the Million Veteran Project (MVP), there were about 57,000 AA samples, however, the EA population consisted of > 209,000 participants (Kranzler et al., 2019). Second, people of African ancestry have more genetic variants and a faster decay of linkage disequilibrium (LD) with an increase in physical distance (Altshuler et al., 2015). Therefore, more independent tagging variants are needed to fully cover the entire genome in AA as compared with other populations. As a result, the traditional genome-wide threshold, 5 x 10E-8, may not be appropriate. Third, the proportion of African and European ancestries differ among AA populations in the U.S. (Dick, Barr, Guy, Nasim, & Scott, 2017). In genetic studies, this admixture is usually modeled by including ancestral principal components (PCs) as covariates in analysis. However, these PCs are a genome-wide adjustment and may result in over- or under- adjustment in some chromosomal regions due to different proportions of local (i.e., region-specific) admixture.
