For the CHRNB3-A6 region, we examined a rather larger segment of the genome upstream of the gene cluster. This was done in order to include several upstream SNPs that have previously been shown to exhibit associations with nicotine dependence or cocaine dependence [17]. Fig 1C shows a regional plot of Tajima’s D values across the sliding windows in the CHRNB3-A6 region. In AFR, there were several windows with extreme Tajima’s D values upstream of CHRNB3 and in the intergenic region between CHRNB3 and CHRNA6. Among the three populations tested, none showed a significant increase in the number of windows with extreme Tajima’s D values when compared to the permutations. The concentration of windows with extreme Tajima’s D values upstream of CHRNB3 is noteworthy in the context of risk for nicotine addiction. Of note, a recent genome-wide association study found that a SNP in this region, rs1451240, was associated with reduced risk for nicotine dependence, measured using the Fagerstrom Test for Nicotine Dependence (FTND) [18]. The LD bin tagged by rs1451240 spans ~66 kb and several other alleles of SNPs in
