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 corresponding TF ChIP-seq data data from ENCODE which matched and supported the mnemonics and state interpretations obtained from the H1 cell-line (Fig. S2). (6) Conserved GERP elements based on 34 way placental mammalian alignments http://mendel.stanford.edu/SidowLab/downloads/gerp/ (Fig. S3). (7) Conserved non-coding GERP elements obtained by subtracting parts of the above mentioned GERP elements that overlap exons.
