Population stratification is a possible strong confounder for association studies of height and other human phenotypes19. We took several steps to ensure that the association signals for height confirmed in our study were not due to population stratification. Association tests in the NHS and PLCO datasets were corrected for residual population structure using principal component methods20; a similar analysis on the unrelated component of DGI did not change association results for the SNPs reported in Table 1 (Supplementary Table 8 online). An analysis of the FINRISK97 replication panels stratified for geographic origins within Finland did not alter the strength of the associations with height reported in Table 1 (Supplementary Table 9 online). Finally, using 279 variants known to correlate with the major axes of ancestry in European-derived populations21, we calculated a small inflation factor (λ) of 1.09 for our height meta-analysis results, suggesting that no substantial stratification is shown even by markers selected for this purpose. Taken together, these results indicate that the genetic associations with height found in our study are unlikely to be due to population stratification.
