In summation, our data facilitate insights into the factors and experimental design criteria that affect eQTL reproducibility and may improve future eQTL studies, replicate many published but nonreplicated eQTLs (e.g. from [31]), support and extend eQTLs identified in other tissues like brain (e.g. FAM119B [53]), identify many novel reproducible liver eQTLs, show that promoters and 3′UTRs are enriched for experimentally accessible functional variation, and support or suggest numerous mechanistic links to biomedically important phenotypes. We believe that this study and others like it will be valuable to the robust discovery and fine-mapping of the genetic basis for complex human diseases.
