In the leave-one-out cross-validation analyses, the replication rate was significantly higher than expected by chance (Table 3). In CC, 18 of 173 tested SNPs across all leave-one out analyses replicated in the left out testing sets (permutation P=0.001) and the proportion of SNPs with the same direction of effect was 59.5% (sign test P=0.005). Of 315 tested SNPs in FS, 43 SNPs replicated (permutation P<0.001) and 77.8% had the same direction of effect (sign test P<0.001). Supplemental Figure S2 displays Manhattan plots of the training set meta-analyses conducted after leaving out each sample.
