As defined by GTEx13, an “eGene” is a gene with at least one significant eSNP after strict correction for multiple marker testing for that gene. There were 8,427 eGenes at FDR ≤ 5%, or 18 eGenes discovered per sample, consistent with a prediction from GTEx. We examined the enrichment of max-eQTLs (defined as the most significant eSNP per gene, if any) in predicted enhancer sequences derived from the Roadmap Epigenomics Consortium and ENCODE across 98 human tissues and cell lines14. Cis-eQTLs were enriched for enhancer sequences present in brain tissues (Kolmogorov-Smirnov (KS) test versus non-brain: D = 1, P = 4.5 × 10−6), and the strongest enrichment is observed in DLPFC enhancers (Z = 9.5) (Fig. 1C).
