Integration of genomic annotations such as chromatin state has been demonstrated to improve power for eQTL discovery8,21–23. For 26 GTEx tissues matched with cell-type specific annotations from the Roadmap Epigenomics project, we applied a Bayesian hierarchical model for eQTL discovery by incorporating variant-level genomic annotations24 that provided a substantial boost to discovery power. Inclusion of genomic annotations (enhancers, promoters and distance to the TSS) increased the total number of cis-eQTL discoveries by an average of 43% (or 1,200 genes) per tissue (Extended Data Fig. 10f), demonstrating the considerable advantage of integrating genomic annotations into eQTL mapping models.
