The pair-wise D' values of 32 SNPs within CHRNA5/A3/B4 were determined using the Haploview program [30]. On the basis of the block definition proposed by Gabriel et al. [31], we found three discernible haplotype blocks within the cluster in the total sample (Figure 1). The first block, with a size of about 10 kb, contains four SNPs between rs169669920 and rs7163730; the second block, with a size of 46 kb, contains 12 SNPs; the third block, with a size of 23 kb, contains only two SNPs — rs11072793 and rs11072794. Considering that (1) no haplotype block was detected within a genomic region of about 108 kb between rs481134 and rs6495316, and (2) the three discernible haplotype blocks did not correspond to the defined genes within this region, we decided to perform haplotype-based association analysis using a sliding window approach with a window size of three consecutive SNPs [32], as described in the following section.
