Figure 3. Functional characterization of cis-eQTLs.

a, Enrichment (x-axis) of eVariants in cis-regulatory elements (CREs) across 128 Roadmap Epigenomics project cell types, for each GTEx discovery tissue (y-axis). Enrichment estimated by comparing to random MAF- and distance-matched variants. Stronger enrichment was observed in matched tissues (coloured dots) than in unmatched tissues (box plots). b, Proportion of eQTLs shared between two tissues (m > 0.9) if the eVariant overlaps the same Roadmap annotation in both tissues (y-axis) or different annotations (x-axis). Points represent the mean across all tissues, coloured by the discovery tissue. c, Enrichment of eVariants (y-axis) in tissue-matched enhancers (black) and promoters (grey) for the first four conditionally independent eQTLs discovered for each eGene (x-axis). d, Proportion of eVariants overlapping tissue-matched DNase I hypersensitive sites (DHS; y-axis) as a function of the probability that a variant is causal (x-axis), coloured by the eQTL discovery tissue. e, Normalized absolute eQTL effect size (x-axis) for each eVariant annotation class (y-axis). f, Median (line) and interquartile range (shading) of normalized absolute eQTL effect size (y-axis), as a function of the number of tissues in which the eGene is expressed (x-axis). Box plots depict the interquartile range (IQR), whiskers depict 1.5× IQR. OR, odds ratio.