Using the Haplo.stats R statistics package [33], we performed haplotype-based association analysis for the three smoking-related phenotypes in both the total and male samples (Tables 3 and 4). In the total sample, we found five major haplotypes between SNPs rs16969948 in CHRNA5 and rs6495316 in the intergenic region downstream from the 5′ end of CHRNB4 that were significantly associated with SI under the additive or dominant model. Of these haplotypes, two were positively, and the remaining three were negatively, associated with SI, with P values ranging from 0.013 for the haplotype ACT, formed by rs950776-rs11072768-rs7166158, to 0.047, for the haplotype TCC, formed by rs16969948-rs481134-rs951266.
