a simulated 300,000 GWAS with a single typed causal variant that explained 0.001 variance of the trait (high effect). We believe this scenario is both realistic and consistent with the GWAS assumptions of COLOC. We then empirically identified the statistical threshold for COLOC and TWAS that would yield a 5% false discovery rate: co-localization statistic PP4 > 0.17 for COLOC, and P<0.05 for TWAS. We note that this empirical COLOC threshold is much less stringent than PP4>0.8 used in the COLOC paper (PP4>0.8 would yield lower power for COLOC in our simulations). These thresholds were subsequently to evaluate the power to detect an expression-trait association in simulations with a true effect (Supplementary Figures S10, 12). The reported power is for a single locus and we did not attempt to quantify genome/transcriptome-wide significance.
