Block structure and interSNP correlations in the NYS were similar to those available from HapMap. Due to the large differences in allele frequencies, LD between SNPs was examined separately in African Americans and Caucasians. The patterns of LD and correlations are shown in Figure 1. In CHRNA6, rs892413 and rs1072003 are in high LD with an r2 of 0.75 in Caucasians and r2 of 0.39 in African Americans. These SNPs also form a weak block with rs2304297. Although rs35389610 is located between rs2304297 and rs89214, it is only polymorphic in Caucasians and so rare that the estimated r2 between it and any other SNP is effectively 0. SNPs rs7004381 and rs4950 upstream of CHRNB3 also showed high LD with r2 of 0.80 in Caucasians and 0.47 in African Americans. All SNPs were in Hardy-Weinberg Equilibrium (HWE) within self-reported ethnic groups.
