To characterize the biological properties of multi-tissue cis-eQTLs, we annotated discovered eVariants using chromatin state predictions from 128 cell types sampled by the Roadmap Epigenomics project2. eVariants were enriched in predicted promoter and enhancer states across all Roadmap cell types (Fig. 3a). However, the eVariants exhibited significantly greater enrichment in promoters and enhancers from matched tissues (Wilcoxon rank sum test, P ≤ 9.3 ×10−4, Extended Data Table 4), illustrating consistent patterns of tissue specificity for cis-regulatory elements and eQTLs (Fig. 3a). Furthermore, eQTL activity was significantly more likely to be shared across pairs of tissues when the eVariant overlaps the same chromatin state in both tissues (Wilcoxon rank sum test, P ≤ 5.0×10−5, Fig. 3b).
