Peak-calling was done using MACS253 on pooled data for DHS, H3K4me1 and H3K27ac. Per cell type, peaks were regarded as significant if the peak summit fell within the upper 1 percentile of the background signal (max values in 92,604 random 1kb non-TSS non-enhancer regions). DHS regions were defined as +/−500 bp around peak summits. Since ChIP-Seq signals for H3K4me1 and H3K27ac often form bimodal peaks around enhancer sites, peak regions were defined as merged regions resulting from overlapping +/− 500 bp regions around MACS2 called peak summits.
