We evaluated the extent to which our xQTLs replicate brain eQTLs and mQTLs found in prior studies. We focused on eQTL and mQTL replication since relevant large-sample datasets are only available for these two xQTL types. Specifically, we assessed the replication rate of brain eQTLs, discovered in the CommonMind23 and Braineac24 studies, and brain mQTLs in a fetal brain study8, in our dataset using the π1 statistics25, which estimates the proportion of these eQTLs (mQTLs) that are also significant in our dataset. π1 of the eQTLs are 0.91 and 0.56 for CommonMind and Braineac, respectively, and π1 of mQTLs is 0.87 for the fetal brain study. All of these results are greater than their respective empirical null mean of 0.11 and 0.33 for eQTLs and mQTLs (p < 0.0001, one-tailed, see Supplementary Information). The lower replication rate of Braineac eQTLs compared to CommonMind eQTLs could be due to its smaller sample size. Also, the Braineac eQTLs were based on false discovery rate (FDR) correction whereas CommonMind eQTLs were defined using Bonferroni correction, and stronger associations captured by more stringent correction
