Table 2: ENCODE data sets and cell lines used for analysis: ChIP-Seq data for RNA Polymerase II (RNAPII), CTCF and various Histone marks, data for DNase I hypersensitive sites (DNase-Seq), methylation data from reduced representation bisulfite sequencing (methyl-RRBS) and sequencing of long polyA+ whole cell RNA (RNA-Seq). For HMEC and HSMM cells RNAPII ChIP-Seq data was not available at the time of our analyses. Datasets were generated at the Broad Institute (BROAD), Cold Spring Harbor Laboratory (CSHL), University of Washington (UW), University of Texas at Austin (UT-A), and Hudson Alpha (HA).

Factor/markPair 1Pair 2
Cell linesCell lines
K562GM12878HSMMHMEC

CTCFBROADBROADBROADBROAD
H3K27acBROADBROADBROADBROAD
H3K27me3BROADBROAD BROADBROAD
H3K36me3BROADBROADBROADBROAD
H3K4me1BROADBROADBROADBROAD
H3K4me2BROADBROADBROADBROAD
H3K4me3BROADBROADBROADBROAD
H3K9acBROADBROADBROADBROAD
H4K20me1BROADBROAD BROADBROAD
RNAPIIUT-AUT-A
DNase-SeqUWUWUWUW
Methyl-RRBSHAHAHAHA
RNA-Seq CSHLCSHLCSHLCSHL