and 400 expected in the absence of any inflation of estimated effect sizes), and 142 replicated with P<0.05 (compared with 21 expected by chance, and 210 expected in the absence of effect size inflation; Supplementary Table 5). These analyses (particularly the directional consistency) shows that most of the loci represent true associations, but also shows that there is a modest inflation in the effect size estimates, due to stratification and/or the winner’s curse. To distinguish between these possibilities, we repeated this analysis, substituting for the family-based samples a random set of studies with similar total effective sample size. The number of replicating loci was only slightly lower in the family-based cohorts than in the random samples (Supplementary Table 5, 12–17 fewer replications attributable to stratification at different P-value thresholds). This indicates that most of the modest inflation in effect estimates is due to the winner’s curse, that a small amount of inflation is due to residual stratification, and that few (upper limit ~15–25; Supplementary Note and Supplementary Table 5) if any of the loci that reach genome-wide significance after single GC correction are likely to be complete false positives due to stratification (that is, no real association whatsoever with height).
