Percentage variance explained by each genome-wide significant SNP was determined based on the final combined discovery data set (Extended Data Fig. 6a) or the discovery combined with the replication samples (Table 1) after correction for covariates using the following equation: Rg∣c2/(1-Rc2)=(t2/((n-k-1)+t2))∗100 where the t-statistic is calculated as the beta coefficient for a given SNP from the regression model (controlling for covariates) divided by the standard error of the beta estimate, and where n is the total number of subjects and k is the total number of covariates included in the model (k = 10) (ref. 40). R2g|c is the variance explained by the variant controlling for covariates and R2c is the variance explained by the covariates alone. R2g|c/(1 − R2c) gives the variance explained by the genetic variant after accounting for covariate effects. The total variance explained by the GWAS (Extended Data Fig. 11b, c) was calculated by first linkage disequilibrium pruning the results without regard to significance (pruning parameters in PLINK:– –indep-pairwise 1000kb 25 0.1). The t-statistics of the regression coefficients from the pruned results are then corrected for
