Functional enrichment of eQTLs was assessed using chromatin state data from the Roadmap Epigenomics Project 27. The data comprised of 25 chromatin states derived from reference epigenomes from 127 cell types. We overlapped target eQTL variants separately with each chromatin state and cell type. We also overlapped 100 sets of control variants with the same annotations and derived an empirical P-value for each enrichment. This was defined as the number of control variant sets (N) that showed a higher overlap with the target annotation than the eQTL lead variants (P = N/100). The empirical P-values were further adjusted for the number of tests (25 states x 127 cell types) within each eQTL set using the Q-value 75 package in R. Annotations with a Q-value < 0.05 were considered significantly enriched. We tested two sets of eQTLs for enrichment: iPSC-specific eQTLs (N = 2,131) and non-specific eQTLs (N = 4,500).
