Figure 1 shows the CHRNA5-CHRNA3-CHRNB4 gene cluster at the top. The red triangle denotes the SNP rs16969968; the other triangles indicate all SNPs in HapMap correlated with it (r2 ≥ 0.8) in the CEU population sample. This figure thus indicates the "r2 bin" of 21 SNPs that, according to HapMap CEU LD patterns, are not likely to be distinguishable even after a replication study in a similar population of European descent. Figure 2 shows the HapMap r2 values among these same SNPs in the Yoruba (YRI) HapMap sample, and indicates that SNP correlations are indeed reduced in this sample. In YRI, only two small non-trivial r2 ≥ 0.8 bins remain, one composed of rs17483721, rs7181486, and rs17483929, and the other of rs7180002, rs951266, and rs1051730. The remaining polymorphic SNPs are singleton bins. One SNP, rs17486278, was not genotyped in the HapMap YRI sample, and four others were monomorphic in YRI: rs17483548, rs17405217, rs17484235, and rs16969968 (the D398N variant). The pairwise r2 for the remaining 16 SNPs is displayed.
