In European and Asian populations, rs16969968 and rs1051730 are highly correlated. However, due to the different LD structure in African Americans, rs16969968 and rs1051730 represent two different sub-bins (r2=0.40 in HapMap 3 Release 2 ASW). In our analysis of African Americans, there is stronger evidence of association between the dichotomous phenotype heavy smoking versus light smoking and the sub-bin tagged by rs16969968 (OR=1.62, 95% C.I.=1.21–2.17, p=1.1×10−3), compared to the sub-bin tagged by rs1051730 (OR=1.15, 95%C.I.=1.03–1.28, p=1.1×10−2). This stronger finding is seen despite the lower minor allele frequency (MAF) and much smaller available sample and for rs16969968 (MAF =0.06, 667 cases/1140 controls) compared to that for rs1051730 (MAF=0.12, 1712 cases/5640 controls).
