Consortium. Only the genes with at least one cis-eQTL at PeQTL < 5 × 10−8 (one of the basic assumptions of SMR) in both Brain-eMeta and eQTLGen were included. We further excluded genes in the major histocompatibility complex (MHC) region because of the complexity of this region, leaving 3943 genes for analysis. We identified 61 genes associated with the traits using the brain eQTL data, 41 of which (67.2%) were in common with a larger set of genes (97) identified using the eQTLGen blood eQTL data (Fig. 5b). Despite the heterogeneity between the two eQTL data sets (Brain-eMeta was based on RNA-Seq and eQTLGen was based on microarray), the strong overlap between the two sets of results is consistent with the strong correlation of eQTL effects between brain and blood estimated above. For SCZ, 19 out of the 24 genes identified using brain eQTL data were replicated using blood eQTL data with an additional 27 genes identified only in the blood data because of its larger sample size (Supplementary Fig. 23). We repeated the SMR analysis using blood eQTL data from the Consortium for the Architecture of Gene Expression (CAGE; n = 2765)9 and observed similar results (Fig. 5b) although
