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The phenotype data on the BXD mouse recombinant inbred lines were downloaded from Nervenet (http://www.nervenet.org/main/databases.html).html

Genotypes for the SNPs represented on the Affymetrix GeneChip® Human Mapping 100 K and 500 K Array Sets of the CEU and YRI cell lines were downloaded from release 22 on the International HapMap project website (www.hapmap.org).hapmap.org

Pharmacological profiles for 24 anticancer drugs across 504 cell lines were downloaded from www.broadinstitute.org/ccle/data.org/ccle/data

Respective ENCODE ChIP-seq datasets for both human and mouse ES cell lines were downloaded (from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC and http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC).ucsc.edu/goldenPath/mm9/encodeDCC

Whole genomic sequencing (125 bp paired-end) reads from three separate Oregon-R lines were downloaded from NCBI (SRX671605, SRX671606, SRX671607).

RNAPII as well as the histone modification data for H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me1, H3K27ac, H3K27me3, H3K36me3, H4k20me1 in all the three cell lines were downloaded from 'Broad Histone' tracks [ 34, 37, 51] in the UCSC browser as mapped reads.

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MBD4 ChIP-sequencing data sets in the hepatocellular carcinoma HepG2 cell line were downloaded from the ENCODE portal (GSE32465; encodeproject.org/ENCODE).org/ENCODE

DNase-seq data for DNase hypersensitivity and ChIP-seq data for 9 modified histones and 45 transcription factors in the K562 cell line were downloaded from UCSC (http://genome.ucsc.edu/encode/dataMatrix/encodeDataMatrixHuman.html).html

The ZIP file will be downloaded.

RRBS DNA methylation data from human H1 cell line was downloaded from Gene Expression Omnibus (GEO accession numbers: GSM621705).

Expression response data following decitabine treatment on the MCF-7 breast cancer cell line was downloaded from the BROAD Institute Connectivity Map [ 22].

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