For our example study, we therefore sampled from the above probabilities to simulate samples of 344 cases and 239 controls assuming minor allele frequencies of 0.3 down to 0.05, corresponding to the two extremes for power: where the allele frequency in the second population is similar to the EA frequency, and where it is notably lower as we see at rs16969968. Each simulated AA dataset was then combined with the real EA data at rs16969968. For simplicity, we used only the data at rs16969968, because this will estimate power to detect cross-population heterogeneity not only at rs16969968 itself, but also at the other SNPs because they have very high r2 with rs16969968 in the EA sample. For each allele frequency, we generated 1000 replicates and recorded the proportion of replicates for which the cross-population heterogeneity was detected (i.e. the population*genotype term was significant) at fixed significance levels.
