Fig. 4 ∣. Induced heterogeneities in marginal effects across local ancestries.

a, Illustrations that different LD patterns across local ancestries can induce differential tagging between a causal SNP and a tag SNP in b or another causal SNP in c. LD strengths between the two SNPs are indicated both in the thickness of arrows and in the color shades of ‘*’ elements in LD matrices. b, Example of single causal SNP with no heterogeneity. Causal effects are the same across local ancestries, and the estimated marginal effects at causal SNP will be also very similar with sufficient sample size. However, because of differential tagging across local ancestries, the estimated marginal effects evaluated at the tag SNP are difference. c, Example of multiple causal SNPs with no heterogeneity. Causal effects for both SNPs are the same across local ancestries. In this example, the correlation between the two causal variants is higher for genotypes in African local ancestries than those in European local ancestries. Therefore, African ancestry-specific genotypes tag more effects, creating different ancestry-specific marginal effects at each causal SNP.