578952 0.9787288 12.3839317 CD276 1572 inside intron -870 disjoint chrX 128920021 128921000 0.93286165 0.20662382 12.3785553 BC0RL1 23349 upstream -712 disjoint chr20 36866729 36867226 0.74240752 -0.28526189 12.3709485 PPP1R16B 535 promoter 394 disjoint chrl 151501619 151502224 0.38589769 1.20249842 12.3691512 LOR 2817 downstream 272824 disjoint chr4 171205682 171206155 0.07257077 0.91646015 12.3678511 AADAT 41602 downstream -20199 disjoint chrl 5 41855579 41855983 1.38428559 0.27423959 12.3658071 ELL3 810 overlaps exon 0 overlap upstream
chrl 7 7084872 7085342 0.2070069 1.19114526 12.3355322 GABARAP 1134 overlaps exon 861 disjoint upstream
chr8 134376194 134376828 0.08535594 0.93094858 12.3348768 NDRG1 1851 inside intron 682 disjoint chr5 89807863 89808231 1.37074685 0.09388259 12.3323337 POLR3G 1427 inside intron -1251 disjoint chr3 196749743 196750465 0.24686724 1.35240769 12.3319774 PPP1R2 896 inside intron 374 disjoint chr5 174092895 174093221 1.56781986 0.19796952 12.328653 MSX2 8715 downstream -560 disjoint chr7 27100171 27100527 1.46867642 0.05637635 12.3259836 HOXAl 1622 inside exon 95 disjoint chrl 6 67975469 67976044 0.14086443 0.80715945 12.3194031 TERF2 1329 overlaps exon 773 disjoint downstream
chr7 148743512 148743910 1.39391562 0.15476864 12.3125063 ZNF777 39395 downstream -34 disjoint chr6 10524118 10524486 1.43059899 0.2071567 12.2970754 TFAP2A 3296 inside intron -814 disjoint chr5 140702278 140703026 -0.43776139 0.46688009 12.2809491 PCDHGA2 3741 inside intron 706 disjoint chrlO 93383136 93383606 -0.05596459 0.94049609 12.2692701 PPP1R3C 299 promoter -9 disjoint chr8 1040622 1041389 2.89326804 1.87841603 12.2663947 ERICH1 369397 upstream 0 cover chrl 9 51059916 51060461 0.32337354 -0.60551553 12.2529711 FOXA3 559 inside intron -268 disjoint chrl 21221476 21222021 0.41078542 1.21483101 12.2496163 EIF4G3 153905 inside intron 153681 disjoint chrl 19845043 19845678 0.33560592 1.17367676 12.2416844 NBL1 1649 inside intron -533 disjoint chrl 43003628 43003996 -0.34678249 0.99355565 12.2269934 LEPRE1 1273 inside intron 805 disjoint chrl 35428773 35429351 0.22689848 0.99262702 12.2240217 SFPQ 1970 covers exon(s) 703 disjoint chr5 92956761 92957126 1.33268417 0.10552244 12.2187197 NR2F1 11963 downstream -175 disjoint chrl 90965663 90966202 1.04106621 0.27546489 12.2159481 BARHL2 10282 upstream -271 disjoint chr2 70977473 70977943 1.17087193 0.26115327 12.206515 VAX2 3284 upstream 2285 disjoint chr5 95091406 95091948 0.47782232 -0.41426296 12.2003719 RHOBTB3 657 promoter 684 disjoint chrlO 8138348 8138851 1.1038895 0.13600016 12.1972342 GATA3 1676 inside intron -13 disjoint chrl 6 53921457 53921861 1.37115696 0.24924467 12.1956148 IRX6 5486 overlaps exon 463 disjoint upstream
chr6 84290603 84291175 2.42264661 1.65824737 12.1949962 PRSS35 11611 inside exon -92886 disjoint chr8 42148000 42148368 2.78304705 1.563722 12.1932505 AP3M2 18240 downstream -17745 disjoint chr7 23604462 23604899 0.56707061 -0.45250377 12.191194 CCDC126 940 inside intron -380 disjoint chrl6 25505486 25505851 0.1007682 1.31554764 12.1896824 HS3ST4 104996 upstream 104605 disjoint chr7 96487256 96487901 0.70697256 -0.09553077 12.1759075 DLX5 4177 overlaps 3' 256 disjoint chrlO 26266825 26267158 -0.20592635 1.0754017 12.1731686 MY03A 3624 inside intron -2797 disjoint chr6 10491114 10491560 1.30292891 0.1503815 12.171138 TFAP2A 29032 downstream 0 overlap chr3 62338145 62338602 1.34662452 0.25514823 12.1671984 FEZF2 4085 upstream -26 disjoint chr6 101953130 101953780 1.62116331 0.98312594 12.1583372 GRK2 0 overlaps 5' 0 overlap chrlO 134651436 134651765 -0.06569074 1.28389651 12.1462852 C10orf93 45383 upstream 2446 disjoint chr5 172602316 172602890 1.35710056 0.51323991 12.1452521 NKX2-5 7449 upstream 545 disjoint chrg 27403538 27404239 0.16462238 1.01876186 12.1382264 EPHX2 322 promoter 336 disjoint chr21 27136479 27136883 -0.04187115 1.05643131 12.1368177 ADAMTS1 2715 covers exon(s) 1546 disjoint chr7 102276939 102277556 0.09106901 0.90638903 12.1352436 FBXL13 224694 inside intron -99611 disjoint chrlO 119794759 119795283 -0.0637596 0.70910856 12.1331785 RAB11FIP2 820 inside intron 532 disjoint chr3 142251877 142252275 1.67377189 0.61899886 12.1286625 SPSB4 1157 promoter 298 disjoint chrl l 124122433 124123078 0.92613226 -0.03042544 12.1255892 VSIG2 4240 overlaps 3' -217 disjoint chr20 55266497 55266865 -0.08428588 1.03473143 12.1243252 BMP7 7842 inside intron 5829 disjoint chrl7 75421508 75422045 0.95081205 -0.13670091 12.1234754 CBX4 5762 overlaps 3' 0 inside chrl2 73886230 73886772 0.15596364 0.88299452 12.1232191 KCNC2 3005 inside intron 576 disjoint chr8 12854455 12855849 0.23090254 1.10138931 12.1217712 C8orf79 931 inside intron -222 disjoint chrl l 69230751 69231411 0.20951674 1.19680985 12.1152058 FGF19 2465 promoter -1641 disjoint chrl 39648388 39648894 0.14497042 1.12372387 12.1151023 MACF1 78992 inside intron -562 disjoint chr5 92934801 92935403 0.74114071 0.02602538 12.1134761 NR2F1 9395 upstream -170 disjoint chr3 144319598 144320103 1.74793261 0.86465379 12.1130202 CHST2 1254 promoter 469 disjoint chr3 170865728 170866093 1.03539481 -0.11210778 12.1093705 MDS1 1561 promoter -1981 disjoint chr7 92076105 92076398 1.52221632 -0.02786618 12.1014061 CD 6 224749 inside exon -18296 disjoint chrlO 118883145 118883589 0.91047732 -0.15352418 12.0971952 VAX1 4212 inside intron 0 overlap chr8 72633402 72633839 0.70140449 -0.38144867 12.0958364 EYA1 196382 upstream -1287 disjoint chrl9 13976651 13977151 0.18847641 1.03483315 12.0947905 RFX1 945 inside intron 381 disjoint chr3 137951951 137952493 -0.33270955 0.58429873 12.0913652 STAGl 1441 inside intron 627 disjoint chrl 104829454 104829834 1.20115669 -0.18273311 12.0796365 POU3F3 8566 upstream -1252 disjoint chrl 7 819867 820271 0.18713114 1.35237908 12.0649638 NXN 9488 inside intron 8212 disjoint chr3 148605658 148606029 1.47387729 -0.00371345 12.0581486 ZIC4 1067 inside intron 3646 disjoint chr22 27167498 27168083 0.02301018 0.87109662 12.057681 CHEK2 299738 downstream 237017 disjoint chr20 3681225 3681755 1.62047769 0.28080678 12.0570382 HSPA12B 19870 inside exon -281 disjoint chrl 8 12278564 12279031 0.64175867 -0.18955471 12.0554427 CTDEA 33777 downstream -1002 disjoint chr4 174683640 174684101 1.08744667 0.07222525 12.0469677 HAND2 3851 downstream 807 disjoint chr2 239418686 239419192 0.2826575 1.14021496 12.036935 FLJ43879 93709 downstream 653 disjoint chr8 100975491 100975992 -0.07649701 0.81129338 12.0284061 COX6C 421 promoter -312 disjoint chrl 5 70307705 70308255 0.11657605 1.14623699 12.0276301 PKM2 2482 inside intron 930 disjoint chrl 8 74598862 74599296 0.35842665 1.3606742 12.0269706 SALL3 241966 upstream -11010 disjoint chrl5 39739042 39739407 1.19063522 0.04141302 12.0172479 TYR03 100519 downstream 420 disjoint chr2 30225217 30225582 1.86663324 0.66334561 12.0167295 YPEL5 1886 inside intron -792 disjoint chr6 5945505 5946241 1.10008687 0.41026416 12.0040936 NRN1 6390 inside intron -719 disjoint chrlO 44198617 44199152 1.05032516 0.17960665 12.0035272 CXCL12 1395 inside intron 568 disjoint chr2 118698878 118699315 1.33257065 0.30703526 12.0014648 INSIG2 136359 downstream 0 overlap chrl l 95295197 95295924 -0.53034065 0.35621202 11.9983383 MTMR2 994 inside intron 636 disjoint chrlO 115990008 115990377 1.33139966 0.25823412 11.9930577 VWA2 1001 inside intron -415 disjoint chrl 7 44001171 44001773 0.87253235 -0.00150245 11.9925054 HOXB3 5035 inside intron -4062 disjoint chr9 109293616 109294011 1.2009432 0.11298237 11.9780023 KLF4 2041 promoter -1135 disjoint chrl 3 47776935 47777564 -0.07834293 0.73546804 11.9751195 RBI 1052 inside intron -433 disjoint chr5 171548675 171549207 1.00316862 0.26380369 11.9680746 STK10 811 promoter -131 disjoint chrX 40832719 40833526 0.58555116 -0.26247383 11.9624621 USP9X 2888 inside intron -2047 disjoint chr2 225613827 225614342 0.14414176 0.99267589 11.9586783 DOCK10 206671 upstream 555 disjoint chr5 172605983 172606393 1.30596753 0.19503162 11.9586312 NKX2-5 11116 upstream ■406 disjoint chr8 17313402 17313764 -0.31672459 0.97139729 11.9569497 MTMR7 1442 inside intron 1210 disjoint chrl3 23743628 23744156 0.24866893 1.09950623 11.9415417 SPATA13 110742 inside intron 35942 disjoint chrl l 31801887 31802441 1.04058522 0.13316255 11.9249033 PAX6 12433 upstream 1267 disjoint chr2 222869357 222869843 1.33556184 0.26429738 11.9159681 PAX3 2100 inside intron 0 overlap chr2 222862301 222862801 0.78881276 -0.11117885 11.9134136 PAX3 9142 inside intron 1169 disjoint chrl2 56299131 56299601 1.56482535 0.56254769 11.9117791 SLC26A10 358 promoter 0 overlap chrl4 92460919 92461707 0.06790611 0.82168887 11.9111358 CHGA 1675 inside intron -1267 disjoint chrlO 71484473 71484838 2.05291789 0.77886655 11.9073098 H2AFY2 2111 inside intron -774 disjoint chr4 81330671 81331039 1.51190073 0.38235698 11.9036078 PRDM8 6209 inside intron -1187 disjoint chrl 176960020 176960493 1.85068019 0.83283323 11.8959976 RALGPS2 429 promoter 98 disjoint chr4 40912317 40912809 1.58043023 0.24209391 11.8887051 APBB2 1073 promoter 262 disjoint chr22 44852227 44852562 -0.11789796 1.12485102 11.8882577 FLJ27365 7984 upstream -5035 disjoint chr2 70984432 70984866 1.47951789 0.51678073 11.8829739 VAX2 3205 inside intron 0 overlap chr3 55492754 55493119 1.38884218 0.21312028 11.8769932 WNT5A 3251 inside intron 0 overlap chrl 9 626584 627179 0.1171439 1.05980057 11.8707327 FSTL3 209 promoter 0 cover chr7 157927670 157928137 0.26232026 1.27595012 11.86992 PTPRN2 145041 inside intron 12512 disjoint chr3 159309696 159310169 0.90027288 -0.04027924 11.8674291 RSRC1 416 promoter 282 disjoint chrl l 35398475 35399247 0.95995674 0.0285861 11.8574057 SLC1A2 795 promoter -17 disjoint chrl 5 20049478 20050383 0.21939009 1.43054501 11.8508868 OR4N4 165642 downstream -823 disjoint chr8 81245325 81245864 1.56263581 0.61681269 11.8415835 TPD52 526 inside intron 11 disjoint chrl 9 13068802 13069339 0.74270113 -0.27842991 11.8409175 NFDC 101219 inside exon 4 disjoint chrl 3 109835764 109836639 2.90547018 1.90734088 11.835097 COL4A2 78133 inside intron 0 cover chrl 62432789 62433187 1.0289996 0.05863001 11.8217288 L1TD1 0 overlaps 5' 0 overlap chr3 186783191 186783601 1.12334007 -0.1094898 11.819547 SENP2 3123 upstream 2912 disjoint chrl2 40825494 40825976 1.55534916 0.4065226 11.8133216 YAF2 92340 downstream -325 disjoint chrl 6 49144201 49144707 0.20594007 1.08354235 11.7990001 N D1 4460 inside intron -3235 disjoint chrl 7 75384018 75384491 1.05277913 -0.03258643 11.7952108 CBX8 993 overlaps exon 776 disjoint downstream
chrl 4 44437674 44438108 -0.19177544 0.77742484 11.7916902 C14orf28 1418 inside intron -816 disjoint chrl 154896748 154897302 0.27198583 1.18500497 11.7852261 BCAN 18385 downstream -2548 disjoint chr8 38761983 38762558 0.99494835 0.28405501 11.7798672 TACC1 1379 promoter 1072 disjoint chr3 55493384 55493746 1.30920655 0.1371347 11.764295 WNT5A 2624 inside intron 383 disjoint chr2 151825427 151825960 0.29787525 1.16237543 11.7536534 C2orf38 662 inside intron 169 disjoint chrl 20682378 20682894 1.53995699 0.41331648 11.7501355 CAMK2N1 2420 overlaps exon 155 disjoint upstream
chrll 7230822 7231223 1.01295717 -0.07891836 11.7446629 SYT9 1066 inside intron -11 disjoint chrl 6 71654712 71655274 0.9935094 0.21870991 11.744265 ATBF1 14938 upstream -96 disjoint chr6 24512676 24513041 1.52213034 0.26582346 11.7414747 MRS2L 1545 inside intron -1011 disjoint chr5 122449676 122450107 1.18345786 0.14911913 11.7159406 PPIC 49353 upstream 2129 disjoint chr5 77181413 77181882 1.4502124 0.38568228 11.7098314 TBCA 73473 upstream 872 disjoint chrl 7 44062558 44063061 0.4059112 1.2010684 11.7085174 H0XB9 3725 upstream 2750 disjoint chr3 65317662 65318201 0.43332629 1.17427563 11.7047431 MAGI1 681347 overlaps exon 0 overlap upstream
chr4 111757920 111758340 1.19389634 0.06590613 11.6987377 PITX2 5362 overlaps 3' 337 disjoint chrl 119343138 119343605 0.87842281 0.01680173 11.6930817 TBX15 9437 upstream 974 disjoint chrl l 2200288 2200827 -0.11326274 0.70038471 11.6703394 ASCL2 47930 downstream 45853 disjoint chrl6 85156171 85156746 0.94952186 0.24650656 11.6682978 F0XC2 1696 promoter 110 disjoint chr20 56858117 56858735 1.16642151 -0.05739069 11.666732 GNAS 9928 inside intron 1389 disjoint chr2 70987642 70988132 1.51138913 0.53985383 11.6584236 VAX2 6415 inside intron 0 overlap chr3 140137166 140137597 1.41269685 0.49119316 11.6410725 F0XL2 10893 downstream 0 overlap chrl 231817533 231817973 1.52628853 0.48025316 11.6371044 KCN 1 1161 inside intron -596 disjoint chrl7 45629132 45629566 0.21888233 1.2012578 11.6326856 C0L1A1 4432 covers exon(s) 2310 disjoint chr7 142817271 142817885 1.12130972 0.3887321 11.6296046 EPHA1 1165 promoter -27980 disjoint chrl2 124239385 124239783 0.96549795 -0.10566052 11.6205293 AACS 123508 downstream -1320 disjoint chrlO 73705129 73705644 0.31164577 1.16136447 11.6198462 DDIT4 1447 inside exon -425 disjoint chrl9 47129200 47129776 -0.11486878 0.92018972 11.6165419 RABAC1 25534 downstream 0 overlap chrl 5 35176138 35176683 0.69881164 -0.19434368 11.6147506 MEIS2 1111 inside intron 784 disjoint chrlO 7495400 7495924 0.53552642 -0.26159984 11.6080609 SFMBT2 1945 promoter -55 disjoint chr20 23348291 23348722 0.02544835 0.94914127 11.607985 NAPB 1358 inside intron 386 disjoint chr20 17242918 17243373 0.24384497 1.2169145 11.5997383 PCSK2 87288 inside intron 752 disjoint chr22 26510755 26511310 0.14385354 1.04558875 11.5964858 MN1 16175 inside intron 11483 disjoint chrl 7 696972 697511 0.34721737 1.16391266 11.5925516 NX 132248 inside intron -5315 disjoint chr8 110724889 110725584 -0.09498457 0.80853874 11.586734 FLJ20366 0 overlaps 5' 387 disjoint chrl 5 38360046 38360444 1.33923903 0.22592922 11.5685399 PA 6 40679 downstream 0 overlap chrl 8 42749495 42750188 0.96857799 0.12877913 11.5677241 PIAS2 1275 inside intron 720 disjoint chrl 6 7077015 7077449 0.19604037 1.29131027 11.5607717 A2BP1 1067883 inside intron 216885 disjoint chr8 97727508 97728011 -0.01338633 0.84686582 11.5593745 PGCP 834 inside intron -389 disjoint chr3 162304876 162305241 0.0303874 1.27645553 11.5580089 B3GALNT1 135 overlaps exon 0 overlap upstream
chr6 158163069 158163500 -0.20593181 0.81948214 11.5458344 SNX9 781 promoter 89 disjoint chrl 7 38795821 38796360 2.56507887 1.79574231 11.5400484 ARL4D 35518 upstream -1621 disjoint chr4 124646418 124646840 1.41588929 0.27215501 11.5389792 SPRY1 106286 downstream 0 overlap chrl 149779875 149780342 0.9868767 0.03791693 11.535486 TUFT1 471 inside intron -52 disjoint chrX 39832369 39832944 0.72881808 -0.22099868 11.5349454 BCOR 8655 inside intron 1372 disjoint chrl 8 5184965 5185401 -0.258223 0.68542722 11.5215647 ZFP161 97911 downstream 842 disjoint chrl 6 8962968 8963402 1.66519716 0.65791399 11.5156499 USP7 1439 inside intron 471 disjoint chrX 24947892 24948470 0.80650145 0.03220486 11.4988023 ARX 4118 upstream 341 disjoint chrl 8 8790289 8790687 0.04075667 1.0850363 11.487076 KIAA0802 82921 inside intron -14645 disjoint chrl 7 63963429 63964242 -0.40841363 0.30609163 11.4825154 WIPI1 967 inside intron 702 disjoint chr6 10526788 10527156 1.27274901 0.15417826 11.4778152 TFAP2A 626 inside intron 229 disjoint chr5 177947876 177948349 0.3480082 1.22951713 11.465052 COL23A1 1812 inside intron 815 disjoint chr4 159310287 159310703 0.13277675 1.27908584 11.4630909 C4orfl8 2289 inside intron 40255 disjoint chrl 90968006 90968440 0.98457613 0.01855502 11.4552436 BARHL2 12625 upstream -2614 disjoint chr8 1032998 1033567 0.37886676 1.18066646 11.4517923 ERICH1 361773 upstream 2399 disjoint chr2 37403852 37404410 -0.32991235 0.49209651 11.4413237 PRKD3 6127 upstream 444 disjoint chr3 196643341 196643815 -0.02946281 0.9334765 11.4409344 CENTB2 1225 inside intron 362 disjoint chrl l 97122493 97123023 0.16479758 1.05444986 11.438862 CNTN5 1274057 upstream 1273730 disjoint chr5 174085329 174085991 1.22533798 0.4134973 11.438809 MSX2 1149 inside intron -359 disjoint chr5 92963404 92963946 0.86569936 0.06987697 11.4302396 NR2F1 18606 downstream 1605 disjoint chrl 148246943 148247343 1.19398301 0.15817805 11.4266316 OTUD7B 1966 inside intron 1434 disjoint chrl l 2797244 2797819 -0.58950587 0.18056702 11.4247668 KCNQ1 357985 inside intron -11784 disjoint chrl 47670715 47671254 1.23328792 0.48500374 11.4236167 FOXD2 3021 upstream 458 disjoint chrl 99241835 99242236 1.24296828 0.33167337 11.4219454 PAP2D 800 inside intron 284 disjoint chr5 2292412 2292810 0.16010113 1.27241347 11.4209976 IRX4 356533 upstream -58945 disjoint chrl 202922432 202923164 0.31005292 0.98996856 11.4115766 LRRN5 1213 promoter -924 disjoint chr4 174658869 174659132 2.04942058 0.41921176 11.4114617 HAND2 28820 downstream 0 overlap chr3 171559303 171559775 0.85334915 -0.33520549 11.4098509 S IL 1094 inside intron -542 disjoint chr2 28827146 28827652 0.1316954 0.97331888 11.4089175 PPP1CB 465 promoter 64 disjoint chrl 67922539 67923049 -0.06223813 0.90710161 11.4076973 GADD45A 421 promoter 452 disjoint chr2 66660724 66661240 1.03684729 0.19225954 11.4055249 MEIS1 144689 downstream 832 disjoint chr3 132093861 132094365 0.13946883 1.12474322 11.4046142 ATP2C1 1758 promoter 607 disjoint chrl 3 44050534 44050956 0.63291734 -0.42915413 11.3980257 TSC22D1 1834 promoter -246 disjoint chr3 148622342 148622677 1.23640722 0.02781989 11.3944224 ZIC1 12472 downstream -91 disjoint chrl 8 72927232 72927735 0.20031223 0.97317285 11.3903041 MBP 46026 inside intron 397 disjoint chrl 2 2671430 2671797 1.910646 0.7694638 11.3852449 CACNA1C 638706 inside exon -107 disjoint chr7 100271682 100272050 1.31123142 0.17300104 11.3823038 EPHB4 8604 upstream 868 disjoint chrl 8 44736097 44736567 -0.05940572 0.8254745 11.3818598 SMAD7 5019 upstream -2735 disjoint chr 113856359 113857294 3.45890463 2.34112001 11.368279 RASA3 58902 inside intron 0 cover chr9 21985928 21986365 1.26460357 0.23884584 11.364968 CDKN2A 1439 promoter -18 disjoint chr6 106548108 106548545 0.6292132 -0.48740613 11.3630366 PRDM1 92342 upstream 134 disjoint chrl3 112048821 112049255 -0.14795451 0.77469936 11.3608433 C13orf28 29414 upstream -2546 disjoint chr4 111756007 111756405 1.20833043 0.19653537 11.3505805 PITX2 7297 downstream 2272 disjoint chr6 10493381 10493916 1.00234549 0.09411868 11.3442592 TFAP2A 26676 downstream 0 overlap chr3 129928575 129929232 -0.2312093 0.9732086 11.3398892 RAB7 907 inside intron -238 disjoint chrl l 64859242 64859685 0.38733975 1.30503423 11.3396033 DPF2 1321 inside intron -823 disjoint chrl2 127864985 127865675 2.2641565 1.47244856 11.3366983 SLC15A4 8818 covers exon(s) 8225 disjoint chrlS 35175031 35175360 1.14075213 -0.01392085 11.3341524 MEIS2 2434 covers exon(s) -125 disjoint chr6 89913593 89914072 1.43599335 0.35934778 11.3167053 ACY1L2 1106 inside intron -336 disjoint chrl9 35632306 35632713 -0.50330708 0.59454978 11.3155842 ZNF536 77139 inside intron 980 disjoint chr4 111752844 111753209 1.73185244 0.60027097 11.3121745 ΡΓΓΧ2 10493 downstream -4 disjoint chrl4 70179453 70179923 1.04803824 0.15256812 11.3089545 ED6 42317 upstream -368 disjoint chrl3 99342529 99342994 1.68273845 0.68915218 11.3023475 CLYBL 285593 overlaps 3' 2179 disjoint chrl3 113620683 113621246 2.94487099 2.12839053 11.3013498 FAM70B 30626 inside intron -4569 disjoint chrl 6 66828058 66828489 1.09483794 0.14499805 11.2953232 RBM35B 422 promoter 0 inside chr6 99401925 99402359 1.40978163 0.50186058 11.2946481 POU3F2 12625 downstream 103 disjoint chr9 100508528 100509031 0.07866008 0.83498327 11.293314 GABBR2 2268 inside intron 369 disjoint chrl l 2196311 2197045 -0.03994823 0.80649523 11.2920245 TH 46701 upstream 49635 disjoint chr7 136051526 136051960 0.04557376 1.00549261 11.2892904 CHRM2 151978 upstream 152434 disjoint chrl3 99345098 99345553 1.10077918 0.06980302 11.2880441 CLYBL 288162 inside intron 0 cover chrlO 32255589 32256119 -0.13080079 0.71323561 11.2856296 ARHGAP12 1656 inside intron 788 disjoint chrl4 68795320 68795991 1.60932469 0.54783862 11.2773332 GALNTL1 676 promoter 12 disjoint chrl l 2197745 2198218 -0.19363174 0.77608981 11.2765893 ASCL2 50539 downstream 48462 disjoint ehr2 81281355 81281847 0.12614626 0.95602032 11.2746669 CTNTMA2 1687722 downstream -5312 disjoint chr9 116414270 116414707 0.03028556 0.97795757 11.2723788 C9orf91 810 inside intron -373 disjoint chrl5 87740929 87741399 0.81829712 -0.07111565 11.2715047 POLG 61900 upstream 2197 disjoint chr6 83128848 83129280 -0.2425073 0.7572414 11.2682688 TPBG 977 promoter 855 disjoint chr2 176697193 176697537 1.65402403 0.41542406 11.2627084 HOXD9 1860 inside exon 46 disjoint chr9 137290261 137291118 2.52684759 1.74403119 11.252682 OLFM1 183270 downstream ' 0 overlap chrl 92268901 92269574 1.27143809 0.47595718 11.2445615 ABHD7 756 inside intron -349 disjoint chr7 69799759 69800193 0.76188734 -0.18763628 11.2441445 AUTS2 1097505 inside intron -1136 disjoint chrl3 71335666 71336244 0.66864282 -0.07427197 11.2434006 DACH1 3086 inside intron 1119 disjoint chr5 111117904 111118335 0.11145007 1.02868963 11.2390391 C5orfl3 2518 inside intron 3002 disjoint chr3 123880752 123881225 -0.25037796 0.4951602 11.2385596 PARP14 19634 upstream 1117 disjoint chr7 44111632 44112207 0.17805742 0.86087741 11.2375213 AEBP1 1148 inside intron 6545 disjoint chr6 30541269 30541826 0.2498323 1.06114051 11.2360138 HLA-E 23423 upstream 182 disjoint chrl l 2650158 2650592 -0.02778269 0.83471144 11.2344926 KCNQ1 210899 inside intron 26394 disjoint chrl3 45323845 45324348 0.12371889 0.92080097 11.2329629 LOC283514 0 overlaps 5' -137630 disjoint chrl 6290289 6291314 2.49226101 1.71892107 11.22752 AC0T7 50276 inside intron -26290 disjoint chr2 174903777 174904133 1.22582784 0.06895008 11.2199332 FLJ46347 6406 downstream -1767 disjoint chr4 54670876 54671099 1.86137165 -0.00695311 11.2099486 GSH2 9922 downstream 0 overlap chrl2 24946336 24946797 1.01050474 -0.03629343 11.2089098 BCAT1 46701 inside intron 69 disjoint chrlO 28860120 28860728 -0.02536036 0.72836964 11.2060148 WAC 977 promoter 467 disjoint chr3 169294012 169294473 0.29583934 1.19764147 11.1970052 GOLPH4 1889 inside intron 1047 disjoint chrl 220859870 220860340 2.4617919 1.60897776 11.1944127 TAFIA 29993 upstream -1164 disjoint chr5 114534627 114535062 1.36395128 0.41700183 11.1856525 TR 36 9079 overlaps 3' -130 disjoint chrl l 6298845 6299273 -0.14844357 0.96411336 11.1815277 PRKCDBP 530 promoter -360 disjoint chrl4 53482427 53482759 1.36439229 0.22372991 11.1747241 BMP4 8260 downstream 295 disjoint chr2 305076 305513 2.52665196 1.64023224 11.1725923 LOC285016 27240 upstream 0 overlap chr5 72566332 72566782 1.28399392 0.3034953 11.1622703 TMEM174 66503 downstream -600 disjoint chrlO 21503775 21504348 1.1941867 0.0956577 11.1587947 NEBL 654 promoter 0 overlap chrll 129208556 129208921 1.83816397 0.73452681 11.1555633 FZD10 4063 upstream 2359 disjoint chrl 7 37561507 37561869 1.99311963 0.72278523 11.1500273 KCNH4 24952 downstream -718 disjoint chr2 1041072 1041539 1.56743406 0.66278627 11.1486722 SNTG2 104518 inside intron 776 disjoint chr4 186173264 186173806 0.23869182 1.01362703 11.1464209 HELT 3270 upstream 430 disjoint chr3 43909185 43909657 0.15781708 1.06108376 11.1396499 ABHD5 201807 downstream 101754 disjoint chr6 15352372 15352839 0.96077565 0.01363627 11.1372487 JARID2 1666 promoter 17 disjoint chr5 153832698 153833257 0.8842727 0.15340675 11.1342146 HA D1 4759 downstream 0 overlap chr4 13156941 13157447 0.37358139 -0.39413592 11.1334487 BAPX1 1806 promoter 221 disjoint chr7 87402629 87402977 -0.48713013 0.60033771 11.1290365 ADAM22 992 inside intron -122 disjoint chr2 176672023 176672526 1.34959551 0.43314254 11.1243779 HOXD12 249 promoter 0 overlap chrl3 35440639 35441100 0.46697094 1.33769666 11.1190395 DCA KL1 162342 inside intron 161940 disjoint chr9 125811422 125811790 1.32576132 0.25701201 11.077911 LHX2 1919 promoter 0 inside chrl3 109229128 109229607 0.16895477 1.10289844 11.0759954 IRS2 7307 inside intron 2860 disjoint chrl2 84197191 84197661 0.96443401 0.10898532 11.0725551 CART1 354 promoter 348 disjoint chrl l 101423720 101424121 -0.05336475 0.9295106 11.0578984 Cllorf70 312 overlaps exon -17 disjoint downstream
chrl 7 68096147 68096683 0.19718237 0.98675079 11.054281 SLC39A11 503743 downstream 2683 disjoint chr6 139392651 139393541 1.37261383 0.44220164 1 1.0472698 REPS1 41561 upstream -218 disjoint chr3 157753814 157754296 0.12616299 1.00158693 11.0447149 SSR3 1332 covers exon(s) 1031 disjoint chrl5 39700016 39700417 -0.32667353 0.75361865 11.0438244 TYR03 61493 downstream 208 disjoint chr22 17020091 17020489 2.4166477 1.4356583 11.0348762 USP18 7334 overlaps exon -7093 disjoint upstream
chr9 76305586 76306126 0.72579163 -0.10460337 11.0305174 RO B 3515 inside intron -1839 disjoint chrl 7 67623025 67623616 1.02502585 0.20738829 11.0251212 SOX9 5139 upstream 0 overlap chrX 136474847 136475400 1.17127285 0.07339791 11.0198597 ZIC3 611 promoter 0 overlap chrX 102489173 102489608 0.97582405 -0.01364143 11.0152644 WBP5 8427 upstream 28369 disjoint chr2 171385173 171385930 1.03045756 0.35936051 11.0138522 GADl 3728 inside intron 0 overlap chr3 185805542 185806029 1.43642482 0.50212969 11.0095501 EPHB3 43262 downstream -574 disjoint chr2 175058791 175059156 -0.00144042 1.21372897 11.005391 GPR155 900 inside intron 454 disjoint chrl7 61727964 61728395 1.32312553 0.32930288 11.0031808 P CA 992 promoter 114 disjoint chrl9 16049988 16050530 0.09496662 0.82723159 11.0028992 TP 4 1664 inside intron -713 disjoint chrl2 64869713 64870149 0.01290724 0.9573754 11.0023674 IRAK3 430 inside intron -101 disjoint chrl l 2742340 2742849 -0.28997805 0.49789827 10.9994317 KCNQ1 303081 inside intron 26142 disjoint chrlO 76836565 76837035 1.21149382 0.46259455 10.9970037 ZNF503 5135 upstream 0 inside chr3 33235959 33236354 1.75430982 0.67358967 10.9948795 FBXL2 57583 upstream -192 disjoint chr8 6411587 6412330 2.56237552 1.7211788 10.9908871 MCPH1 135108 inside intron 0 cover chr5 94980251 94980688 1.8675215 0.93327414 10.9902765 GPR150 1047 promoter 698 disjoint chrB 45683296 45683769 -0.06484164 0.75078865 10.9892667 LOC220416 314 promoter -158276 disjoint chrl3 30673288 30673653 -0.18320365 0.85607597 10.9794017 B3GALTL 1157 inside intron -254 disjoint chr5 76974164 76974703 0.67199778 -0.11905665 10.9781122 OTP 3887 upstream -1424 disjoint chrl 46539276 46539707 -0.01991979 0.8658461 10.9761791 LRRC41 1917 inside intron 305 disjoint chr3 180652882 180653413 0.1 1056391 0.82939587 10.9648644 GNB4 818 promoter -598 disjoint chrl 238842426 238842907 0.01215114 0.97817344 10.9565707 GREM2 342 promoter -119083 disjoint chr9 78824299 78824703 1.05101829 -0.04878127 10.9448044 FOXB2 0 overlaps 5' 0 inside chrl 2 116888258 116888948 0.00496365 0.8721665 10.9400733 RFC5 49944 upstream 2025 disjoint chrl 219116608 219116973 1.19001553 0.10997054 10.9399042 HLX1 2408 promoter 98 disjoint chr5 908281 909123 2.7165341 1.9127995 10.9381044 ZDHHC11 4181 upstream -6511 disjoint chr22 29147679 29148209 0.11297733 1.20573035 10.930992 SEC14L2 24747 inside intron 1190 disjoint chrl 6229994 6230429 0.28467689 1.12978852 10.9249479 GPR153 13192 downstream -944 disjoint chrl6 2997995 2998393 0.86735544 -0.11303019 10.9235287 CLDN9 3813 upstream -3679 disjoint chr5 140199856 140200272 -0.05391144 0.93099283 10.9180747 PCDHA7 5704 inside intron 919 disjoint chrl l 128062763 128063209 1.19772091 0.38702197 10.9144796 FLU 5989 upstream 2104 disjoint chr3 24538947 24539345 1.45537944 0.46111582 10.9096866 THRB 27631 upstream -367 disjoint chrl 7 60984043 60984498 -0.21445631 0.80992079 10.9088536 AXIN2 3728 overlaps exon 1866 disjoint downstream
chr20 55271171 55271722 1.03787897 0.37135108 10.9080068 BMP7 2985 inside intron 972 disjoint chr7 56141094 56141420 -0.34870077 0.92816033 10.906647 CHCHD2 260 inside intron 0 overlap chrl 7 41214998 41215399 0.09873197 1.0752817 10.8924431 CRHR1 2049 promoter 1048 disjoint chrl2 26157097 26157579 0.98283759 -0.20596333 10.8905497 BHLHB3 11533 downstream 746 disjoint chrX 119014627 119015199 -0.47682618 0.24357145 10.8805575 NKAP 52865 upstream 2680 disjoint chr4 36924025 36924570 0.27188648 1.08052563 10.8630867 C4orfl9 337679 upstream -651 disjoint chrl 2 113360936 113361578 0.7706759 -0.10525403 10.8624399 TBX5 30307 upstream 948 disjoint chr5 133736159 133736680 -0.08713242 0.72035053 10.8574599 UBE2B 1391 inside intron -368 disjoint chrl 2 106677497 106678003 -0.03508871 0.80980867 10.8525319 PRDM4 1040 inside intron 521 disjoint chr7 100397492 100397927 0.04328804 0.9463404 10.8406724 MUC17 52156 upstream -979 disjoint chr7 139987811 139988248 1.76098675 0.72975077 10.8392309 DENND2A 767 promoter -206 disjoint chrl 6 55525219 55525698 -0.03629934 0.87377455 10.8375791 HERPUD1 1971 inside intron -1242 disjoint chrl 6 6011909 6012383 -0.05293258 0.87043899 10.8354609 A2BP1 2777 inside intron -1507 disjoint chr2 176698852 176699280 1.06235719 0.12732481 10.827772 HOXD9 3519 downstream -1019 disjoint chr8 77747698 77748133 1.1005683 0.17691481 10.8271443 ZFHX4 30701 upstream 4589 disjoint chrl9 16298196 16298531 1.06149275 -0.08485005 10.8253494 LF2 1546 inside intron 0 inside chrl 7 14142703 14143137 0.59654095 -0.36785929 10.8246081 HS3ST3B1 2093 promoter 0 overlap chrl 47672848 47673316 1.54661892 0.32070687 10.8091143 FOXD2 959 promoter 0 overlap chrX 35554044 35554409 2.68609765 1.60531548 10.8078217 CXorf22 293369 upstream 0 overlap chr2 172660446 172660808 1.08187608 0.03322204 10.8038952 DLX1 1993 inside intron -41 disjoint chr2 10181223 10182034 0.32770902 1.15030251 10.7880174 RRM2 1038 covers exon(s) -291 disjoint chrl 9 48809384 48809959 3.05114482 2.17660868 10.7878647 ZNF428 5886 inside intron 5366 disjoint chrl3 43614940 43615453 -0.13557576 0.9007033 10.7841539 C13or£21 230524 upstream -698 disjoint chr3 109293787 109294236 2.35037057 1.43744663 10.7795487 CD47 1163 promoter -557 disjoint chr7 157065146 157065753 0.20448766 0.98210648 10.7693305 PTPRN2 .1007425 inside intron -2991 disjoint chr6 11381707 11382216 2.3503773 1.58109409 10.7679858 NEDD9 40824 upstream -179054 disjoint chr2 241858990 241859430 0.33387291 1.30023725 10.7649939 HDLBP 1493 inside intron 532 disjoint chrl 50663979 50664446 0.81763193 0.03755417 10.7465477 FAF1 534077 downstream 0 overlap chrl9 63766801 63767165 0.01756971 1.16052763 10.7316966 MZF1 9588 inside intron -234 disjoint chr6 167232262 167232777 2.91949845 2.16743256 10.728328 RNASET2 57289 downstream 0 inside chrl 204748387 204748809 0.10748486 1.08277131 10.7281509 RASSF5 886 inside intron -320 disjoint chrl l 61198697 61199253 -0.10083193 0.79294235 10.7252913 Cllorfl l 5232 upstream 4922 disjoint chrl 216164502 216164837 -0.29424522 0.86103112 10.7111021 SPATA17 293185 downstream 97 disjoint chr5 76967601 76968035 0.82051991 -0.09033672 10.7080681 OTP 2242 inside intron 38 disjoint chrl2 120728532 120728963 0.19194299 1.06964538 10.7077443 RHOF 12556 upstream -759 disjoint chrS 469944 470654 2.75894119 1.94963754 10.7016844 AHR 112654 inside intron 3570 disjoint chrl 2 64420844 64421140 1.40194684 0.14677863 10.698797 H GA2 83366 upstream 247 disjoint chr5 131158851 131159288 0.19935681 1.1396706 10.6922981 FNIPl 1319 inside intron 540 disjoint chrl 6 49744784 49745188 0.90954571 -0.19841917 10.6880947 SALL1 2132 promoter 0 inside chr7 123458332 123458697 -0.04628223 0.98570093 10.686819 SPAM1 105768 downstream 602 disjoint chr8 67505252 67506162 0.66448673 -0.05364035 10.6855632 RRS1 1436 overlaps 3' -587 disjoint chr6 27769990 27770529 0.73166283 0.01967772 10.6836252 HIST1H2BL 113158 downstream -6304 disjoint chr6 49537734 49538276 -0.01143139 0.71530081 10.6833704 MUT 534 inside intron 617 disjoint chr8 2405276 2405968 0.06185081 0.89019978 10.6801122 YOM2 424622 downstream 374 disjoint chr8 1 1604591 11605061 0.96012402 0.12742376 10.6782763 GATA4 5430 inside intron 0 overlap chrl 8 11899190 11899615 -0.50968238 0.55876226 10.6711084 MPPE1 550 promoter -108 disjoint chr2 119327413 119327781 1.36153006 0.31032897 10.6612957 EN1 5185 upstream 0 overlap chrl l 129446506 129446976 -0.08359444 0.78356335 10.6515058 APLP2 1496 inside intron -498 disjoint chr22 36531591 36531956 0.13989017 1.20836431 10.6514315 H1F0 532 inside exon 0 overlap chrl l 61199482 61199919 0.50242235 1.40049427 10.6514078 Cl lorfl l 4566 upstream 4256 disjoint chrl2 113608115 113608412 1.49623855 0.16498364 10.6500393 TBX3 1764 promoter 700 disjoint chr6 10529699 10530290 1.35699887 0.15478891 10.6499196 TFAP2A 1917 promoter 0 overlap chrlO 65627570 65627941 0.17871104 1.30538895 10.6494909 REEP3 676442 downstream -26674 disjoint chr6 167235322 167235885 2.77478925 2.07811944 10.6482663 RNASET2 54181 downstream 0 inside chr8 79878487 79878953 -0.23362482 0.60024295 10.6352697 IL7 1359 inside intron 283 disjoint chrl 7 28279615 28280516 -0.67679039 0.13023489 10.6339186 TMEM98 575 inside intron -110 disjoint chr2 172682422 172683046 1.1761885 0.31761993 10.6297776 DLX2 6699 upstream -934 disjoint chr7 96488760 96489086 1.49437636 0.35007757 10.6231683 DLX5 2992 inside intron 0 inside chr4 120351829 120352312 1.66500386 0.62588013 10.6191533 MYOZ2 75361 downstream 700 disjoint chr8 103204213 103204647 0.09904621 0.94395347 10.6176199 NCALD 1090 inside intron 443 disjoint chrl 8010745 8011113 -0.04787245 0.9864084 10.6159267 ERRFIl 1803 promoter -1304 disjoint chr22 44848396 44848827 0.4303134 1.3712114 10.6151239 FLJ27365 11719 upstream -1204 disjoint chr20 9766334 9766774 -0.16606912 0.78265865 10.6141116 PAK7 747 inside intron 497 disjoint chr21 42107141 42108745 2.92123595 2.14624627 10.6138389 PRDM15 63914 inside intron 349 disjoint chrl 35815937 35816401 1.17101375 0.16232775 10.6117989 TFAP2E 4380 inside intron 0 overlap chr4 110869064 110869462 1.66014002 0.73048376 10.6087661 PLA2G12A 1197 inside intron 688 disjoint chr4 75184194 75184639 -0.08123412 0.99992701 10.6078906 CXCL2 419 promoter -51 disjoint chrl4 81068568 81069081 -0.41006372 0.51777833 10.6032868 SEL1L 804 inside intron 423 disjoint chr6 8379416 8379748 -0.34509114 0.78638905 10.601663 SLC35B3 875 covers exon(s) 565 disjoint chrl7 46597874 46598338 1.11969174 0.25185787 10.5998811 NME2 0 overlaps 5' 281 disjoint chr21 46626295 46627398 3.42586889 2.4075511 10.5944392 PCNT 57813 inside intron 0 overlap chrl 87574858 87575226 0.42232434 1.44782722 10.5866823 LM04 8120 inside intron -1018 disjoint chr7 20784720 20785539 1.16466738 0.34302616 10.5866769 SP8 7490 downstream 0 overlap chrl9 51076617 51077120 1.29410944 0.4314546 10.5843749 IRF2BP1 4095 downstream 747 disjoint chrl 2 6531345 6531710 0.06201827 1.15883384 10.5794896 HOM-TES- 3779 inside intron 2976 disjoint
103
chrl 117466611 117466976 2.32657686 1.22122232 10.5727822 TR1M45 678 promoter 0 overlap chr3 189353072 189353404 1.93368189 0.75329897 10.5722226 LPP 60010 upstream 765 disjoint chr6 160101820 160102320 0.16382924 0.80023685 10.571135 ACAT2 754 promoter 99 disjoint chrX 39833277 39833912 0.79711149 -0.1832463 10.5709345 BCOR 7687 inside intron 404 disjoint chr8 42867604 42868230 0.47008376 1.2423507 10.5698677 RNF170 2708 inside intron 2139 disjoint chrl4 74965715 74966149 0.06212111 0.99177852 10.5655922 JDP2 2440 promoter -493 disjoint chr9 126061179 126061619 -0.15068447 0.76218268 10.5391625 NEK6 1110 inside intron -617 disjoint chrl5 57519073 57519510 2.79182832 1.94265342 10.5385014 FAM81A 1410 inside intron -1043 disjoint chr9 139116223 139117248 3.34124812 2.46233927 10.5340434 MAN1B1 15024 inside intron 419 disjoint chrl4 68799250 68800012 0.33651435 1.07088216 10.5245431 GALNTL1 2583 inside intron -1104 disjoint chr2 29994974 29995609 -0.12472471 0.53446931 10.5189468 ALK 2326 inside intron 726 disjoint chr4 36900406 36900738 0.02287703 1.08075909 10.5155522 C4orfl9 361511 upstream 20907 disjoint chr6 42640851 42641246 -0.5432982 0.4256095 10.5148323 UBR2 816 inside intron -581 disjoint chr6 109884443 109885083 0.032929 1.15505026 10.5027279 MICALl 561 promoter -105 disjoint chr6 131499094 131499711 -0.02574566 0.81618759 10.4941254 AKAP7 8442 upstream -244 disjoint chrl 2 113321781 113322252 0.85264422 0.05714293 10.4905871 TBX5 3833 overlaps exon 443 disjoint upstream
chr5 1315294 1315665 0.06345876 1.19827158 10.4878104 TERT 32496 inside intron -5072 disjoint chr5 92954473 92954808 1.35686486 0.17614114 10.4809732 NR2F1 9675 inside intron 216 disjoint chrl 4 72773466 72773795 1.0224913 -0.15737018 10.4752212 PAPLN 212 promoter 12 disjoint chr7 25865300 25865761 1.34340324 0.42822269 10.4737124 NFE2L3 292623 upstream -4 disjoint chr7 148474894 148475256 1.04499332 0.03914685 10.464425 ZNF398 20454 inside intron 0 overlap chrl 2 113363807 113364387 1.50603593 0.50793875 10.4600481 TBX5 33178 upstream -269 disjoint chr22 17797744 17798145 -0.09015066 0.84224177 10.4580212 HIRA 1073 inside intron 600 disjoint chrl l 10784882 10785425 0.12826944 1.08904851 10.4559092 EIF4G2 1732 covers exon(s) 512 disjoint chrlS 78776243 78776647 2.25254007 1.27387147 10.4515817 KIAA1199 82119 upstream -524 disjoint chr2 222870771 222871211 1.23118748 0.13366675 10.4502617 PAX3 732 inside intron 0 overlap chrl 8 28305471 28306073 1.29665062 0.28272594 10.4490618 FAM59A 1027 promoter -128 disjoint chrl 2 84195829 84196296 1.13631993 0.3610481 10.4454557 CART1 1719 promoter 1713 disjoint chrl4 20561693 20562130 1.33522075 0.48053872 10.4442634 DRG2 973 inside intron 445 disjoint chr3 185500586 185501071 0.58690847 1.34205405 10.4433613 PSMD2 871 covers exon(s) -479 disjoint chr6 138468351 138468686 1.75109327 0.54249199 10.437986 PERP 1593 inside intron 1195 disjoint chrl7 24014197 24014670 -0.43814472 0.5045301 10.4355502 SUPT6H 769 inside intron -679 disjoint chrlO 45193425 45194063 0.18741823 0.93036138 10.4258248 ALOX5 3791 inside intron -3263 disjoint chr7 89678196 89678630 1.02490454 0.08860828 10.4206194 STEAP2 305 promoter 119 disjoint chrl l 62406443 62406991 0.00300633 1.29620859 10.4204804 SLC3A2 1581 overlaps exon -706 disjoint upstream
chrl l 85454923 85455324 -0.40285751 0.52975688 10.4166191 PICALM 2431 inside intron 2049 disjoint chr21 27257505 27257964 -0.28193704 0.8445655 10.4147702 ADAMTS5 2738 inside intron 1763 disjoint chr9 95367230 95367727 0.23704279 1.15366274 10.413282 FAM120A 113237 inside exon 860 disjoint chr6 41578972 41579386 0.81357033 -0.02010379 10.4118386 FOXP4 42755 upstream 1408 disjoint chr6 36672395 36672820 -0.1066266 1.08242581 10.411827 SFRS3 2252 covers exon(s) -2005 disjoint chr8 28328765 28329028 -0.0870391 1.39784853 10.3942134 FBX016 74674 downstream -2856 disjoint chrlO 101283794 101284288 1.46690125 0.65184035 10.3860649 N X2-3 1095 inside intron 145 disjoint chrl2 122413621 122414163 0.0886482 0.83614463 10.3837059 SBN01 12681 upstream 407 disjoint chrl6 55260117 55260687 1.34067917 0.30103259 10.3810001 MT1H 587 promoter 201 disjoint chr7 27152662 27153150 1.39651664 0.58016366 10.3781938 HOXA6 742 inside intron 302 disjoint chr5 155086101 155086534 -0.06458171 0.81265512 10.3779574 SGCD 599810 upstream 1163 disjoint chr22 24007196 24007801 -0.2690961 0.58815678 10.3707818 LOC91353 36086 upstream 775 disjoint chr3 89238613 89238975 1.80834722 0.80917985 10.3563463 EPHA3 388 promoter 7347 disjoint chrl5 72251806 72252205 0.36175754 1.34010201 10.3490837 ISLR 934 promoter 2461 disjoint chrlO 94809396 94809800 1.51496582 0.58632663 10.3417633 EXOC6 211175 downstream 216 disjoint chr7 100401677 100402078 0.32038067 1.24979574 10.3417481 MUC17 48005 upstream -5164 disjoint chr3 148604713 148605150 1.1567849 0.28809915 10.341199 ZIC4 1946 inside intron 4525 disjoint chrl4 60173085 60173785 1.13365849 0.36755521 10.3408248 SKI 12147 downstream 0 overlap chrlO 25282566 25282892 -0.00729102 1.19979088 10.3356609 PRTFDC1 1028 promoter -660 disjoint chr2 176735472 176735803 1.53277275 0.46877176 10.3331655 HOXD3 1247 promoter 60 disjoint chr9 107360882 107361480 2.47648572 1.62558876 10.3326368 FCMD 638 inside intron -421 disjoint chr8 76367304 76367636 -0.16667281 1.02477888 10.3263039 HNF4G 247121 upstream 114369 disjoint chr9 85786583 85787068 1.32809505 0.48524444 10.3195754 RMI1 1051 inside intron -621 disjoint chrl2 47650559 47651056 0.76979611 -0.0576195 10.3184855 WNT10B 753 overlaps exon 0 overlap upstream
chr3 73916837 73917235 0.34849866 1.33777283 10.3173049 PDZRN3 160076 upstream -159775 disjoint chrl 219116260 219116520 1.54853984 0.0757792 10.3093245 HLX1 2861 upstream 551 disjoint chr3 87183887 87184408 2.64787309 1.69430557 10.3045226 VGLL3 60941 upstream 46 disjoint chrl 9 47123216 47123650 0.56700767 -0.31038534 10.2980008 ARHGEF1 42931 downstream 106 disjoint chr7 127081147 127081512 1.91934973 0.96169736 10.2972815 SND1 1710 inside intron -1360 disjoint chr2 120822209 120822631 1.18185664 0.13640296 10.292443 INHBB 2741 inside intron 785 disjoint chr7 69699360 69699695 1.41562202 0.24994331 10.2912267 AUTS2 997106 inside intron 0 overlap chr7 154422262 154422663 2.73384083 1.80749816 10.2850229 PAXEP1 2951 inside intron 2287 disjoint chr3 135610027 135610556 1.49078715 0.67662911 10.2819779 AMOTL2 33932 upstream -1469 disjoint chrlO 38187253 38187642 -0.15592114 0.83607321 10.2784296 ZNF248 762 promoter -143 disjoint chr2 170393445 170393930 -0.17816856 0.68366136 10.2748848 METTL5 3847 upstream -570 disjoint chr7 157162835 157163267 0.48607601 1.31200005 10.2690477 PTPRN2 909911 inside intron 6380 disjoint chrl 3 22309771 22310292 -0.08924871 0.87514561 10.2632684 SGCG 342798 upstream 0 overlap chr21 36988933 36989298 0.6805974 -0.34564047 10.2614354 SIM2 4562 upstream 765 disjoint chr5 174093240 174093575 1.16381102 0.08792825 10.2511503 MSX2 9060 downstream -905 disjoint chr2 183290201 183290647 -0.05250408 0.75768665 10.2506851 DNAJC10 958 inside intron -754 disjoint chrl6 1953676 1954092 0.98996575 0.10078904 10.2480982 RPS2 735 inside intron 73 disjoint chrl 7 63800424 63801519 1.09667094 0.24198559 10.2476517 SLC16A6 1425 promoter -297 disjoint chr8 72632631 72633071 0.88691877 -0.01809861 10.2441951 EYA1 195611 upstream -516 disjoint chrl5 61754054 61754521 2.61010767 1.84758338 10.2439771 HERC1 158618 overlaps exon -73090 disjoint upstream
chr4 111749994 111750464 1.62826459 0.96932562 10.2340817 PITX2 13238 downstream 1632 disjoint chr6 27756710 27757751 1.34481056 0.49395207 10.2300776 HIST1H2BL 125936 downstream -726 disjoint chrl 6 86639490 86640011 3.04503424 2.20634644 10.2249447 BA P 96952 inside intron 18963 disjoint chr4 38848471 38849061 2.79380021 1.83105802 10.2222265 WDR19 11357 upstream 0 cover chrl l 6905172 6905642 0.25343304 1.01679129 10.2170696 ZNF215 943 covers exon(s) -384 disjoint chrl 7 53437779 53438216 0.10205333 1.003107 10.2147577 SFRS1 1370 overlaps two 533 disjoint exons
chrl 2 70121556 70122098 0.10724426 0.79213639 10.2135731 LGR5 1477 inside intron -900 disjoint chr2 144807731 144808096 1.47855782 0.46355056 10.2126472 GTDC1 1233 promoter -864 disjoint chrlO 134388042 134388491 2.67713318 1.67824327 10.2016004 INPP5A 186700 inside intron 1316 disjoint chr5 151765213 151765608 0.52900023 1.41472367 10.1997065 NMUR2 197 promoter -480196 disjoint chrl3 32060799 32061194 -0.11708394 0.80996368 10.1975238 APRIN 2176 inside intron -964 disjoint chr2 174904668 174905162 0.85683204 0.09466623 10.1974261 FLJ46347 5377 downstream 2547 disjoint chrl2 63957917 63958348 0.97389997 0.0384547 10.1965643 MSRB3 406 promoter 310 disjoint chi9 70511650 70511976 -0.4799844 0.62426523 10.1856156 PIP5K1B 1215 inside intron -893 disjoint chrl 39646066 39646434 1.20199228 0.20481964 10.1852533 MACF1 76670 inside intron 171 disjoint chrlO 124756501 124756932 -0.20595549 0.70057396 10.1823333 D ZF5 1371 covers exon(s) 816 disjoint chrl 7 71646816 71647283 0.98162664 0.27594251 10.1803288 FOXJl 877 inside intron 234 disjoint chrl 179339723 179340193 1.35875876 0.61132435 10.1761558 IER5 15463 downstream 347 disjoint chr4 122942411 122942740 -0.39674351 0.6808623 10.1730931 EXOSC9 490 covers exon(s) -203 disjoint chrl l 59082053 59082418 0.87679083 -0.2374464 10.1724556 OSBP 57774 downstream 2295 disjoint chr3 15441419 15441751 -0.27959612 0.85035132 10.1695269 METTL6 2263 covers exon(s) 2185 disjoint chrl 8 55039862 55040296 1.19906308 0.25993555 10.1678953 GRP 1483 inside intron -1217 disjoint chrl4 52687631 52687963 -0.21213059 0.87334792 10.1602508 DDHD1 1786 inside intron 652 disjoint chrl4 100263839 100264306 0.54294082 1.25428927 10.1528469 DLK1 834 inside intron -587 disjoint chr6 130727749 130728114 1.4241164 0.4549441 10.1521835 IAA1913 71840 upstream 0 overlap chrl l 61105976 61106552 -0.12000628 0.71354079 10.149857 SYT7 1103 promoter -362 disjoint chrl l 62449510 62449908 1.34615952 0.32311436 10.1473217 CHRM1 3923 upstream 41 disjoint chr7 138369938 138370267 0.11710442 1.15588746 10.1472033 ZC3HAV1L 1047 overlaps exon 317 disjoint upstream
chrl6 2902926 2903396 0.52022455 1.35335458 10.1461996 FLYWCH1 946 inside intron -393 disjoint chr5 170765553 170766023 0.16191373 1.01722263 10.1418714 PM1 18151 overlaps exon 12342 disjoint upstream
chrll 44297424 44297831 1.14124604 0.04690863 10.1415306 ALX4 9133 upstream 10 disjoint chrl l 31782268 31782558 1.32688126 0.02865007 10.121135 PAX6 6875 inside intron 0 overlap chr 131350984 131351533 0.14291175 1.22866554 10.1203763 C9orf50 71342 downstream 444 disjoint chrlO 126124594 126124923 -0.0489467 1.08520816 10.1100022 LHPP 15478 upstream 876 disjoint chr8 94782864 94783334 0.33671046 1.15009697 10.0995939 RBM12B 39029 downstream -343 disjoint chr5 178918264 178918954 0.7665121 0.08006629 10.0985246 RUFY1 8088 inside intron 165 disjoint chrlS 50871464 50871869 0.92737638 0.0066449 10.0970233 ONECUT1 1964 promoter -473 disjoint chrlO 105200290 105200895 0.30630296 1.14732855 10.0959773 FAM26B 1169 overlaps exon 1045 disjoint downstream
chr2 127132367 127132630 -0.22661168 1.14302373 10.0894939 GYPC 2214 inside intron -1726 disjoint chrlO 97880957 97881391 0.92147946 -0.00629243 10.0773165 ZNF518 1496 inside intron -555 disjoint chr5 158465582 158465944 2.10798602 1.12645999 10.0745972 EBF1 6236 upstream 191 disjoint chr7 72608365 72609137 0.34913771 1.12023406 10.0738918 BCL7B 822 inside intron 326 disjoint chrl l 124176041 124176439 -0.36981301 0.53874062 10.0676292 Cl lorf61 533 promoter -312 disjoint chr7 25864291 25864755 0.74913184 -0.11231904 10.0656398 NFE2L3 293629 upstream 7 disjoint chrl 5 34967461 34967982 0.45529552 -0.32386931 10.0583351 MEIS2 209812 downstream -387 disjoint chrll 103540808 103541242 1.88114452 1.0009311 10.0563015 PDGFD 572 promoter -540 disjoint chrl 2 33481678 33482043 0.55439787 1.57094013 10.0558297 SYT10 1977 inside intron 987 disjoint chr2 96568598 96568963 1.34053201 0.3391967 10.0544923 ARID5A 2408 inside intron -1084 disjoint chr2 241368447 241368848 0.43302009 1.4124418 10.0486685 KIF1A 39448 inside intron -73 disjoint chr7 818904 819233 0.07639301 1.24613606 10.0482638 UNC84A 3544 upstream 253 disjoint chr8 133857662 133858060 -0.46983858 0.51285105 10.0441716 PHF20L1 877 inside intron -589 disjoint chrl 9 41043984 41044421 1.05380629 0.13549043 10.0416207 KIRREL2 4321 covers exon(s) 0 overlap chrlO 124904740 124905138 -0.03303127 0.96979454 10.0352069 BUB3 881 inside intron -24 disjoint chrl2 31703612 31704007 -0.31599393 0.59401519 10.0339959 MOC50559 225 inside intron -42845 disjoint chr2 176763241 176763672 1.34394497 0.47379511 10.0325707 H0XD1 1689 inside exon -645 disjoint chrl 63558079 63558447 1.22792425 0.23204335 10.031607 FOXD3 2870 upstream 0 inside chrl3 99433509 99434010 0.52410948 -0.16202088 10.0262313 ZIC2 1190 inside intron 0 overlap chrlO 134771833 134772237 -0.03404586 0.89452653 10.02058 GPR123 37411 inside intron -2868 disjoint chr20 37023055 37023755 1.21932484 0.03579891 10.0134058 DHX35 658 promoter 276 disjoint chrl 7 44150637 44151071 0.48305027 -0.41526955 10.0106061 PRAC 3809 downstream 162 disjoint chrl4 94311602 94312000 1.11769178 0.19580728 10.0089833 GSC 5351 upstream -1508 disjoint chrl2 180990 181355 2.23879999 1.25682364 10.0076623 SLC6A12 11397 covers exon(s) 1497 disjoint chr5 150439475 150439942 0.33058349 1.20506107 10.0059584 TNIP1 1247 inside intron 337 disjoint chr4 169638566 169638967 -0.18542698 0.74467909 10.0048758 PALLD 15824 upstream -266 disjoint chrlO 15248633 15249067 1.49011319 0.63561807 10.0026277 NMT2 1633 inside intron 763 disjoint chrl 3 36393936 36394298 2.46837758 1.51351485 10.0003259 ALG5 77178 downstream -1184 disjoint
[0125] Table 7. Regions of differential methylation between iPS cells and ES cells.
These DMRs were defined by using a absolute area cutoff of 10.0 which corresponds in magnitude to the 5% FDR cutoff of the R-DMRs.
Columns are chromosome, start, end, iPS M value, ES M value, absolute area, gene, distance to gene, relation to gene, distance to CGI, and relation to CGI. chrl 5 97225652 97227801 0.227471611 1.080152523 51.5937901 IGF1R 215365 inside intron -12153 disjoint chr6 27633621 27634805 0.108399472 1.289575618 38.81697032 ZNF184 84764 upstream -38573 disjoint chr5 43072850 43074823 1.466157509 0.5817001 37.26230862 LOC389289 1274 close to 3' 0 cover chr20 9437038 9438216 0.051275945 0.987698218 31.22453135 C20orfl03 5054 upstream -1149 disjoint chrl 4 28316507 28317651 0.760956759 -0.17642005 28.07687865 FOXG1B 10470 downstream 0 cover chr3 182923968 182925746 0.127063354 0.656520447 24.87669495 SOX2 11553 downstream 1354 disjoint chrl 6 7291918 7293162 0.946999718 0.249556214 24.58553596 A2BP1 1282786 inside intron 1172 disjoint chrl 3 87125868 87126896 0.804579041 -0.00432374 24.19527842 SLITRK5 2998 inside exon 499 disjoint chrX 144705410 144706639 0.759028942 0.127530373 20.54209095 SLITR 2 402 promoter 416 disjoint chr20 41249967 41250675 1.036819093 -0.12875618 19.57020325 PTPRT 1295 inside intron 214 disjoint chrl 2 129208556 129209275 0.663237433 -0.25861014 19.31325005 FZD10 3709 upstream 2005 disjoint chrl 2 53004646 53005713 0.284782964 0.872195098 18.63588133 COPZ1 0 overlaps 5' -43391 disjoint chrX 82652439 82653443 1.072618267 0.207597033 18.59974597 POU3F4 2499 close to 3' -7 disjoint chr2 171282410 171283336 0.667048044 0.000469203 17.58159857 SP5 2304 overlaps 3' -260 disjoint chrl 9 42099017 42099878 0.155797937 0.977802648 17.49715532 ZNF568 0 overlaps 5' 0 overlap chrl 9 42400743 42401903 -0.01612304 0.602185605 16.67966062 ZNF383 7302 upstream 0 overlap chrl 9 49552384 49553848 0.234164936 0.756906337 16.38921482 ZNF228 0 overlaps 5' 0 cover chr3 6879643 6880824 0.981606416 0.394324387 16.13497527 GR 7 1717 inside intron -2 disjoint chi9 33282156 33283079 1.367725662 0.672429276 15.99862229 NFX1 1647 inside intron -1153 disjoint chr5 77303281 77304177 0.575424342 -0.09411442 15.98740855 AP3B1 322106 downstream 0 overlap chr6 170325252 170329737 1.427295144 0.405051902 15.42982794 DLL1 111884 downstream 257 disjoint overlaps exon chr4 40085410 46086419 0.854054556 0.145270204 14.92037612 GABRA2 282 upstream 241 disjoint chr3 53899007 53900125 0.704645462 0.150267931 14.53929982 SELK 903 inside intron 353 disjoint chrl l 22410755 22411366 0.57100791 1.251003689 13.93228098 SLC17A6 94513 downstream 0 cover chrl 228624603 228625670 0.612607913 0.030782173 13.86369936 PGBD5 44614 upstream 2056 disjoint chr3 114944217 114944963 1.08854428 0.408940172 13.8249113 NAT13 2822 inside intron 2161 disjoint chrl6 7294546 7295117 0.84066923 -0.27172958 13.60284679 A2BP1 1285414 inside intron 0 overlap chrl2 113314751 113315770 0.535799537 0.019715542 13.58108062 TBX5 10315 inside intron 2524 disjoint chrl 9 63407589 63408222 0.868644635 1.842826113 13.10886679 ZNF274 21382 inside intron 0 overlap chrl5 41880102 41880940 0.459955412 1.02971503 13.09355453 HYPK 190 covers exon(s) 0 overlap chrl4 28313268 28313880 0.638323011 -0.08319744 12.90767825 F0XG1B 7231 downstream 0 overlap chr9 1037266 1038126 0.128659603 0.751999684 12.9006026 DMRT2 3487 upstream -872 disjoint chr4 82609891 82610762 0.680195878 0.166337626 12.78775147 RASGEF1B 1322 inside intron 872 disjoint chrl4 28312464 28312934 0.933404745 -0.07146545 12.77512602 FOXG1B 6427 downstream 220 disjoint overlaps exon
chr7 27169657 27170448 0.967586842 0.47682675 12.71832918 HOXA9 1225 upstream 0 overlap chrl9 41955960 41956400 -0.66328949 0.391187285 12.64560433 ZNF790 64720 inside intron -37 disjoint chrl3 105981768 105982682 0.819916711 0.316123238 12.62887987 EFNB2 2655 inside intron 1787 disjoint chrl l 14883295 14884165 0.402081489 1.007264281 12.50814439 CYP2R1 12969 upstream 0 inside chrl 149639234 149640163 0.848459762 0.203289892 12.29849568 PSMB4 570 covers exon(s) -28 disjoint chrl 177811966 177813166 0.814919212 0.349471835 12.25303575 NPHS2 276 promoter -36 disjoint chr2 100804245 100805192 1.099654132 0.688956238 12.24446839 NPAS2 1201 inside intron -360 disjoint chrlO 79064308 79065116 0.991115036 0.409319809 12.13252135 KCNMA1 2466 inside intron 985 disjoint chrl4 88326545 88327399 0.76264982 0.217787804 12.03025764 EML5 1510 inside intron 750 disjoint chrlO 102970690 102971604 0.640026818 0.19939173 12.01443698 LBX1 7102 downstream 688 disjoint chrl 4 50365422 50366312 0.612093416 0.12914268 11.98509471 NIN 1276 inside intron 165 disjoint chrlO 101283761 101284528 0.653430826 0.013044699 11.98208146 N X2-3 1062 inside intron 0 overlap chr9 1039754 1040188 0.162076199 1.16412108 11.95685953 DMRT2 1425 promoter 0 overlap chrl4 28307849 28308529 0.691004283 -0.02261013 11.77346482 FOXG1B 1812 inside exon -266 disjoint chrl 165459041 165459893 0.862462127 0.349489691 11.51606237 POU2F1 2275 inside intron -1056 disjoint chrl 9 52544342 52545345 -0.14160207 0.373788344 11.4568994 DHX34 0 overlaps 5' 0 overlap chrl 9 42155962 42156849 0.649135866 1.069810155 11.23448186 ZNF568 56889 downstream 0 overlap overlaps exon
chrl 9 12652946 12653452 0.507728551 1.234012862 11.11472675 DHPS 224 downstream 0 overlap overlaps exon
chr6 50911061 50911933 0.75742851 0.200796632 11.10587079 TFAP2B 16520 upstream 6668 disjoint chrl 8 55039895 55040683 0.709173498 0.260202288 11.09244726 GRP 1516 inside intron -1250 disjoint chr6 146391395 146392107 -0.0325721 0.560549252 11.06317243 GRM1 4 promoter 108 disjoint chr3 16898002 16898748 0.813418781 0.17760569 10.88160233 PLCL2 50837 upstream 1637 disjoint chr8 57188202 57188882 0.672038702 1.253061001 10.8502335 MOS 212 inside exon 0 inside chrlO 93549479 93550266 0.481093269 0.060932357 10.71373998 TN S2 1431 inside intron -800 disjoint chrl 199407658 199408489 1.212560664 0.549121877 10.67460732 TMEM9 17418 upstream -531 disjoint chrll 16590686 16591544 0.261277965 -0.24639575 10.65714883 Cllorf58 125225 upstream 0 overlap chrlS 33397919 33398533 0.916481955 0.22102909 10.58726287 BRUNOL4 1407 inside intron 372 disjoint chr2 10780095 10781000 0.601211078 0.21284729 10.58321445 ATP6V1C2 870 covers exon(s) -262 disjoint chr3 144162925 144163569 1.134445992 0.575984538 10.56635759 PAQR9 1298 inside exon 255 disjoint chrl6 29891819 29892361 1.07322243 0.376415556 10.50638294 BOLA2 220766 inside intron 0 overlap chrl 27771242 27771886 1.089082223 0.352457353 10.47939058 AHDC1 30804 inside intron 2361 disjoint chrl5 60468042 60468548 0.926802392 0.155411332 10.42803734 FLJ38723 139757 upstream 1246 disjoint chr7 8442214 8443068 0.275755867 -0.17450799 10.38775953 NXPH1 2105 inside intron -490 disjoint chrl6 65841434 65842369 0.498297373 0.120004317 10.31332647 SLC9A5 1079 inside intron -781 disjoint chrl l 75205444 75206301 0.822656516 0.368584985 10.16164583 UVRAG 1585 inside intron -870 disjoint chrl4 28322452 28323093 0.366469326 -0.18297536 10.12176953 FOXG1B 16415 downstream 1023 disjoint chr5 3642696 3643410 1.247996089 0.714909805 10.0431625 IRX1 5757 upstream 234 disjoint
[0126] Table 8. Gene ontology functional categories enriched in differentially methylated regions between iPS cells and ES cells.
Fold
Methylation GO ID Term Count % P Value
Enrichment
Hypermethylated in GO:0007275 multicellular organismal 14 31.82% 2.69251 6.81E-04 iPS compared to ES development
GO:0032501 multicellular organismal 18 40.91% 2.163279 7.23E-04 process
GO:0048731 system development 11 25.00% 2.823529 0.00294
GO:0065007 biological regulation 20 45.45% 1.724951 0.00477
GO:0007399 nervous system 7 15.91% 4.054299 0.00575 development
GO:0045944 positive regulation of 4 9.09% 10.5676 0.00579 transcription from RNA
polymerase II promoter
Hypomethylated in GO:0050794 regulation of cellular 12 70.59% 2.778833 1.63E-04 iPS compared to ES process
GO:0050789 regulation of biological 12 70.59% 2.582055 3.36E-04 process
GO:0065007 biological regulation 12 70.59% 2.345934 8.57E-04
GO:0006355 regulation of 8 47.06% 3.368421 0.00303 transcription, DNA- dependent
GO:0006351 transcription, DNA- 8 47.06% 3.293928 0.00345 dependent
GO:0032774 RNA biosynthetic process 8 47.06% 3.28996 0.00348
GO:0045449 regulation of transcription 8 47.06% 3.153195 0.00446
GO:0019219 regulation of nucleobase, 8 47.06% 3.082017 0.00509 nucleoside, nucleotide and
nucleic acid metabolic
process
GO:0006350 transcription 8 47.06% 3.039703 0.00551
GO:0043283 biopolymer metabolic 11 64.71% 2.101101 0.00588 process
GO:0010468 regulation of gene 8 47.06% 2.968116 0.00632 expression
GO:0010467 gene expression 9 52.94% 2.500271 0.00792
GO:0031323 regulation of cellular 8 47.06% 2.851375 0.00795 metabolic process
GO:0019222 regulation of metabolic 8 47.06% 2.753613 0.00968 Fold
Methylation GO ID Term Count % P Value
Enrichment process
[0127] Table 9. Relationship between differential gene expression and differential methylation at reprogramming differentially methylated regions (R-DMRs).
Columns are chromosome, start, end, transcriptional start site (TSS), strand,distance between DMR and TSS, Gene Name, ΔΜ (Fibroblast minus iPS), differential expression
(log2(fib/iPS)), absolute area for RDMR, pvalue for differential expression, FDR for differential expression, and state and relationship to CpG island.
"state" indicates the degree of methylation. "On" indicates some methylation, "Off1 is no methylation, "+" is more and "-" is less. chrl2 52000502 52001366 52001648 -! -282 AAAS -1 -0.32 20 0.067 0.086 OffiOn Shore chr4 56948879 56949726 56948395 -1 484 AASDH -0.79 -0.63 15 0.00095 0.0015 OffiOn Shore chr3 51984311 51985098 51984125 1 -186 ABHD14A -1.4 1.5 20 5.60E-07 7.50E-07 On:On- Shore chrl l 107497934 107498656 107497468 1 -466 ACAT1 -0.92 0.41 17 0.0065 0.012 On:On- Shore chr4 8492954 8493382 8493352 -1 0 ACOX3 -1.1 1.3 13 0.009 0.0083 OffiOn Shore chrlO 72102810 72103593 72102565 1 -245 ADAMTS14 -0.71 -0.055 12 0.74 0.78 OffiOn Shore chrl6 76027004 76027721 76026512 -1 492 ADAMTS18 -0.78 -0.36 12 0.014 0.023 On:On- Shore chrl4 23874374 23874985 23874117 -1 257 ADCY4 0.69 0.54 12 0.16 0.17 On.Orri- Shore chr22 39072915 39074068 39072509 1 -406 ADSL -0.79 -0.98 13 1.00E-05 1.80E-05 OffiOn Shore chrlO 1 16154742 116155284 116154505 -1 237 AFAP1L2 0.71 -3.1 11 2.40E-08 2.10E-08 On:Off Shore chrl 50260778 50261886 50262159 -1 -273 AGBL4 -0.37 0.034 11 0.75 0.8 OffiOn Shore chr6 143424084 143424766 143423729 1 -355 AIG1 0.87 -0.84 17 0.0071 0.0072 On:Off Shore chr9 111582761 111583859 111582540 1 -221 AKAP2 -0.67 0.32 21 0.0046 0.014 OffiOn Shore chrl l 43859115 43860200 43858971 1 -144 ALKBH3 -1.1 1.6 18 1.10E-08 3.50E-08 On:On- Shore chr7 101891278 101892048 101892293 -1 -245 ALKBH4 -0.66 -0.065 11 0.49 0.59 On:On- Shore chr2 128358078 128358950 128358904 0 AMMEC 1L -0.92 0.14 22 0.17 0.26 On:On- Shore chr9 128923507 128924325 128924734 -1 -409 ANGPTL2 -0.67 1.6 15 7.90E-05 6.30E-05 OffiOn Far chr4 125850864 125852360 125851382 0 A KRD50 -0.87 0.026 36 0.87 0.89 OffiOn Shore chr9 71476098 71476586 71477042 -456 APBA1 -0.95 1.5 12 4.30E-05 3.60E-05 On-.On- Shore chrl 8 10443546 10444154 10444625 1 471 APCDD1 0.68 -0.89 12 0.079 0.08 On:Off Shore chrl l 6458220 6458873 6459171 -1 -298 ARFIP2 -0.71 0.21 10 0.17 0.22 On:On- Shore chrl l 119713523 119714134 119713156 1 -367 ARHGEF12 -0.65 0.054 11 0.65 0.71 OffiOn Shore chrl 3 110604579 110605190 110604086 1 -493 ARHGEF7 -0.63 -0.44 11 0.002 0.0044 OffiOn Shore chrX 24942581 24943519 24943775 -1 -256 ARX 0.86 -0.81 18 0.0023 0.0025 On:Off Shore chr2 9262997 9263873 9264345 1 472 ASAP2 0.76 1.5 14 2.30E-06 2.50E-06 On:Off Shore chr20 30410772 30412250 30411211 1 0 ASXL1 -0.97 1.7 34 1.70E-07 2.50E-07 OffiOn Shore chr6 32202746 32203633 32203995 -1 -362 ATF6B -0.96 0.8 24 0.011 0.011 OffiOn Far chr4 47181803 47183461 47182167 1 0 ATP10D -0.85 4.5 38 8.20E-07 4.80E-07 OffiOn Far chrl9 47188555 47189803 47190222 -1 -419 ATP1A3 -0.81 -2.8 19 1.50E-08 1.60E-08 On:On- Shore chr3 132096464 132097406 132096124 -340 ATP2C1 -0.73 0.63 18 0.0031 0.004 OffOn Shore chrl7 37864479 37865925 37864388 -91 ATP6V0A1 -1.8 1.2 74 0.00022 2.00E-04 OffiOn Shore chr7 128287130 128289657 128290134 477 ATP6V1F -0.6 0.87 12 9.90E-06 2.20E-05 On:On- Shore chr20 49818737 49819207 49818274 -1 463 ATP9A -1.1 1.4 14 6.30E-07 9.70E-07 On:On- Shore chrl 44218171 44219358 44217695 -476 B4GALT2 -0.73 0.61 23 0.0027 0.0036 On:On- Shore chr9 95755626 95756444 95755534 -1 92 BARXl 0.8 0.22 18 0.076 0.12 On. ff inside chr6 31777467 31778888 31779172 -1 -284 BAT5 -0.93 -0.1 37 0.47 0.53 OffiOn Shore chrl2 24945810 24947103 24946497 -1 0 BCAT1 1.1 0.032 38 0.74 0.8 On:Off Shore chrl l 101693010 101693830 101693404 0 BIRC3 -0.86 0.88 18 0.071 0.072 On:On- cover chrlO 102035372 102036295 102036436 -1 -141 BL0C1S2 -0.92 -0.11 24 0.13 0.26 OffiOn Shore chr7 43763958 43764428 43764797 369 BLVRA 1.7 1.7 23 4.20E-06 3.70E-06 On:Off Shore chrl 9 45663927 45664709 45663517 -1 410 BLVRB -1.2 0.84 26 1.70E-05 3.50E-05 On:On- inside chr22 48605680 48606150 48605552 -1 128 BRD1 -0.84 -0.58 11 4.20E-05 0.00018 OffiOn Shore chrl 166170606 166171425 166171857 -1 -432 BRP44 -0.58 1.1 12 1.30E-05 1.60E-05 OffiOn Shore chrl l 62230533 62231948 62231446 -1 0 BSCL2 1.3 -0.69 53 0.0043 0.005 On:Off Shore chrl 84717584 84718520 84717538 -46 BXDCS -0.56 0.027 13 0.82 0.86 OffiOn Island chr2 201385610 201386475 201385153 -457 BZW1 -1.4 0.19 33 0.0078 0.05 OffiOn Shore chrlO 76859938 76861143 76861217 74 ClOorfl l 0.85 1.1 29 0.026 0.025 On:Off Shore chrl l 67794646 67795503 67795997 -1 -494 Cllor£24 -0.69 1.2 16 3.50E-05 3.70E-05 OffiOn Shore chrll 124176005 124177056 124175509 -1 496 CllorfSl -0.81 -1.3 18 6.90E-05 6.30E-05 OffiOn Shore chrl l 107843062 107843604 107843468 -1 0 C110rf65 -0.79 0.91 12 0.0016 0.0016 OffiOn Far chrll 101423651 101424121 101423399 -252 Cl lorf70 -0.86 1.7 11 0.0033 0.0028 OffiOn Shore chrl l 67130174 67130749 67130753 -1 -4 Cllorf72 -0.62 -0.14 10 0.49 0.53 On:On- Shore chrl 2 31703504 31703977 31703889 0 C12orf72 -0.81 0.045 10 0.78 0.82 OffiOn Far chrl 4 22494938 22495932 22496158 -1 -226 C14orf94 -1 -1 22 5.10E-06 9.10E-06 OffiOn Shore chrl5 32289759 32291074 32289515 -1 244 C15or£29 -0.67 0.48 14 0.046 0.052 On:On- Shore chrl 7 6859256 6859972 6858848 -408 C17orf49 -1.4 0.3 27 0.066 0.087 OffiOn Shore chrl 7 260730 261485 260434 -296 C17orf97 -0.74 0.75 16 0.072 0.073 OffiOn Shore chrl 8 45266539 45267302 45267602 -1 -300 C18orf32 -0.68 0.51 12 0.00044 0.0012 On:On- Shore chrl 53457779 53458427 53458866 -1 -439 Clorfl23 -0.54 0.66 9.8 0.00092 0.0013 OffiOn Shore chrl 224252595 224253728 224253689 -1 0 Clorf55 -0.72 0.58 23 0.067 0.071 OffiOn Island chrl 7 40401554 40402060 40401170 -1 384 C1QL1 0.69 -0.22 9.7 0.082 0.12 Orr.Off Island chr5 159730318 159730788 159730226 -1 92 C1QTNF2 -1.7 1.9 22 1.30E-05 1.00E-05 OffiOn Shore chr20 42371931 42372890 42373303 -1 -413 C20orfl42 -0.88 0.81 24 0.0058 0.006 OffiOn Shore chr20 1113011 1113525 1113117 -1 0 C20orf46 -1.4 -1.3 16 2.40E-08 1.30E-07 OffiOn Shore chr22 40804540 40805148 40805645 497 C22orf32 -1.1 0.33 19 0.006 0.015 On:On- Shore chr2 54410456 54411106 54411575 469 C2orf73 -0.58 0.18 10 0.18 0.23 OffiOn Shore chr3 49288985 49289455 49289456 -1 -1 C3orf62 -1.2 0.21 15 0.23 0.27, OffiOn Shore chr4 88031560 88032189 88032599 -1 -410 C4orS6 -0.63 0.22 11 0.32 0.35 On:On- Shore chr4 140419505 140420580 140420942 -1 -362 C4orf49 0.73 1.9 17 2.50E-06 2.00E-06 On:On+ Shore chr5 31568507 31569549 31568156 -351 C5orf22 -0.75 1.2 13 0.00062 0.00057 On:On- Shore chr6 139390108 139391026 139391512 486 C6orfil5 0.84 -0.68 20 4.10E-06 2.60E-05 On:Off Shore chr6 36961967 36962531 36961618 -349 C6orf89 -0.77 3.1 12 1.10E-07 8.30E-08 OffiOn Shore chr9 34371708 34372214 34371598 -1 110 C9orf24 0.71 -0.49 9.9 1.60E-05 0.00019 On:On+ Shore chr9 90794820 90795852 90795598 0 C9orf47 0.69 0.072 17 0.85 0.87 On:Off Island chr9 116413976 116414707 116413527 -449 C9orf91 -1.1 -0.059 15 0.81 0.83 Off: On Shore
Figure imgf000189_0001
chrl9 9981288 9981833 9982147 -1 -314 COL5A3 -0.78 0.63 10 0.12 0.13 OffiOn Shore chrl8 491107 491721 490685 -1 422 COLEC12 1.2 1.3 18 0.028 0.027 On:Off Shore chr3 130450233 130451091 130451143 1 52 COPG -0.89 0.85 11 3.00E-04 0.00037 OffiOn Shore chr4 84175616 84176520 84175263 1 -353 COPS4 -0.66 0.63 13 0.00084 0.0013 OffiOn Far chrl2 119451528 119452403 119451336 -1 192 COQ5 -0.9 -0.75 17 7.50E-O6 2.80E-05 OffiOn Shore chr8 100974995 100976166 100975071 -1 0 C0X6C -0.68 0.11 18 0.037 0.21 OffiOn Shore chrl 152198040 152198938 152197667 -1 373 CRTC2 -0.47 -0.11 12 0.18 0.31 On:On- Shore chrl2 54980539 54981173 54980442 -1 97 CS -0.67 0.14 11 0.12 0.22 On:On- Shore chr3 37879135 37879725 37878673 1 -462 CTDSPL -0.62 0.29 9.9 0.07 0.093 OffiOn Shore chr8 104453246 104454370 104452919 1 -327 CTHRC1 -1.6 3.6 50 7.40E-07 4.60E-07 OffiOn Shore chrlO 102016917 102017744 102017427 -1 0 CWF19L1 -0.82 0.024 17 0.95 0.96 On:On- cover chr4 75184086 75185125 75183861 -1 225 CXCL2 -0.62 0.38 17 0.52 0.54 OffiOn Shore chr2 237142786 237143842 237143119 1 0 CXCR7 -0.42 -2.5 12 0.011 0.0096 OffiOn Shore chrlO 135190290 135190832 135190857 1 25 CYP2E1 -0.71 1.2 11 9.10E-O5 8.60E-05 On:On- Shore chr6 39868512 39869858 39868120 1 -392 DAAM2 -0.9 1.8 34 0.00023 0.00017 OffiOn Shore chrl 9 3920026 3921580 3920826 -1 0 DAPK.3 -0.84 1.1 25 5.90E-06 8.50E-06 OffiOn Shore chrl2 49919269 49920589 49918877 1 -392 DAZAP2 -1.3 2 34 3.90E-08 5.40E-08 On:On- Shore chrl l 6632319 6633173 6633656 -1 -483 DCHS1 -1.8 -0.063 42 0.8 0.82 OffiOn Shore chrl 6 30347855 30348662 30348874 -1 -212 DCTPP1 -0.55 -0.16 11 0.46 0.5 OffiOn Shore chr4 169638218 169638967 169638213 -1 5 DDX60L -1.2 2.6 25 1.10E-06 8.00E-07 OffiOn Shore chr9 125732538 125733041 125732238 -1 300 DENNDIA 0.79 1.7 11 1.60E-05 1.20E-05 On:On+ Far chr22 30480380 30481547 30480069 1 -311 DEPDC5 -0.7 -0.13 20 0.29 0.36 On:On- Shore chr22 17511567 17512037 17512190 -1 -153 DGCR14 -0.85 0.35 11 0.097 0.11 OntOn- Shore chrl 9 12652982 12653416 12653682 -1 -266 DHPS -0.77 0.43 9.3 0.0022 0.0049 On:On- Shore chr5 5463692S 54638868 54639278 -1 -410 DHX29 -0.75 0.079 22 0.24 0.42 OffiOn Shore chr20 37023085 37024004 37024409 1 405 DHX35 0.66 -1.4 11 5.90E-07 9.10E-07 On:Off Shore chrl 35166288 35167307 35167773 -1 -466 DLGAP3 -0.76 -0.95 13 1.20E-05 2.20E-05 On:On- Shore chrl 50660079 50661308 50661729 -1 -421 D RTA2 0.95 -0.15 32 0.38 0.43 OmOff inside chrl4 72430928 72432018 72430562 -1 366 DPF3 0.66 3.3 20 4.00E-07 2.60E-07 On:Off Shore chrl 8 63332626 63333027 63332855 -1 0 DSEL -1 4 11 5.30E-09 4.50E-09 OffiOn Shore chr8 29260747 29261964 29262241 -1 -277 DUSP4 0.9 -1.3 31 0.027 0.026 On:Off Shore chrl 7 7077773 7078276 7078587 -1 -311 DVL2 -0.69 -0.12 9.6 0.33 0.4 OffiOn Shore chr20 57308251 57308721 57308877 1 156 EDN3 -0.74 -0.7 9.6 0.0024 0.0029 OffiOn Shore chrl 3 77390303 77390839 77390946 -1 -107 EDNRB 0.73 -5.2 11 7.50E-08 4.60E-08 On:Off Island chr2 37236911 37237348 37237694 -346 EEF2AK2 -0.81 0.19 9.7 0.074 0.13 OffiOn Shore chr5 95323642 95324707 95323531 111 ELL2 0.95 4.1 27 2.80E-09 2.60E-09 On:On+ Shore chr2 119322444 119323646 119322229 215 EN1 1.4 4.8 47 0.00054 0.00038 On.Off cover chrl 7 4795269 4795949 4795131 1 -138 EN03 0.66 -1.9 12 2.30E-07 2.60E-07 On:On+ Shore chrl 38002227 38003186 38003411 -1 -225 EPHA10 -0.52 0.05 14 0.69 0.75 On.On- Island chr3 89238541 89239014 89239364 1 350 EPHA3 0.74 2.7 9.6 0.03 0.028 On:On+ Far chr8 27403289 27404341 27404562 1 221 EPHX2 -0.91 -2.5 21 1.80E-08 2.10E-08 OffiOn Shore chrl 9 60878879 60879600 60878404 1 -475 EPN1 -0.71 0.28 9.3 0.0015 0.011 OffiOn Shore chr7 27247106 27248568 27248689 1 121 EVX1 1 0.62 38 0.014 0.016 On:Off Shore chr4 122942025 122942740 122941922 1 -103 EXOSC9 -0.94 0.31 15 0.013 0.027 OffiOn Shore chrl 7 38149309 38150205 38150574 -1 -369 EZH1 -0.7 -0.24 13 0.17 0.2 OffiOn Shore chr6 159158101 159158840 159159254 -1 -414 EZR 0.92 -0.91 18 2.00E-04 0.00024 On.Off Shore chr5 76150933 76152517 76150610 1 -323 F2RL1 0.86 -0.65 38 0.031 0.032 On:Off cover chrl 94778820 94779461 94779903 -1 -442 F3 0.78 0.61 14 0.26 0.27 On:On+ Shore chrl3 24643853 24644635 24644426 -1 0 FAM123A -0.8 -0.97 18 0.00024 0.00026 Off:On Shore chr8 139576964 139577962 139578247 -1 -285 FA 135B -0.9 0.059 25 0.53 0.63 OffiOn Shore chr2 276748 277287 276919 -1 0 FAM150B 0.74 -4 11 3.20E-12 l.lOE-11 On:On+ Shore chr5 74198292 74198969 74198371 -1 0 FAM169A 0.83 -0.68 16 0.00023 4.00E-04 On:Off Shore chr5 93472282 93472911 93473096 -1 -185 FAM172A -0.61 1.4 10 5.50E-09 4.00E-08 On:On- Shore chr4 17390905 17391682 17392046 -1 -364 FAM184B -0.93 -0.33 17 0.039 0.055 On.On- Shore chrl 27210387 27211486 27211914 -1 ■428 FAM46B 0.98 -4.3 31 3.00E-09 2.60E-09 Orr.Off Shore chrl 26020046 26020853 26019906 1 -140 FAM54B -0.99 1.2 13 6.40E-07 1.30E-06 On:On- Shore chrl 149244804 149245524 149245897 -373 FAM63A -0.82 -0.15 16 0.39 0.44 OffiOn Shore chr9 130838923 130840220 130838745 1 -178 FAM73B -0.79 -0.45 24 0.025 0.031 OffiOn Shore chrlO 90739545 90740380 90740268 1 0 FAS -1.1 3.3 25 4.60E-06 2.80E-06 Off: On Shore chr5 41960469 41961005 41961113 1 108 FBX04 -1.1 3.3 17 2.90E-08 2.30E-08 OffiOn Shore chr7 19151445 19152404 19151569 -1 0 FERD3L 1.1 0.32 31 0.013 0.026 OmOff Island chrl 7 7282621 7283406 7283413 1 7 FGF11 0.61 -4 13 8.90E-08 5.90E-08 On:Off Shore chr8 16903999 16904728 16903936 -1 63 FGF20 0.85 0.3 14 0.13 0.15 On:Off Shore chrl 201586761 201587330 201586912 -1 0 FMOD -1.1 1.5 16 0.034 0.033 OffiOn Far chrl 9 51059637 51060566 51059358 1 -279 F0XA3 0.9 -4.4 23 9.00E-I2 1.90E-11 On:Off Shore chrl 47672083 47674387 47674276 1 0 F0XD2 0.75 0.58 39 0.0025 0.0036 On:Off cover chrl 7 71649451 71650173 71648966 -1 485 F0XJ1 0.6 -0.1 12 0.47 0.53 On:Off Shore chrl 6 85167510 85169756 85169616 1 0 FOXL1 0.91 0.33 57 0.03 0.045 On:Off Shore chrl 9 626554 627215 627389 1 174 FSTL3 -0.94 2.6 16 1.00E-05 6.50E-06 On:On- cover chrl 9 40321848 40322481 40321568 1 -280 FXYD1 -0.63 -0.13 10 0.67 0.7 On:On- Shore chr3 198959502 198960777 198961018 1 241 FYTTDl -1 2.5 36 6.00E-09 8.70E-09 OffiOn Shore chr4 46085231 46086026 46086153 -1 -127 GABRA2 -0.67 0.046 12 0.65 0.73 OffiOn Shore chrl 67922539 67923115 67923471 1 356 GADD45A -0.9 1.5 14 8.50E-06 7.60E-06 OffiOn Shore chrl2 50070725 50071156 50071467 -1 -311 GALNT6 0.9 2.4 11 7.10E-08 7.00E-08 On:On+ Shore chrl l 22645348 22645994 22646230 1 236 GAS2 -0.65 0.0015 12 1 1 OffiOn Shore chr9 73952498 73953630 73954113 1 483 GDA -1.4 -0.13 23 0.48 0.52 On:On- Shore chr7 30511040 30511780 30510942 -1 98 GGCT -0.79 -1.3 13 1.20E-05 1.30E-05 OffiOn Island chrl 9 14468413 14469157 14467944 -1 469 GIPCl -0.89 1 12 0.00035 0.00036 On:On- Shore chrl 2 40825422 40825976 40824940 -1 482 GLT8D3 0.95 -0.36 11 0.12 0.14 On:On+ Shore chr7 79600875 79601729 79602076 1 347 GNAI1 0.84 1.1 14 9.70E-06 1.40E-05 On:Off Shore chr9 36248709 36249074 36248450 -1 259 GNE -0.94 1.6 9.4 4.20E-08 9.50E-08 OffiOn Shore chr3 195600216 195601199 195601284 -1 -85 GP5 0.87 0.19 19 0.11 0.17 On;On+ Shore chrX 48866007 48866759 48867095 -1 -336 GPKOW -0.65 0.36 12 0.048 0.061 OffiOn Shore chrl l 93772648 93773901 93774066 -1 -165 GPR83 -0.78 -0.81 17 0.014 0.014 On:On- Shore chr7 112514479 112514916 112515015 -1 -99 GPR85 -0.78 2.6 9.3 7.20E-06 4.70E-06 OffiOn Far chrl 238841218 238842631 238842085 -1 0 GREM2 -0.69 4.2 24 1.60E-05 9.10E-06 OffiOn Far chrl2 14023240 14023922 14024319 -1 -397 GRIN2B -0.66 0.098 12 0.2 0.34 OffiOn Shore chrl4 94306491 94307170 94306252 -1 239 GSC 1.2 0.072 19 0.64 0.69 On:Off Shore chr4 54659618 54660658 54660955 1 297 GSX2 0.63 0.26 18 0.047 0.074 On:Off Shore chrlS 57736104 57736642 57737005 -1 -363 GTF2A2 -0.77 0.49 12 0.0028 0.0048 OffiOn Shore chr22 36531453 36532130 36531060 1 -393 H1F0 -1.5 0.62 29 0.029 0.031 OffiOn Shore chrl l 118471800 118472824 118471369 -1 431 H2AFX -0.55 -0.12 10 0.56 0.6 On:On- Shore chr2 172487203 172488023 172487204 1 0 HAT1 -1.1 0.013 25 0.89 0.92 OffiOn Island chr6 30050571 30052040 30050871 1 0 HCG9 0.84 0.071 28 0.4 0.52 On:Offi Shore chr5 140995658 140996167 140996607 -440 HDAC3 -0.92 -0.39 13 0.032 0.042 θη.Όη- Shore chrl7 55510037 55510756 55511074 -318 HEATR6 -0.84 -0.29 17 0.0088 0.023 OffiOn Shore chr6 26125295 26126121 26125939 0 HIST1H1A -0.96 0.24 22 0.66 0.68 On:On- Far chr6 26151595 26154569 26151864 -1 0 HIST1H2BB -0.97 0.41 68 0.012 0.018 OffiOn cover chr6 27890663 27891301 27890801 1 0 HIST1H2BM -0.6 -0.28 10 0.28 0.3 Off:On Shore chrl l 118460915 118461730 118460797 1 -118 H BS -0.76 -0.69 16 0.006 0.0068 OffOn Shore chrl 183970441 183971496 183970306 1 -135 HMCN1 -0.75 1 22 0.074 0.074 OffiOn Shore chr7 27191794 27192297 27191360 -1 434 HOXA11 0.74 1.5 10 0.0049 0.0043 On:Off Island chr7 27206734 27209251 27206250 -1 484 HOXA13 1 1.6 71 0.07 0.069 On:Off Shore chr7 27108771 27111401 27108919 -1 0 HOXA2 1.1 3.1 65 1.50E-05 9.30E-06 On:Off cover chr7 27163715 27164048 27164080 -1 -32 HOXA7 1.1 1.4 9.5 1.80E-06 2.20E-06 On:On+ Shore chr7 27171724 27172368 27171596 128 HOXA9 -0.83 5.7 15 1.10E-05 6.00E-06 OffiOn inside chrl 7 43977471 43978326 43977392 79 HOXB2 0.67 4.2 16 1.70E-06 9.80E-07 On:Off Shore chrl 7 44037719 44038556 44037333 386 HOXB6 0.72 3.9 17 0.00038 0.00026 On:Off Shore chrl 7 44047783 44048609 44047300 -1 483 HOXB8 0.8 0.48 16 0.013 0.017 On.Off Shore chr2 176672197 176672601 176672776 1 175 HOXD12 0.87 0.34 9.5 0.05 0.065 On:Off Island chr2 176734095 176734646 176733865 1 -230 HOXD3 0.93 2.6 14 0.0032 0.0026 On:Off Shore chr2 176723900 176724580 176724359 1 0 HOXD4 0.82 0.48 16 0.004 0.0065 On.Off Shore chr3 150329148 150329864 150330061 1 197 HPS3 -0.95 -0.33 19 0.0018 0.0075 OffOn Shore chrlO 100985942 100987462 100985609 -1 333 HPSE2 1.2 0.067 54 0.47 0.58 On:Off Shore chr4 88531132 88531577 88531347 0 HSD17B11 -0.84 0.55 9.2 0.0043 0.006 OffOn Far chr6 78228778 78229530 78229900 -370 HTR1B 0.63 0.3 13 0.026 0.043 On:Off Island chrl 6217310 6218162 6218631 -469 IC T -0.71 0.26 13 0.057 0.087 On:On- Shore chrl 7 70519198 70520157 70520371 1 214 ICT1 -0.87 0.26 17 0.0041 0.019 Off:On Shore chrl l 303520 304360 304171 1 0 IFITM1 1.2 -1.9 28 0.00099 0.00077 On:Off Shore chr3 130642132 130644404 130641658 1 -474 IFT122 -0.75 -0.6 14 0.0026 0.0035 0ff:0n Shore chrl l 1 17362678 1 17363607 117362319 1 -359 IL10RA -1 0.21 25 0.14 0.18 OffOn Shore chr8 79879836 79881043 79880313 -1 0 IL7 -0.79 1.3 22 0.036 0.035 OffOn Shore chrl 151909016 151909732 151910103 -1 -371 ILF2 -0.5 -0.28 9.9 0.11 0.13 OffiOn Shore chrl 154808516 154809265 154809020 -1 0 IQGAP3 -0.47 0.27 9.9 0.17 0.2 Off:On cover chr3 12982883 12983533 12983960 -1 -427 IQSEC1 -0.82 0.14 15 0.51 0.55 On:On- Shore chr21 45172606 45173110 45173181 -1 -71 ITGB2 -0.94 0.57 11 0.013 0.015 OfEOn Far chrl4 92649334 92650885 92651377 -1 -492 ΓΓΡΚ1 0.93 -0.84 41 6.20E-05 9.80E-05 On:On+ Shore chr21 25932552 25933367 25933455 1 88 JAM2 -0.76 -2.3 15 0.0019 0.0015 Off:On Shore chrl6 56327520 56328725 56328618 1 0 ATNB1 -0.8 -1.1 27 0.00014 0.00014 Off:On Shore chrl 209374491 209374964 209374080 -1 411 KCNH1 -0.71 0.58 9.2 0.0013 0.0021 On:On- Shore chrlO 103593842 103594483 103593667 -1 175 KCNEP2 1.1 0.057 20 0.76 0.79 On:On+ Shore chrH 87863066 87863734 87863004 -1 62 KCN 10 -1 -0.4 16 0.0056 0.01 Off:On Shore chr7 4782072 4782584 4781790 1 -282 KIAA0415 -0.86 0.62 12 0.00026 0.00054 OffOn Shore chrl 154170172 154170923 154170812 -1 0 KIAA0907 -0.62 -0.86 13 1.90E-05 3.70E-05 Off:On Island chrl5 77512317 77512856 77511913 1 -404 KIAA1024 0.71 0.99 11 0.0026 0.0026 On:Off Island chr2 96666287 96667361 96667810 -1 -449 KIAA1310 -0.96 0.25 29 0.011 0.034 OffOn Shore chrl 8 32663397 32664218 32663078 1 -319 IAA1328 -0.69 0.71 16 0.0017 0.0021 OffOn Shore chrl 231008306 231009193 231007812 1 -494 KIAA1383 0.78 0.41 19 0.0015 0.0041 On:On+ Shore chr8 22517137 22517846 22518202 1 356 KIAA1967 -0.74 -0.97 10 0.00016 0.00019 OffiOn Shore chr9 115901027 115901533 115901377 -1 0 KIF12 1.2 -0.44 17 0.00016 0.00094 On:Off Island chrl 10194252 10194746 10194261 1 0 KJF1B -0.72 -1.5 9.3 1.50E-06 1.70E-06 Off:On Shore chr2 26059335 26059736 26058947 -i 388 KIF3C 0.95 -0.99 10 0.00011 0.00013 On:On+ Shore chrlO 32385805 32386284 32385334 -1 471 KIF5B -1.1 0.56 14 6.00E-04 0.0012 On:On- Shore chrX 56274838 56275275 56275632 1 357 KLF8 0.84 -2.2 10 1.10E-08 1.80E-08 On:Off Shore chrl 18678954 18679794 18680090 1 296 KLHDC7A -1.2 0.33 20 0.00016 0.0026 On:On- Shore chrl7 8219S04 8220660 8220754 -1 -94 K BA2 -1.1 0.0065 21 0.97 0.98 OffiOn Island chr3 135853020 135854290 135853168 -1 0 KY -0.77 0.37 21 0.0012 0.0047 On:On- Shore chrl 62432789 62433259 62433084 1 0 L1TD1 1.2 -6.4 16 4.50E-15 4.00E-14 On:Off Shore chrl2 48962715 48963500 48963557 -1 -57 LIMA1 -0.88 1.6 19 6.30E-06 5.60E-06 OffiOn Far chr!2 79855960 79856864 79855825 -1 135 LIN7A 1.2 -0.5 30 0.28 0.29 OmOff Shore chrl 8 45342733 45343341 45342425 1 -308 LIPG 0.59 -3.3 9.9 8.10E-05 5.10E-05 On:Off Shore chr2 96768747 96769571 96769528 -1 0 LMAN2L -0.53 -0.13 12 0.21 0.31 OffiOn Island chr3 199171748 199172774 199171468 1 -280 LMLN -0.92 0.43 21 0.0051 0.009 OffiOn Shore chrl 163592931 163593654 163592576 -1 355 LMX1A 0.98 0.024 16 0.83 0.87 On-.Off Shore chrl l 58099384 58099854 58099910 -1 -56 LPXN -1.3 4.4 16 1.70E-07 1.00E-07 OffiOn Far chr7 127457740 127458222 127458238 -1 -16 LRRC4 1 -1.2 13 0.00013 0.00012 On:On+ Shore chrl3 45683296 45683802 45684084 1 282 LRRC63 -1.1 0.067 15 0.48 0.58 OffiOn Far chr6 31742123 31742806 31741867 1 -256 LY6G5B -1.1 0.27 21 4.00E-04 0.0073 OffiOn Shore chr2 160361641 160362537 160362999 -1 -462 LY75 -0.64 1.9 16 1.00E-05 7.50E-06 Off: On Shore chr22 19666979 19668016 19666558 1 -421 LZTR1 -0.56 0.88 14 3.50E-05 5.60E-05 OffiOn Shore chr8 20204860 20205402 20205754 -1 -352 LZTS1 0.62 1.1 9.2 0.024 0.023 On:Off Island chrl 3 34948736 34949770 34949346 -1 0 MAB21L1 0.97 3 27 0.0096 0.0084 On:Off Shore chr4 151722068 151723752 151722753 1 0 MAB21L2 0.98 0.74 41 0.44 0.46 On:Off Shore chrX 30158366 30158800 30158474 1 0 MAGEB3 -0.8 0.027 9.6 0.68 0.79 OffiOn Far chr8 120290374 120291295 120289893 1 -481 MAL2 1 -8.4 27 1.40E-14 4.10E-14 On:Off Shore chrl5 89248045 89248620 89248424 1 0 MAN2A2 0.71 0.53 11 0.0019 0.0031 On:On+ Shore chrl 9 12637664 12638408 12638828 -1 -420 MAN2B1 -0.64 -0.6 9.6 0.014 0.016 OffiOn Shore chr5 68747086 68748117 68746710 1 -376 MARVELD2 1.4 -4.5 38 5.10E-09 4.10E-09 On:Off Shore chr3 153467976 153468929 153468519 1 0 MBNL1 -1.2 3.4 31 6.90E-09 6.40E-09 OffiOn Shore chr3 184627355 184628068 184628549 -1 -481 MCF2L2 0.92 -0.23 18 0.26 0.29 On:Off Shore chrl 5 92576194 92576805 92575955 1 -239 MCTP2 0.57 -0.36 9.7 0.43 0.45 On:Off Shore chr22 19191935 19193907 19191905 1 -30 MED15 -0.58 1.2 23 6.90E-07 1.50E-06 OffiOn Island chrl3 47566161 47567199 47567268 -1 -69 MED4 -0.61 -0.54 17 0.003 0.0046 OffiOn Island chr5 88213307 88214646 88214780 -1 -134 MEF2C -0.79 2.6 28 2.10E-07 1.70E-07 OffiOn Shore chr5 126654790 126655682 126654514 1 -276 MEGF10 0.69 -7.3 17 1.70E-13 3.30E-13 On:Off Shore chrl5 39738621 39739440 39739902 1 462 MGA 1 -1 23 1.60E-07 8.10E-07 On:Off Shore chr7 141341765 141342307 141342148 1 0 MGA -1.3 0.74 19 0.099 0.1 On:On- Far chrl4 36737068 36737872 36736907 1 -161 MIPOLl -0.75 0.017 14 0.94 0.95 OffiOn Shore chrl l 118497944 118498502 118497498 1 -446 MIZF -0.62 -1 9.3 6.90E-05 7.90E-05 OffiOn Shore chrl 5 21361048 21361443 21361547 1 104 KRN3 -1.1 0.24 12 0.0021 0.019 On:On- Far
Chrl 7 53650943 53651554 53651600 -1 -46 MKS1 -1.1 0.48 19 7.70E-05 0.00048 OffiOn Shore chr4 146758835 146759622 146759990 1 368 M AA -0.7 1.5 15 1.10E-05 9.40E-06 OffiOn Shore chrl5 54543859 54544535 54544627 -1 -92 MNS1 -0.79 0.17 11 0.33 0.37 OffiOn Shore chr2 198087702 198088714 198089016 1 302 MOBKL3 -0.67 -0.18 18 0.046 0.11 OffiOn Shore chr8 72919481 72921712 72919285 -1 196 MSC 1.4 1.2 77 4.90E-05 5.10E-05 On:Off Shore chrl2 63957815 63958453 63958755 1 302 MSRB3 0.85 3.4 14 3.90E-09 4.00E-09 On:Off Shore chrl 6 55260075 55260759 55261227 1 468 MT1H 1.1 -1.3 14 9.00E-05 8.10E-05 On:Off Shore chr6 49537734 49538834 49538990 -1 -156 MUT -0.45 0.4 14 0.00052 0.0024 OffiOn Shore chrl7 4404264 4404980 4405430 -1 -450 MYBBP1A -0.5 -0.61 10 0.0023 0.0032 OffiOn Shore chrl2 79625531 79628584 79625583 1 0 MYF6 1.2 -0.074 110 0.64 0.68 On:Off cover chr4 89837197 89837971 89838409 -1 -438 NAP1L5 -0.64 1.7 9.7 3.40E-06 3.00E-06 On:On- Far chr7 102575855 102576658 102576749 -1 -91 NAPEPLD -0.61 0.59 12 0.052 0.055 OffiOn Shore chrH 20561657 20562621 20561326 -1 331 NDRG2 1.1 -2.9 24 3.60E-06 2.30E-06 On:On+ Shore chi21 43185676 43186113 43186447 1 334 NDUFV3 -0.81 0.82 9.7 2.40E-06 9.90E-06 On:Qn- Shore chrl 16640066 16640925 16639820 1 -246 NECAP2 -0.62 1.5 14 1.30E-07 2.60E-07 OffiOn Shore chrl 116184777 116185508 116185270 -1 0 NHLH2 -0.91 0.63 18 0.0031 0.0039 OffiOn Shore chrX 118622731 118623446 118623874 -1 -428 NKRF -0.97 -0.57 17 0.047 0.051 OffiOn Shore chr5 172595175 172597606 172594868 -1 307 N X2-5 1.1 0.69 69 0.073 0.076 On:Off cover chrl 7 46586034 46587188 46586734 1 0 NME2 -0.49 0.2 11 0.086 0.14 OffiOn Shore chr5 151764850 151765680 151765017 -1 0 UR2 -1.1 0.3 22 0.0039 0.014 On:On- Far chrlO 71871600 71874437 71871429 -1 171 NODAL 0.79 -3.7 20 2.20E-07 1.40E-07 OnrOff Shore chrl 9 51166677 51168019 51168497 -1 -478 NOVA2 -1.3 0.18 48 0.094 0.16 OffiOn Far chrl 24615289 24616878 24614903 1 -386 NPAL3 -1.1 3.1 49 1.50E-07 1.10E-07 OffiOn Island chrl 177811864 177813130 177811691 -1 173 NPHS2 -0.67 0.51 19 0.0034 0.0053 Off: On Shore chrl 5 71713104 71713830 71712806 -1 298 NPTN -0.62 0.4 10 1.60E-07 0.00015 OffiOn Shore chr4 164473281 164474139 164473198 83 NPY1R -0.5 -3.5 11 2.10E-05 1.30E-05 OffiOn Shore chrl 115060068 115060883 115061038 -155 NRAS -0.59 0.53 14 0.0046 0.0066 OffiOn Far chrl 9 54095725 54096386 54095851 1 0 NUCB1 -0.79 1.1 13 0.0011 0.0011 OffiOn Shore chr6 34468801 34469585 34468419 -1 382 NUDT3 -1.1 -0.51 18 0.00042 0.0011 On:On- Shore ehrl l 71467424 71468965 71469221 -256 NUMAl -0.87 -0.29 25 0.0027 0.013 On:On- Shore chr9 132990145 132990579 132990802 1 223 NUP214 -0.85 -0.98 10 0.00026 0.00028 OffiOn Shore chr6 150108944 150109798 150109507 -1 0 NUP43 -0.57 -0.67 14 0.0011 0.0015 OffiOn cover chrl 9 9908S04 9909001 9908228 -1 276 OLFM2 0.97 -3.6 13 1.10E-06 6.60E-07 On:Off Shore chr3 31998257 31998980 31998242 -1 15 OSBPL10 0.78 -3.6 13 6.10E-05 3.80E-05 On.Off Shore chrl4 56346232 56347277 56346940 -1 0 OTX2 0.67 -8.8 20 1.00E-14 3.10E-14 On:Off Shore chr3 25806629 25807557 25806575 1 -54 OXSM -0.58 1.5 12 9.10E-07 1.10E-06 OffiOn Far chr6 163069241 163069816 163069258 1 0 PACRG -0.68 -0.37 11 0.17 0.18 OffiOn Shore chr8 82187100 82188417 82186858 -1 242 PAG1 0.97 2.2 21 0.0025 0.002 On:On+ Shore chr5 138704696 138705235 138705418 1 183 PAIP2 -0.76 -0.59 11 0.00022 0.00052 On:On- Shore chr20 9766334 9767024 9767479 -1 -455 PAK7 -0.86 -2 15 4.30E-05 3.00E-05 OffiOn Shore chr20 3816429 3817376 3817486 1 110 PANK2 -0.61 -0.29 13 6.40E-05 0.0035 On:On- Shore chrl4 72772610 72773969 72773958 1 0 PAPLN 0.93 -3.4 20 4.80E-08 3.60E-08 On:Off Shore chr20 48781985 48782595 48781488 1 -497 PARD6B 1.3 -0.15 22 0.11 0.19 On:Off Shore chr2 113753158 113753700 113752958 -1 200 PAX8 1 0.58 15 0.00068 0.0013 On:On+ Shore chrH 36194933 36196159 36196533 1 374 PAX9 0.73 0.27 24 0.035 0.059 On:Off cover chr5 140206443 140207435 140207541 1 106 PCDHA9 -1.4 -0.067 39 0.6 0.66 OffiOn Shore chr5 140551701 140553038 140552136 1 0 PCDHB10 -0.61 -0.5 15 0.33 0.35 OffiOn Shore chr5 140582954 140584599 140583130 1 0 PCDHB14 -0.9 -1 41 7.80E-05 8.80E-05 OffiOn Shore chr5 140604555 140605784 140605165 1 0 PCDHB15 -0.59 -0.19 18 0.076 0.13 OffiOn Shore chr5 140481143 140482033 140481765 1 0 PCDHB4 -0.76 -0.11 19 0.32 0.41 On:On- Shore chr5 140509530 140510381 140510023 1 0 PCDHB6 -1.1 -0.18 25 0.48 0.51 On:On- Shore chrS 140532162 140532975 140532519 1 0 PCDHB7 -1.1 0.62 24 0.023 0.025 On:On- Shore chr5 140836087 140837886 140835753 1 -334 PCDHGA12 -0.95 0.81 48 8.30E-06 2.3ΌΕ-05 OffiOn Island chr5 140843995 140845397 140844925 1 0 PCDHGA12 0.59 0.12 23 0.14 0.26 On.Off cover chrl4 70442988 70443498 70443875 1 377 PCNX -1.2 -0.84 17 7.10E-05 0.00011 On:On- Shore chrll 103540657 103541430 103540237 -1 420 PDGFD 0.76 -0.069 13 0.92 0.92 On:On+ Shore chrl 158520001 158521672 158521555 -1 0 PEX19 -0.51 -0.72 23 0.0021 0.0025 OffiOn Far chrl l 71633228 71634225 71632852 -1 376 PHOX2A 0.66 0.37 12 0.013 0.022 On:Off Shore chrX 48659428 48660766 48661228 -1 -462 P 2 1.5 -3.4 51 4.80E-10 7.20E-10 On:Off Shore chr4 111778292 111780100 111777957 -1 335 PITX2 1.4 2.6 70 0.0013 0.00098 Orv.Off Shore chr3 173011251 173011852 173010929 -1 322 PLD1 -1.4 0.96 17 0.00038 4.00E-04 OffiOn Shore chr8 96214135 96214836 96215208 372 PLEKHF2 0.99 0.35 19 0.063 0.078 On:Off Shore chrl 4 64239302 64240573 64241068 495 PLEKHG3 1.8 -1.3 66 9.40E-08 3.00E-07 On:Off Shore chr3 147361955 147362709 147361972 -1 0 PLOD2 -0.6 2 13 0.00051 0.00038 OffiOn Shore chrl 8 55715765 55717799 55718172 373 PMAIP1 1.9 -2.6 58 0.00087 0.00065 On-.Off Shore chrl l 66876851 66877387 66877593 -1 -206 P0LD4 -0.86 1.9 13 6.00E-07 5.70E-07 OffiOn Shore chr 37475959 37476776 37476438 0 P0LR1E -0.68 0.33 14 0.16 0.18 OffiOn Shore chr5 89806822 89808231 89806437 -385 POLR3G 0.87 -2.4 24 2.10E-07 1.80E-07 On:Off Shore chr9 133368639 133369913 133369427 0 POMT1 -0.74 0.23 27 0.15 0.18 OffiOn Shore chr7 94901476 94902012 94902197 -1 -185 PON2 -0.77 0.36 12 0.0075 0.015 OffiOn Shore chr6 35418842 35420016 35418369 -473 PPARD -1.1 0.94 36 0.00053 0.00056 OffiOn Shore chr2 28826837 28827718 28828184 466 PPP1CB -0.88 0.13 15 0.025 0.14 OffiOn Shore chrl 9 54067836 54069153 54067490 -346 PPP1R15A -1.1 1.9 38 0.00026 0.00019 OffiOn Shore chr20 36866660 36867292 36867762 470 PPP1R16B 0.86 -3.1 15 2.20E-10 4.60E-10 On:Off Shore chrlO 93381686 93382700 93382838 -1 -138 PPP1R3C -0.95 5 26 9.00E-07 5.10E-07 OffiOn Shore chr4 81325458 81326417 81325448 -10 PRDM8 1.1 0.45 29 0.026 0.032 On:Off Shore chr5 176663857 176664507 176663441 -416 PRELIDl -0.75 -0.053 11 0.69 0.74 OffiOn Shore chrX 48930018 48930419 48929766 -1 252 PRICKLE3 1.4 -0.28 15 0.18 0.21 On:Off Shore chrl4 93323873 93324487 93323858 -1 15 PRIMA 1 1.3 -4.9 22 5.40E-07 3.10E-07 On:Off inside chrll 6298776 6299273 6298294 -1 482 PRKCDBP -1 3.1 13 5.50E-08 4.40E-08 OffiOn Shore chrl 148560625 148561272 148560642 0 PRPF3 -0.77 -0.3 14 0.031 0.05 OffiOn Shore chrl9 750120 751356 750345 0 PTBP1 -0.69 -0.54 17 0.00011 4.00E-04 OffiOn Shore chrl4 51849417 51850462 51850863 401 PTGER2 -1.2 2.1 33 0.0015 0.0012 OffiOn Shore chrl2 28015165 28016172 28016183 -1 -11 PTHLH 0.92 2.1 24 0.00021 0.00015 On:Off Shore chr2 120233007 120233390 120233677 287 PTPN4 1 -2.3 10 4.60E-08 5.00E-08 On:Off Shore chrlO 1 19794759 119795631 119796104 -1 -473 RAB11F1P2 -0.67 1.2 16 1.50E-06 2.40E-06 OffiOn Shore chr2 135526326 135527009 135526323 -3 RAB3GAP1 -0.67 0.62 13 0.00028 0.00056 OffiOn Far chrl 204009733 204010446 204010747 -1 -301 RAB7L1 0.83 1 17 0.00073 0.00072 On:On+ Shore chrl 176960092 176960598 176961002 404 RALGPS2 0.98 -0.12 14 0.77 0.79 On:On+ Shore chrl 9 5393S924 53936460 53935782 -1 142 RASIPl 0.69 -0.83 10 0.087 0.088 On:On+ Shore chrlO 6170285 6170752 6171013 261 RBM17 -1.3 -0.6 17 6.30E-05 0.00021 OffiOn Shore chrl6 66827848 66828699 66827637 -1 211 RBM35B 0.92 -5.3 22 2.00E-16 3.10E-14 On:Off inside chr2 151826574 151827312 151826623 -1 0 RBM43 -0.84 2 17 6.00E-07 5.50E-07 OffiOn Shore chrl l 66201115 66201646 66201851 -1 -205 RBM4B -0.76 -0.34 11 0.021 0.033 OffiOn Shore chrl 144218454 144219982 144218995 0 RBM8A -1.2 -0.94 48 0.00024 0.00027 OffiOn cover chr3 140740202 140740814 140741180 -1 -366 RBP1 0.68 -2.5 12 0.034 0.032 On:On+ cover chr8 30360106 30361089 30361486 397 RBPMS 1 -2.4 21 2.70E-07 2.20E-07 On:Off Shore chrl 9 54723072 54723575 54722687 -385 RCN3 -0.94 2.8 13 4.30E-06 2.80E-06 OffiOn Shore chr5 112286167 112286949 112285811 -1 356 REEP5 -0.98 1.2 22 3.70E-07 8.40E-07 OffiOn Shore chr4 39043102 39044198 39044390 -1 -192 RFC1 -0.64 -0.26 19 0.00012 0.0063 OffiOn Shore chrl5 91433927 91434679 91433437 -1 490 RGMA 0.58 -3.6 12 4.80E-08 3.50E-08 On:On+ Shore chrl 239587526 239588078 239587153 -1 373 RGS7 -0.81 -0.0033 10 0.98 0.99 OffiOn Shore
Figure imgf000196_0001
chr6 34833041 34833889 34833275 1 0 SNRPC -0.77 -0.095 17 0.17 0.33 OffOn Island chr8 101730241 101730747 101731069 -1 -322 SNX31 0.71 -0.11 9.9 0.49 0.54 On:Off Shore chrl l 120828566 120829482 120828130 1 -436 S0RL1 0.71 -4.5 17 1.50E-07 8.90E-08 On:On+ Shore chrl 109742562 109743134 109742086 -1 476 SORT1 0.87 1.7 14 3.70E-06 3.30E-06 On:Off Shore chrl7 7433706 7434084 7434212 -1 -128 SOX15 1.1 -2.7 11 7.20E-08 6.40E-08 On:Off Shore chr4 168392603 168393497 168392316 -1 287 SPOC 3 -0.88 -0.52 20 0.1 0.11 OffiOn Shore chrl 9275528 9277565 9275571 1 0 SPSB1 -1.3 1.2 20 6.20E-05 6.20E-05 0£f:On Far chr2 54639368 54639978 54639035 1 -333 SPTBN1 0.61 -0.39 10 0.12 0.13 On:Off Shore chr2 54535446 54536496 54536958 1 462 SPTBN1 0.83 -0.19 22 0.41 0.44 On:Off Shore chrl l 18611177 18612196 18612596 -1 -400 SPTY2D1 -0.74 0.64 21 0.00015 0.00033 OffiOn Shore chrl2 107774108 107775136 107775480 -1 -344 SSH1 -1.4 0.5 42 0.00067 0.0017 OffiOn Shore chrl 154256172 154257128 154257374 -1 -246 SSR2 -0.87 0.97 24 9.00E-08 7.80E-07 On:On- Shore chr3 188869372 188870572 188870895 -1 -323 SST -0.75 -0.38 23 0.36 0.38 On:On- Shore chr7 89677688 89678738 89678936 1 198 STEAP2 0.86 -0.18 25 0.67 0.69 On:Off Shore chrl 47551001 47552215 47552406 -1 -191 STIL -0.47 -0.039 12 0.79 0.82 OffiOn Shore chr2 219245295 219245942 219245053 1 -242 STK36 -0.59 -0.8 11 1.30E-06 7.20E-06 OffiOn Shore chr3 33235923 33236354 33235711 -1 212 SUSD5 0.96 -2.1 12 0.04 0.038 On:On+ Shore chr6 10995074 10996149 10995346 1 0 SYCP2L 1 -3.1 25 3.00E-08 2.60E-08 On:Off cover chrl l 7229084 7229482 7229757 1 275 SYT9 0.85 -0.028 9.3 0.77 0.83 On:Off Shore chr6 42126489 42127322 42126253 1 -236 TAF8 -0.72 -0.28 16 0.063 0.088 On:On- Shore chrl 158159568 158160878 158160131 -1 0 TAGLN2 -0.62 2.3 22 7.80E-08 8.20E-08 OffiOn Shore chrX 9391085 9391600 9391369 1 0 TBL1X 0.73 -0.043 10 0.84 0.86 On:Off Shore chrl 7 56887322 56888176 56888589 1 413 TBX4 0.71 0.24 17 0.013 0.039 On:Off inside chrX 101268226 101269819 101268459 1 0 TCEAL2 -0.82 -3.8 21 1.80E-08 1.40E-08 OffiOn Far chr6 134251392 134252647 134251969 1 0 TCF21 0.88 2.2 29 0.00045 0.00033 On:Off Island chr3 49424826 49425483 49424643 1 -183 TCTA -1.3 2.1 19 8.20E-07 6.70E-07 Off: On Shore chrl2 122721273 122722037 122721615 1 0 TCTN2 -0.77 -0.003 12 0.97 0.98 On:On- Island chrl2 2939709 2940808 2939223 1 -486 TEAD4 1.1 -1.4 34 1.80E-05 1.60E-05 On:Off Shore chr6 10523611 10525546 10523297 -1 314 TFAP2A 0.71 0.57 38 0.0052 0.0068 On:Off Shore chrl 6 31390203 31390640 31390985 1 345 TGFB1I1 -0.78 3.7 9.3 1.70E-10 2.60E-10 OffiOn Shore chr2 85407474 85408262 85408622 -1 -360 TGOLN2 -1.1 0.33 23 0.00046 0.0039 OffiOn Island chrl 9 4782004 4782405 4782716 -1 -311 TICAMl -1.5 3 17 2.20E-10 4.80E-10 OffiOn Shore chrl 7 847468 848181 847107 1 -361 TIMM22 -0.86 -0.019 11 0.96 0.97 OffiOn Shore chrl5 64435469 64436062 64436083 -1 -21 TIPIN -0.76 -0.55 12 0.0048 0.0067 OffiOn Island chr9 70979378 70980658 70979030 1 -348 TJP2 -0.54 -1.9 19 1.30E-05 9.90E-06 OffiOn Shore chrl 7 8019634 8020484 8020439 -1 0 TMEM107 -0.71 2 16 3.60E-05 2.60E-05 OffiOn Shore chr4 4300981 4301622 4300835 -1 146 TMEM128 -0.72 -0.15 13 0.26 0.32 OffiOn Shore chrl2 128952367 128953608 128953837 -1 -229 TMEM132D -1.3 -1.1 45 0.05 0.049 OffiOn Shore chr7 142691474 142692970 142692185 1 0 TMEM139 0.9 -2.1 38 1.20E-09 3.90E-09 On:On+ Far chr6 10830535 10831023 10831324 1 301 T EM14C -0.84 0.069 10 0.22 0.44 OffiOn Shore chr4 122904262 122904903 122904899 -1 0 TMEM155 0.84 1.2 15 0.037 0.036 On:On+ Shore chr2 216655231 216656193 216654887 -344 TMEM169 1 0.68 28 0.14 0.14 On:On+ Shore chr22 36999136 36999534 36998962 -1 174 TMEM184B -0.86 0.26 9.5 0.00083 0.01 OffiOn Shore chrl l 62316149 62316757 62316056 -1 93 TMEM223 -0.78 -0.83 13 0.00039 0.00048 On:On- Shore chrl l 117907452 11790791 117907145 1 -307 TMEM25 0.99 0.19 13 0.56 0.59 On:Off Shore chrl 32311554 32312090 32311109 1 -445 TMEM39B -0.67 -0.47 10 0.0049 0.0078 OffiOn Shore chr3 186698092 186699058 186699516 -1 -458 TMEM41A -0.6 0.31 11 0.0087 0.021 On:On- Shore chr7 77264267 77265259 77265683 -1 -424 TMEM60 -0.78 0.39 22 6.60E-05 0.00099 OffiOn Shore chrl7 7699109 7700071 7699101 1 -8 TMEM88 0.73 -1.5 20 0.003 0.0026 OniOff cover chrX 101656865 101657878 101658355 -1 -477 TMSB15A -0.86 -1.9 24 0.053 0.051 OffiOn Shore chr5 150439475 150440357 150440769 -1 -412 TNIP1 -1.1 1.1 20 4.50E-06 7.70E-06 OffiOn Shore chrl l 56849443 56850228 56848989 -1 454 TN S1BP1 -0.55 -0.93 12 8.00E-06 1.60E-05 OffiOn Shore chrl7 50333350 50334071 50333203 1 -147 TOM1L1 0.65 -0.74 11 0.00045 0.00063 On:Off Shore chr2 73817431 73818006 73817980 -1 0 TPRKB -1.2 0.25 20 0.13 0.16 OffiOn Island chi9 99920320 99921033 99921301 -1 -268 TRIM14 0.69 -1.2 14 0.062 0.062 On:On+ Shore chr9 118489681 118491029 118489430 1 -251 TRIM32 -1.1 1 39 0.00014 0.00014 Off:On Shore chr7 99355191 99355658 99355090 -1 101 TRIM4 -1.1 2.2 15 0.00019 0.00013 Off: On Shore chr5 180565221 180566392 180564783 -1 438 TRIM7 0.71 0.4 10 0.0016 0.0046 On:Off Shore chrl2 48003463 48004245 48003238 1 -225 TROAP -0.49 0.81 11 0.00045 0.00055 OffiOn Shore chrX 111211423 111212208 111212660 -1 -452 TRPC5 0.53 0.056 12 0.54 0.64 On:Off cover chr9 73250569 73251492 73251640 -1 -148 TRPM3 0.87 0.1 23 0.084 0.25 On.Off Shore chr3 151607828 151608438 151608812 1 374 TSC22D2 -0.58 0.55 9.8 0.00017 0.00052 OffiOn Shore chrl4 80491499 80492035 80491528 1 0 TSHR 0.78 0.25 12 0.036 0.066 On:Off Shore chrl 229731204 229731962 229731022 1 -182 TSNAX -0.53 0.043 11 0.46 0.65 OffiOn Shore chr6 80769881 80770735 80771078 1 343 TT -0.63 -1.3 15 0.00022 0.00019 OffiOn Shore chrl 32418706 32419500 32418253 1 ^53 TXLNA -0.87 0.84 19 3.10E-06 1.10E-05 OffiOn Shore chrX 46938532 46939422 46938187 1 -345 UBA1 -0.51 -0.059 13 0.52 0.62 OffiOn Shore chr8 59486870 59487586 59486377 1 -493 UBXN2B 0.77 -1.5 15 0.00065 0.00053 On:Off Shore chrl 9 4406171 4408176 4406295 -1 0 UBXN6 -0.73 1.6 37 6.20E-07 7.20E-07 OffiOn Shore chrl 7 70430028 70430531 70430946 -1 -415 USH1G -0.88 -0.36 12 0.0023 0.0071 OffiOn Shore chrl2 121944829 121946259 121946665 -1 -406 VPS37B -1.1 1 45 9.20E-06 1.50E-05 OffiOn Shore chrl 149428682 149429431 149429290 -1 0 VPS72 -0.57 -0.61 12 0.00015 0.00036 OffiOn Far chrll 124127304 124128078 124127344 -1 0 VSIG2 0.75 0.33 15 0.28 0.3 On:Off Far chrl 27687239 27688914 27689256 -1 -342 WASF2 -0.84 0.39 24 0.002 0.0056 OffiOn Shore chrX 48341327 48342037 48340845 1 -482 WDR13 -1.1 1.1 21 1.90E-07 6.70E-07 On:On- Shore chrl5 41906504 41907907 41906470 1 -34 WDR76 -1.2 1.1 35 0.0014 0.0014 OffiOn Shore chr4 6321509 6322012 6322478 1 466 WFS1 -0.86 0.71 12 0.0012 0.0015 OffiOn Shore chrl 2 47650415 47651506 47651768 -1 -262 WNT10B 0.96 0.28 27 0.37 0.39 On:Off Shore chrl l 32407847 32408446 32408935 -1 -489 WT1 0.69 -0.18 9.7 0.32 0.36 On:Off Shore chrl9 48770878 48771345 48771555 -1 -210 XRCC1 -0.78 -0.39 10 0.011 0.018 OffiOn Shore chr9 128607581 128608455 128607126 1 -455 ZBTB43 -0.83 -0.23 15 0.36 0.39 OffiOn Shore chrl 9 63721519 63722392 63722733 -1 -341 ZBTB45 -0.97 0.29 19 0.19 0.21 OffiOn Shore chr6 33530421 33530924 33530334 1 -87 ZBTB9 -0.71 -1.5 9.2 7.80E-07 1.10E-06 OffiOn Shore chrl 37711731 37712267 37712753 1 486 ZC3H12A -0.83 -0.24 12 0.27 0.3 On:On- Shore chr8 135794905 135795380 135794463 -1 442 ZFAT -1 -0.46 10 0.0049 0.0082 On:On- Shore chrl 6 71640082 71641654 71639775 -1 307 ZFHX3 1.3 1.5 58 6.40E-06 6.20E-06 On:Off Shore chr8 77755277 77755839 77756078 1 239 ZFHX4 1 1.1 13 0.0015 0.0014 On:Off Shore chrl 7 4922633 4923139 4922478 1 -155 ZFP3 -0.75 1.5 11 0.005 0.0044 OffiOn Shore chr9 114858938 114859513 114858817 -1 121 ZFP37 -0.8 -0.41 13 0.056 0.066 OffiOn Shore chr4 189154018 189154425 189153919 1 -99 ZFP42 1.3 -3.5 14 5.20E-15 7.10E-13 On:Off Shore chr3 15114165 15115540 15115659 -1 -119 ZFYVE20 -0.75 0.2 25 0.026 0.074 OffiOn Island chr3 148607740 148609393 148609871 1 478 ZIC1 1 2.2 46 0.091 0.09 On:Off Shore chrl 9 62044119 62044730 62043876 -1 243 ZM2 -1.3 0.24 16 0.014 0.041 OffiOn Shore chr5 140060142 140061040 140060216 1 0 ZMAT2 -0.8 0.29 16 0.06 0.083 OffiOn Far chrl6 3102802 3103758 3102575 -227 ZNF205 -0.83 -0.3 23 0.0025 0.011 OffiOn Far chrlO 43388640 43389600 43390038 -1 -438 ZNF239 -1.2 -0.036 34 0.89 0.9 OffiOn Shore chrlO 38305564 38305995 38305561 -1 3 Z F25 -0.84 3.7 10 6.70E-10 8.50E-10 OffiOn Shore chrl9 62395171 6239S851 62394681 -490 ZNF264 -0.68 0.22 13 0.077 0.12 OffiOn Shore chrl9 49022069 49023126 49023313 187 ZNF283 -0.94 0.29 20 0.097 0.12 On:On- Far chrl9 63653791 63654547 63654778 231 ZNF324B -0.85 0.67 15 0.046 0.048 OffiOn Shore chr20 2436261 2437534 2437561 -1 -27 ZNF343 -1.7 1.8 52 5.70E-07 5.90E-07 OffiOn Island chrl9 57181221 57181826 57181891 -1 -65 ZNF350 -0.88 -0.39 15 0.18 0.19 On:On- Far chrl9 61711327 61712169 61711024 -303 ZNF471 -1.5 0.65 32 0.017 0.018 OffiOn Shore chrl9 42553301 42553879 42553899 20 ZNF527 -0.74 0.095 12 0.58 0.62 OffiOn Island chrl 8 54679424 54681238 54681041 0 ZNF532 1.1 -1.1 57 1.30E-06 2.80E-06 On:Off Shore chrl9 42777801 42778352 42777622 -179 ZNE540 -0.81 0.38 11 0.17 0.18 OffiOn Shore chrl9 9469617 9470258 9470279 -1 -21 ZNF560 -0.83 -0.38 15 0.19 0.21 On:On- Island chrl9 41396541 41397313 41397410 -1 -97 ZNF565 -0.82 -0.47 16 0.0033 0.0057 On:On- Shore c rl9 42099161 42100176 42099106 -55 ZNF568 -0.86 0.8 19 0.019 0.019 OffiOn Shore chrl9 47263164 47264370 47264704 334 ZNF574 -1.1 -1.2 30 1.50E-05 1.70E-05 OffiOn Far chrl9 63612375 63612845 63611875 -500 ZNF584 -0.9 1 12 0.00014 0.00015 OffiOn Shore chr3 48257189 48257590 48257600 10 ZNF589 0.97 -2.9 11 1.00E-07 8.20E-08 On:Off Shore chrl 40716028 40716633 40715889 -139 ZNF642 -1.5 -0.69 22 0.049 0.051 OffiOn Shore chrl9 63528728 63530011 63530197 186 ZSCAN22 -1.4 0.8 25 3.90E-05 7.40E-05 OffiOn Shore ohrl 159274588 159275028 159275377 -1 -349 0.77 -6.3 9.2 4.60E-14 1.90E-13 On:On+ Shore chrX 74882540 74883454 74883688 -1 -234 -0.72 1.9 10 8.80E-05 6.40E-05 OffiOn Far chrl l 1727832 1728500 1728397 -1 0 -1 1.6 19 0.0089 0.008 On:On- Shore chrl 9 60690067 60691236 60691676 440 -0.7 1.5 22 1.50E-05 1.40E-05 OffiOn Shore chr8 37713884 37714843 37714102 -1 0 -0.91 1.4 25 2.40E-06 2.70E-06 OffiOn Shore chr6 42966431 42967006 42966504 -1 0 -1 1.3 16 8.90E-06 9.70E-06 OffiOn Island chrl5 39310960 39311676 39310729 -231 -0.63 0.91 13 0.00058 0.00063 OffiOn Shore chr22 44859823 44860326 44860541 215 -0.8 0.84 11 0.0051 0.0052 On:On- Shore chrl 7 38576961 38578O10 38576772 -189 -0.54 0.82 12 0.00013 0.00019 OffiOn Shore chr7 47984240 47985303 47985771 -1 -468 -0.69 0.8 19 7.80E-05 0.00013 OffiOn Shore chr6 31727318 31728076 31728149 -1 -73 -0.52 -0.57 11 0.00021 0.00053 OffiOn Shore chr22 29696207 29696807 29696663 0 0.82 -0.54 12 0.0039 0.0057 On:On+ Shore chr6 32230156 32231601 32229850 -306 -0.51 -0.5 18 0.026 0.031 On:On- Island chrl l 122435593 122436765 122435340 -1 253 -0.72 0.48 16 0.016 0.02 OffiOn Shore chr7 65217354 65218154 65217240 -114 -0.64 -0.37 12 0.0038 0.0093 OffiOn Island chr7 55608160 55608828 55607694 -1 466 1.3 0.36 20 0.00019 0.002 On:Off Shore chr6 31903659 31910233 31903667 0 -0.94 0.34 19 0.36 0.38 OffiOn Island chrlO 112392344 112393466 112392533 -1 0 0.64 0.31 15 0.0047 0.014 On:Off Shore chrl 9 12641873 12642417 12641517 -356 -0.9 -0.29 14 0.034 0.055 OffiOn Shore chrl l 95762951 95763667 95762591 -1 360 -0.7 0.19 14 0.099 0.16 OffiOn Shore chr6 3181501 1 31815654 31815776 122 -0.7 -0.18 11 0.41 0.44 OffiOn Shore chrl 8 52963741 52965315 52965371 56 -2 0.15 45 0.12 0.21 OffiOn Far chrX 103104235 103105108 103103880 -355 -0.9 0.13 22 0.58 0.62 OffiOn Shore chrl l 116474825 116475226 116474347 -1 478 -1 -0.12 11 0.58 0.62 OffiOn Shore chr8 57148494 57149184 57149014 -1 0 -0.92 -0.078 17 0.00048 0.28 OffiOn Shore chr6 30797531 30799046 30797330 -201 -0.97 0.063 21 0.42 0.56 OffiOn Shore chr5 140546831 140547958 140547077 0 -0.74 -0.056 14 0.57 0.66 OffiOn Shore chrl4 23754493 23755818 23755081 -1 0 -0.58 0.025 19 0.83 0.86 OffiOn Shore chr22 19728700 19729843 19730270 1 427 -0.62 0.013 9.9 0.82 0.89 Off:On Shore
[0128] Table 10. Reprogramming differentially methylated regions (R-DMRs) and the DMRd that distinguish iPS cells from ES cells, overlap with cancer-specific differentially methylated regions (C-DMRs).
Figure imgf000200_0001
* FDR cutoff of 0.05.
** Absolute area cutoff of 10.0.
P values based on 10,000 permutations. Random values are averages over all 10,000 iterations.
[0129] Table 11. Primer sequences and location of CpG sites examined using bisulfite pyrosequencing.
Figure imgf000201_0001
/5Biosg = 5' biotin added
F = forward
[0130] Although the invention has been described with reference to the above example, it will be understood that modifications and variations are encompassed within the spirit and scope of the invention. Accordingly, the invention is limited only by the following claims.

Claims

What is claimed is:
1. A method of identifying an induced pluripotent stem (iPS) cell comprising:
comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of an iPS cell, wherein a similarity in methylation status is indicative of the putative cell being an iPS cell.
2. The method of claim 1, wherein the one or more nucleic acid sequences are within a gene.
3. The method of claim 1 , wherein the one or more nucleic acid sequences are upstream or downstream of a gene.
4. The method of claim 1 , wherein the one or more nucleic acid sequences are selected from the group consisting of differentially methylated region (DMR) sequences as set forth in Tables 2, 6, 7, 9, Figures 1B-1C, Figures 4C-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
5. The method of claim 1, wherein the methylation status is performed by one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequencing, single-strand conformation polymorphism (SSCP) analysis, restriction analysis, microarray technology, and proteomics.
6. A method of identifying an induced pluripotent stem (iPS) cell comprising:
comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, to a known methylation status of the one or more nucleic acid sequences of a corresponding somatic cell from which the iPS cell is induced or embryonic stem (ES) cell, wherein an alteration in methylation status is indicative of the putative cell being an iPS cell.
7. The method of claim 6, wherein the one or more nucleic acid sequences are within a gene.
8. The method of claim 6, wherein the one or more nucleic acid sequences are upstream or downstream of a gene.
9. The method of claim 6, wherein the methylation status of the one or more nucleic acid sequences of the putative iPS cell are compared to the methylation status of the one or more nucleic acid sequences of a corresponding known parental somatic cell from which the iPS cell is induced.
10. The method of claim 9, wherein the one or more nucleic acid sequences are selected from the group consisting of differentially methylated region (DMR) sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNFl 84 gene, the IGF1R gene, and any combination thereof.
11. The method of claim 6, wherein the methylation status of the one or more nucleic acid sequences of the putative iPS cell are compared to the methylation status of the one or more nucleic acid sequences of a corresponding known ES cell.
12. The method of claim 11, wherein the one or more nucleic acid sequences are selected from the group consisting of differentially methylated region (DMR) sequences as set forth in Table 6, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNFl 84 gene, the IGF1R gene, and any combination thereof.
13. The method of claim 6, wherein the alteration in methylation status is
hypomethylation.
14. The method of claim 6, wherein the alteration in methylation status is
hypermethylation.
15. The method according to claim 6, wherein the methylation status is performed by one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PGR, bisulfite pyrosequenceing, single-strand conformation polymorphism (SSCP) analysis, restriction analysis, microarray technology, and proteomics.
16. A plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in the reprogramming of a somatic cell to generate an induced pluripotent stem (iPS) cell.
17. The plurality of nucleic acid sequences of claim 16, wherein the nucleic acid sequences are selected from the group consisting of the differentially methylated region (DMR) sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene.
18. The plurality of nucleic acid sequences of claim 16, wherein the nucleic acid sequences are hypermethylated in the iPS cell as compared to the somatic cell.
19. The plurality of nucleic acid sequences of claim 16, wherein the nucleic acid sequences are hypomethylated in the iPS cell as compared to the somatic cell.
20. The plurality of nucleic acid sequences of claim 16, wherein the plurality is a microarray.
21. A plurality of nucleic acid sequences, wherein the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the methylation status of the nucleic acid sequences is altered in an induced pluripotent stem (iPS) cell as compared to an embryonic stem (ES) cell.
22. The plurality of nucleic acid sequences of claim 21 , wherein the nucleic acid sequences are selected from the group consisting of the differentially methylated region (DMR) sequences as set forth in Table 7, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBP1 gene, the ZNF184 gene, and the IGF1R gene.
23. The plurality of nucleic acid sequences of claim 21, wherein the nucleic acid sequences are hypermethylated in the iPS cell as compared to the ES cell.
24. The plurality of nucleic acid sequences of claim 21, wherein the nucleic acid sequences are hypomethylated in the iPS cell as compared to the ES cell.
25. The plurality of nucleic acid sequences of claim 21 , wherein the plurality is a microarray.
26. A method for providing a methylation map of a region of genomic DNA isolated from an induced pluripotent stem (iPS) cell, comprising:
performing comprehensive high-through array-based relative methylation (CHARM) analysis on a sample of labeled, digested genomic DNA isolated from the iPS cell, thereby providing a methylation map for the iPS cell.
27. The method of claim 26, further comprises performing one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequencing, single-strand conformation polymorphism (SSCP) analysis, and restriction analysis.
28. A method of characterizing the methylation status of the nucleic acid of an induced pluripotent stem (iPS) cell, comprising:
a) hybridizing labeled and digested nucleic acid of an iPS cell to a DNA microarray comprising at least 2000 nucleic acid sequences, with the proviso that the nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island; b) determining a pattern of methylation from the hybridizing of (a), thereby characterizing the methylation status for the iPS cell.
29. The method of claim 28, further comprising comparing the methylation status profile to a methylation profile from hybridization of the microarray with labeled and digested nucleic acid from a parental somatic cell from which the iPS is induced.
30. The method of claim 29, wherein the one or more nucleic acid sequences are selected from the group consisting of differentially methylated region (DMR) sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, and the IGF1R gene.
31. The method of claim 28, further comprising comparing the methylation profile to a methylation profile from hybridization of the microarray with labeled and digested nucleic acid from an embryonic stem (ES) cell.
32. The method of claim 31, wherein the one or more nucleic acid sequences are selected from the group consisting of differentially methylated region (DMR) sequences as set forth in Table 7, Figures 4C-4G, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, and the IGF1R gene.
33. A method of generating an induced pluripotent stem (iPS) cell comprising:
contacting a somatic cell with an agent that alters the methylation status of one or more nucleic acid sequences of the somatic cell, the one or more nucleic acid sequences being outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 2 kb in distance from a CpG island, and wherein the nucleic acid sequences are differentially methylated in reprogrammed somatic cells as compared with parent somatic cells, thereby generating an induced pluripotent stem (iPS) cell.
34. The method of claim 33, wherein the one or more nucleic acid sequences are selected from the group consisting of differentially methylated region (DMR) sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
35. The method of claim 33, further comprising detecting the methylation status profile of the one or more nucleic acid sequences of the induced iPS.
36. The method or claim 33, further comprising comparing the methylation status profile to a methylation status profile of the one or more nucleic acid sequences of a parental somatic cell from which the iPS is induced.
37. The method of claim 36, wherein the one or more nucleic acid sequences are selected from the group consisting of differentially methylated region (DMR) sequences as set forth in Tables 2, 6, 9, Figures 1B-1C, Figures 4A-4G, the BMP7 gene, the GSC gene, the TBX3 gene, the HOXD3 gene, the PTPRT gene, the POU3F4 gene, the AZBPl gene, the ZNF184 gene, the IGF1R gene, and any combination thereof.
38. The method of claim 33, wherein the agent is a nuclear reprogramming factor.
39. The method of claim 38, wherein the nuclear reprogramming factor is a nucleic acid encoding a SOX family gene, a KLF family gene, a MYC family gene, SALL4, OCT4, NANOG, LIN28, or the expression product thereof.
40. The method of claim 38, wherein the nuclear reprogramming factor is one or more of POU5F1, OCT4, SOX2, KLF4, or C-MYC.
41. An induced pluripotent stem (iPS) cell produced using the method of claim 33.
42. A population of induced pluripotent stem (iPS) cells produced using the method of claim 33.
43. A method of treating a subject comprising:
a) obtaining a somatic cell from a subject;
b) reprogramming the somatic cell into an induced pluripotent stem (iPS) cell using the method of claim 33;
c) cultoing the pluripotent stem (iPS) cell to differentiate the cell into a desired cell type suitable for treating a condition; and
d) introducing into the subject the differentiated cell, thereby treating the condition.
44. The method of claim 1, wherein methylation is determined as methylation density.
45. The method of claim 44, wherein methylation density is about 0.3 to 0.6.
46. A method of identifying an induced pluripotent stem (iPS) cell comprising:
comparing the methylation status of one or more nucleic acid sequences of a putative iPS cell, with the proviso that the one or more nucleic acid sequences are outside of a promoter region of a gene and outside of a CpG island, and wherein the methylation status is determined as methylation density of about 0.3 to 0.6.
47. The method of claim 33, wherein methylation is determined as methylation density.
48. The method of claim 47, wherein methylation density is about 0.3 to 0.6.
49. A method of generating an induced pluripotent stem (iPS) cell comprising:
contacting a somatic cell with an agent that alters the methylation status of one or more nucleic acid sequences of the somatic cell, the one or more nucleic acid sequences being outside of a promoter region of a gene and outside of a CpG island, and wherein the nucleic acid sequences are up to about 0.3 to 0.6 in methylation density, thereby generating an induced pluripotent stem (iPS) cell.
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Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012037456A1 (en) * 2010-09-17 2012-03-22 President And Fellows Of Harvard College Functional genomics assay for characterizing pluripotent stem cell utility and safety
WO2014194884A3 (en) * 2013-06-07 2015-04-09 Klaus Olek Method for locating nucleic acids, nucleic acids, and complementary oligonucleotides for identifying biological material, and method for identifying biological material and kit
US10626445B2 (en) 2013-06-10 2020-04-21 President And Fellows Of Harvard College Early developmental genomic assay for characterizing pluripotent stem cell utility and safety
US11085067B2 (en) 2013-06-10 2021-08-10 President And Fellows Of Harvard College Early developmental genomic assay for characterizing pluripotent stem cell utility and safety
CN105233290A (en) * 2015-07-31 2016-01-13 北京泱深生物信息技术有限公司 C22orf26 gene and application of expression product of C22orf26 gene to preparing Parkinson diagnosis and treatment preparation
CN105233290B (en) * 2015-07-31 2018-02-09 北京泱深生物信息技术有限公司 The application of C22orf26 genes and its expression product in Parkinson's diagnosis and treatment reagent is prepared
CN105238790A (en) * 2015-11-26 2016-01-13 河南省农业科学院畜牧兽医研究所 Promoters for regulating pig AEBP1 and construction method, and transfection carriers and construction method and application
CN105238790B (en) * 2015-11-26 2018-01-30 河南省农业科学院畜牧兽医研究所 A kind of regulation and control pig AEBP1 promoter and construction method, transfection carrier and construction method, application

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