To find signals that are specific to certain groups, we tested whether any individual SNPs detected in non-EUR GWASs are conditionally independent of signals detected in EUR GWASs. We fitted an approximate joint model that includes GWS SNPs identified in EUR and non-EUR, using LD reference panels specific to each ancestry group. After excluding SNPs in strong LD (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${r}_{{\rm{LD}}}^{2}$$\end{document}rLD2 > 0.8 in either ancestry group), we found that 2, 17, 49 and 63 of the GWS SNPs detected in SAS, AFR, EAS and HIS GWASs, respectively, are conditionally independent of GWS SNPs identified in EUR GWASs (Supplementary Table 9). On average, these conditionally independent SNPs have a larger MAF and effect size in non-EUR than in EUR cohorts, which may have contributed to an increased statistical power of detection. The largest frequency difference relative to EUR was observed for rs2463169 (height-increasing G allele frequency: 23% in AFR versus 84% in EUR) within the intron of PAWR, which encodes the prostate apoptosis response-4 protein. Of note, rs2463169 is located within the 12q21.2
