For GWS regions that were identified, all genotyped and imputed variants within that region that had a missing rate <0.05, Hardy-Weinberg P-values >0.0001, and MAF >3% were tested using the same model as in the admixture mapping, except the global African ancestry index was replaced by PCs (the first four PCs in COGA and the first three PCs in other samples as in the original studies (Lai, Wetherill, Bertelsen, et al., 2019; Lai, Wetherill, Kapoor, et al., 2019)) to adjust for population stratification among AA. RVTESTS (Zhan et al., 2016) was used to perform association tests within each cohort separately, then results from each cohort were meta-analyzed using METAL (Willer et al., 2010). The significance threshold was determined by the estimated effective number of tests using the R package matSpDlite (Li & Ji, 2005; Nyholt, 2004), which decomposes the LD between variants to arrive at the approximate number of independent variants.
