We next linked Cortex-EUR cis-eQTLs to variants associated with brain-related traits and diseases. We determined the linkage-disequilibrium (LD) overlap between cis-eQTLs and GWAS SNPs, which indicated that primary eQTLs were 2.6-fold more likely to be in LD with a GWAS SNP compared with non-primary eQTLs (Fisher’s exact test, P = 7.4 × 10−125; Supplementary Note and Supplementary Table 10). To more formally test whether there was evidence for sharing the same genetic effect between cis-eQTLs and 31 neurological traits, we conducted MR using the Wald ratio method and co-localization analyses (Supplementary Table 11). Among the 359,763 Wald ratios tested across 11,270 genes, 1,531 Wald ratios for 1,088 genes passed a suggestive P-value threshold (P < 5 × 10−5; Supplementary Table 12). Of the cis-eQTL instruments from these findings, 294 were also cell-type ieQTLs. There were 549 significant Wald ratios that passed Bonferroni’s correction (P < 1.43 × 10−7), from which 186 also co-localized between the eQTL and GWAS traits when using coloc28 (posterior probability for co-localization of significant signals PP4 > 0.7; Fig. 5a and Supplementary Fig. 21), confirming that
