The 5,055 SNPs that were included for BMI replication on Metabochip included 1,909 independent SNPs (r2 < 0.1 and > 500 kb apart), of which 1,458 displayed directionally consistent effect estimates with those reported previously5. To estimate the number of Metabochip SNPs truly associated with BMI, we counted the number of SNPs with directional consistency (DC) between ref. 5 and a meta-analysis of non-overlapping samples for these 1,909 SNPs. We then calculated DC in the presence of a mixture of associated and non-associated SNPs assuming P(DC ∣ associated) = 1 and P(DC ∣ not associated) = 0.5. In this formulation, DC = R/2 + S, meaning that S = 2DC – T, in which T equals the total number of SNPs, R equals the number of SNPs not associated with BMI, and S equals the number of SNPs associated with BMI. With DC = 1,458 and T = 1,909, we estimate S to be 2DC – T = 2 × 1,458 – 1,909 = 1,007.
