By requiring consistent genetic effects across the three populations, we can refine a genetic association to variants that are more likely to reflect potential functional variants. Two SNPs in bin A are the most frequently reported from previous meta-analyses of smoking behavior in European ancestry subjects: rs16969968 and rs1051730. They are highly correlated (r2=1) in European ancestry and Asian populations, but display only modest correlation in African Americans (r2=0.40) (HapMap 3 Release 2 ASW). We can leverage this difference in LD architecture to differentiate the association of heavy smoking with these two variants.
