Changing focus to minor allele frequencies, it is possible that, regardless of the reported OR, genotyped marker SNPs with lower MAFs are more efficient in tagging low frequency causal variants. If that were the case, patterns of replicability may change as a function of the MAF of associated SNPs. Nevertheless, we observed similar rates of effective replicability across all the frequency spectrum of disease-associated SNPs, with no drastic decrease for markers of increasingly smaller MAFs (Figure 6).
