Fig. 3: Selection and classification of cCREs to build the registry of candidate cis-regulatory elements.

We began by filtering and clustering DNase peaks to create representative DHSs (rDHSs). We then selected those rDHSs with high DNase signal (maximal Z-score or max-Z across all biosamples with data; see Methods) and high signal for at least one other assay (H3K4me3, H3K27ac or CTCF) to be cCREs. In total, we defined 926,535 cCREs in human and 339,815 cCREs in mouse. On the basis of combinations of signal and genomic context, we classified cCREs into one of these groups: PLS, pELS, dELS, DNase–H3K4me3, or CTCF-only, and their counts are indicated (k, thousand; M, million). Human and mouse silhouettes were adapted under Public Domain Mark 1.0 and Public Domain Dedication 1.0 licenses, respectively.