We are interested in the power to filter a SNP from consideration when the association is detected in one population but has no effect in the second population. This power depends on the allele frequency of the SNP in the second population and can be estimated by simulating the second population under an odds ratio of 1 and specified allele frequencies for the SNP, assuming Hardy-Weinberg equilibrium. It is important to note that no adjustment for LD is needed here; we are evaluating our ability to rule out the specific, genotyped SNP. The simulated data is then analyzed together with the real data at the SNP of interest for the first population, using the logistic regression approach above, and power to detect cross-population heterogeneity is estimated by the proportion of replicates which achieve a given significance level.
