We therefore proceeded to identify quasi-independent GWS SNPs from the multi-ancestry meta-analysis by performing a COJO analysis of our METAFE, using genotypes from around 350,000 unrelated EUR participants in the UK Biobank (UKB) as an LD reference. We identified 12,111 quasi-independent GWS SNPs, including 9,920 (82%) primary signals with a GWS marginal effect and 2,191 secondary signals that only reached GWS in a joint regression model (Supplementary Table 10). Figure 1 represents the relationship between frequency and joint effect sizes of minor alleles at these 12,111 associations. Of the GWS SNPs obtained from the non-EUR meta-analyses above that were conditionally independent of the EUR GWS SNPs, 0/2 in SAS, 5/17 in AFR, 27/49 in EAS and 27/63 in HIS were marginally significant in our METAFE (Supplementary Table 9), and 24 of those (highlighted in Fig. 2) overlapped with our list of 12,111 quasi-independent GWS SNPs.
