Following the MR analysis, co-localization analysis was performed on the MR findings that passed the suggestive threshold to determine whether the eQTL and trait shared the same underlying signal. We ran co-localization28 using both the default parameters (p1 = p2 = 10−4 and p12 = 10−5) and parameters based on the number of SNPs in the region (p1 = p2 = 1/(number of SNPs in the region) and p12 = p1 / 10). We considered the traits to co-localize if either of the parameter runs yielded PP4 > 0.7. In addition, a systematic co-localization analysis was performed to compare findings between Cortex-EUR eQTLs and other existing cortex eQTL datasets (Supplementary Note).
