The ultimate goal of the GTEx project is to provide a framework for biological interpretation of disease-related variants. To evaluate the relevance of the discovered eQTLs in disease mapping studies, we tested the eQTLs identified in each tissue for association with disease using the Wellcome Trust Case Control Consortium (WTCCC) studies of seven complex disorders (45) (see Fig. 8A). Using eQTLs identified in whole blood, we found an enrichment for top associations with autoimmune diseases (shown as a leftward shift from the null distribution in the Q-Q plot in Fig. 8A), for Crohn’s disease, rheumatoid arthritis, and type 1 diabetes among eQTLs (P < 2.2 × 10−16 for each disease), consistent with the utility of blood and lymphoblastoid cell lines (LCLs) in trait mapping for autoimmune disorders (46, 47). In contrast to the autoimmune disorders, we found no enrichment for association (no shift in P value distribution) with bipolar disorder or type 2 diabetes among the blood eQTLs (P > 0.05) (Fig. 8A). This tissue specificity of autoimmune enrichment results suggests they are not due to the confounding effects that
