The functional annotations used were as follows (All coordinates were relative to the hg19 version of the human genome): (1) CpG islands obtained from the UCSC table browser. (2) Exons, genes, introns, transcription-start-sites (TSSs) and transcription end sites (TESs), 2Kb windows around TSSs and 2Kb windows around TESs based on the GENCODEv10 annotation (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGencodeV10/) restricted to long transcripts. (3) Expressed and non-expressed genes, their TSSs and TESs. Genes were classified into the expressed or non-expressed class based on their RNA-seq expression levels in the H1-ESC (Fig. 4c) and GM12878 (Extended Data 2b) cell-lines. A gaussian mixture model with 2 components was fit on expression levels of all genes to obtain thresholds for the two classes. (4) Zinc finger genes (obtained by searching the ENSEMBL annotation for genes with gene names starting with ZNF). (5) Transcription factor binding sites (TFBS) based on ENCODE ChIP-seq data in the H1-ESC cell-line. The uniformly processed TF ChIP-seq peak locations were downloaded from the ENCODE repository: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/. We also computed % TF binding site coverage for states calls in the GM12878 and K562 cell-lines using
