genetic trait-associated SNPs. If a specific eQTL from the full set was not tested in the meta-analysis conducted on the pruned set, this eQTL was assigned the higher FDR value corresponding to the next eQTL tested in the pruned set. We used an FDR threshold of 0.05 (corresponding to P<8.3×10−6) to declare a trans-eQTL effect significant. Similarly, in the eQTS analysis, we used a set of 1,873 uncorrelated (Pearson R2<0.1) PGSs and performed an analogous FDR calculation. The FDR threshold for eQTS corresponded to P<3.02×10−6. We analyzed only SNP/PGS–gene pairs tested in at least two cohorts.
