For each of the seven deeply-profiled reference epigenomes (Fig. 2j) we independently learned chromatin states on observed data for all available histone marks or variants, and DNase in the reference epigenome. The same binarization and model learning procedure was followed as for the core set of 5 marks. We chose to consistently focus on a larger set of 50-states to capture the additional state distinctions afforded by using additional marks (Fig. S4). Enrichments for annotations, including some of those described above for the 15-state model, were computed using ChromHMM. The HiC domains were obtained from 106, the lamina associated domains are described below, conserved element sets were the hg19 lift-over from 72, repetitive elements are from RepeatMasker.
