Adjusting for the overall coverage and variability of each state, we then studied differences in the relative fraction of the genome annotated to each chromatin state between cell types (Fig. 5b, Extended Data 5b, S6c-e). Immune cells show a consistent and previously unrecognized depletion of active and bivalent promoters (TssA, TssBiv) and weakly transcribed states (TxWk), which may be related to their capacity to generate sub-lineages, replicate, and enter quiescence (reversible G0 phase). ESCs and iPSCs show enrichment of TssBiv, consistent with previous studies57, and a depletion of ReprPCWk (defined by weak H3K27me3), possibly due to restriction of H3K27me3-establishing Polycomb proteins to promoter regions. Surprisingly, IMR90 fetal lung fibroblasts, which were previously used as a somatic reference cell type58 are in fact a strong outlier in multiple ways, showing higher levels of Het, ReprPC and EnhG, and a depletion of Quies chromatin states.
