Pruning of the summary statistics to find near-independent lead SNPs (using the FUMA default settings), identified 358 lead SNPs for the down-sampled EXT-minus-23andMe, as compared to 842 in the full-sample version. (Note that the number of lead SNPs reported here for EXT differs from the 855 reported in the original study because that study used a restricted-access genetic reference panel and somewhat different settings for the pruning parameters.) Thus, down-sampling reduced the number of lead SNPs by 57.5%, which could appear problematic. However, the results of the following three checks of the concordance in coefficients (see Step 1) suggested no strong reason for concern (Figure S4). First, all the 842 lead SNPs identified in the full-data version had a consistent direction of effect, meaning the null hypothesis of near-perfect sign concordance (99%) could not be rejected (P = 1). Moreover, there was 100% sign concordance among all 130,176 SNPs with P < 1 × 10–5 (in the full-data GWAS). Second, we identified only 21 lead SNPs (out of the 842; 2.5%) for which the down-sampled coefficient fell outside the 95%
