We used SMR37 as our primary method to identify SNPs which might mediate association with schizophrenia through effects on gene expression. The significance for SMR is set at the Bonferroni corrected threshold of 0.05/M where M is the number of genes with significant eQTLs tested for a given tissue. Significant SMR associations imply colocalization of the schizophrenia associations with eQTL. We applied the HEIDI test37 to filter out SMR associations (PHEIDI < 0.01) due to linkage disequilibrium between SCZ-associated variants and eQTLs. cis-eQTL summary data were from three studies: fetal brain (N=120)38, adult brain (n = ~1,500)39 and blood (n = ~32,000)40. Linkage disequilibrium (LD) data required for the HEIDI test37 were estimated from the Health and Retirement Study (HRS)41 (n = 8,557). We included only genes with at least one cis-eQTL at PeQTL < 5×10−8, excluding those in MHC regions due to the complexity of this region. For blood, we included only genes with eQTLs in brain. This left 7,803 genes in blood, 10,890 genes in prefrontal cortex and 754 genes in fetal brain for analysis (see Supplementary Note
