To assess whether SNPs detected in non-EUR were independent of signals detected in EUR, we performed another COJO analysis of ancestry groups GWAS by fitting jointly SNPs detected in EUR with those detected in each of the non-EUR GWAS meta-analyses. For each non-EUR GWAS, we performed a single-step COJO analysis only including SNPs identified in that non-EUR GWAS and for which the LD squared correlation (\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) with any of the EUR signals (marginally or conditionally GWS) is lower than 0.8 in both EUR and corresponding non-EUR data. Single-step COJO analyses were performed using the --cojo-joint option of GCTA, which does not involve model selection and simply approximates a multivariate regression model in which all selected SNPs on a chromosome are fitted jointly. LD correlations used in these filters were estimated in ancestry-matched samples of the 1000 Genomes Project (1KGP; release 3). More specifically, LD was estimated in 661 AFR, 347 HIS (referred to with the AMR label in 1KGP), 504 EAS, 503 EUR and 489 SAS 1KGP participants. We used the same LD reference samples in these analyses as for our main discovery analysis described at the beginning of the section.
