Could our results be biased because of ascertainment in the data, data analysis or interpretation? We carefully adjusted phenotypes for systematic differences and applied thorough quality control to the SNP data (Online Methods). We show by principal component analysis (PCA) of African, Asian and European populations that all of our samples are of European ancestry (Supplementary Fig. 2a,b). We demonstrate further by PCA of European populations only that our samples show close relationship to the UK population and do not show an apparent cline across Europe (Supplementary Fig. 2c,d). We performed REML analysis by fitting the first two, four and ten eigenvectors from the European-only PCA as covariates. The results show little to no systematic difference in the estimates of the variance explained by fitting up to ten eigenvectors (Supplementary Table 1). Furthermore, we performed single-SNP association analysis between 1,286 ancestry-informative markers (AIMs) and height, and did not detect a significant inflation of the test statistic for these AIMs (Supplementary Fig. 3; P = 0.219). All these results suggest that our estimate of variance explained by all SNPs is unlikely
