Our conclusion is that among these genotyped SNPs, rs16969968 should be prioritized for follow-up because it exhibits the strongest evidence for a comparable odds ratio in both the EA and AA groups; the other 6 SNPs that survived filtering also remain as potential SNPs of interest, while three have been ruled out. This similar odds ratio at rs16969968 is observed despite the fact that the A allele has very different allele frequencies in EAs and AAs (0.33 versus 0.05 respectively). In contrast, the flanking SNP rs951266 has a similar level of allele frequency discrepancy (0.33 versus 0.08, which leads to a reduction in r2 between it and rs16969968 in the AA sample (Figure 3)), but has an odds ratio of 0.95 in the AAs versus 0.68 in the EAs. Thus a discrepancy in allele frequency on its own does not indicate whether the odds ratio for the allele effect will be similar or not in the two groups. By including a "population" covariate in the overall model, we can adjust for differences in population rates, and then test for the significance of the population-by-genotype interaction.
