A pure transmission based analysis was performed in seven cohorts for SNPs representing 416 signals of association (Supplementary Note), selected after repeating meta-analysis excluding these studies, with single GC correction. Filtering of low imputation quality SNPs in the studies was followed by inverse variance method of meta-analysis of the family based results. Because of the presence of related individuals, family based studies have lower power at a given sample size. For each study, we calculated the effective sample size (the size of a sample of unrelated individuals that would have the equivalent power; see Supplementary Note and Winkler et al. 24). Estimation of winner’s curse in our data set was performed by repeating the meta-analysis excluding either the family-based studies or excluding random sets of studies from GIANT matched by effective sample size to the family based studies. Independent genome-wide significant loci were selected from each meta-analysis. Power for replication in the excluded samples was estimated at different P-value thresholds and the deficit in replications (number of replications expected minus number observed) was calculated. The contribution of the winner’s curse
