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% confidence interval of the full-data estimate. Among the 130,176 SNPs, we found 2202 such outliers (1.7%). We marked these SNPs in the disseminated summary statistics, but otherwise interpret their small number as unproblematic for the comparability of the down-sampled multivariate GWAS. Third, regression analysis of the down-sampled coefficients on the full-data estimates with the 842 lead SNPs found an intercept close to zero (~0.0005, P = 0.045), a regression coefficient statistically different from but still near unity (~0.898, P = 5.24 × 10–5), and high adjusted R2 = 0.86. We found similar results for the 130,176 SNPs (reported in Figure S4). The regression results suggest the down-sampling induced some, but not marked, attenuation of the coefficients. Overall, these results demonstrate satisfactory concordance for the down-sampled multivariate coefficients.
