We conducted MR between the Cortex-EUR eQTLs and 31 neurological traits (21 neurological disease outcomes, two quantitative traits and eight brain-volume outcomes; Supplementary Table 11). For this purpose, we used the Wald ratio method, which computes the change in disease risk per s.d. change in gene expression, explained through the cis-eQTL instrument(s) for that gene. To obtain our instruments, Cortex-EUR eQTLs at a genome-wide significant P-value threshold (P < 5 × 10−8) were selected and then LD-clumped using the ld_clump() function in the ieugwasr package v0.1.4 (ref. 98) with the default settings (10,000 kb clumping window with r2 cut-off of 0.001 using the 1000 Genomes EUR reference panel). SNP associations for each of the eQTL instruments were then looked up in the outcome GWAS. If the SNP could not be found in the outcome GWAS using the dbSNP rsid, then a proxy search was performed to extract the next closest SNP available in terms of pairwise LD, providing a minimum r2 threshold of 0.8 with the eQTL. These steps were performed using the associations() function in the ieugwasr package. To
