As a foundation for integrative analysis, we learned a common set of combinatorial chromatin states40 across all 111 epigenomes, plus 16 additional epigenomes generated by the ENCODE project (127 epigenomes in total), using the core set of five histone modification marks that were common to all. We learned a 15-state model (Fig. 4a,b, Table S3a) consisting of 8 active states and 7 repressed states (Fig. 4c) that were recurrently recovered (Extended Data 2a), and showed distinct levels of DNA methylation (Fig. 4d), DNA accessibility (Fig. 4e), regulator binding (Extended Data 2b, Fig. S2), and evolutionary conservation (Fig. 4f, Fig. S3). The active states (associated with expressed genes) consist of active TSS-proximal promoter states (TssA, TssAFlnk), a transcribed state at the 5’ and 3’ end of genes showing both promoter and enhancer signatures (TxFlnk), actively-transcribed states (Tx, TxWk), enhancer states (Enh, EnhG), and a state associated with zinc finger protein genes (ZNF/Rpts). The inactive states consist of constitutive heterochromatin (Het), bivalent regulatory states (TssBiv, BivFlnk, EnhBiv), repressed Polycomb states (ReprPC, ReprPCWk), and a quiescent state (Quies) which covers on average 68%
