enhancers, weak enhancers, and CTCF binding sites, but significantly depleted in repressed regions (Fig. 1b). Identified cis-eQTL were also notably enriched within regions containing histone modifications indicative of regulatory activity (Additional file 2: Figure S3). We additionally tested for enrichment, among our high confidence cis-eQTL, of variants that we have previously found to be associated with altered DNA methylation (mQTL) in the human fetal brain [10]. Consistent with an association between DNA methylation and gene expression [20, 21], fetal brain mQTL were enriched sixfold among fetal brain cis-eQTL (P = 3.13 × 10− 19).
