Our CIDR genotyping included the CHRNA3 SNPs rs1317286 and rs6495308 recently reported by Berrettini et al. to be associated with cigarettes-per-day with p-values of 0.0000026 and 0.000069 respectively (Berrettini et al., 2008). With our comprehensive coverage we are thus able to make a direct comparison and confirm that their results are in line with our two distinct findings represented by rs16969968 and rs578776. In our sample, rs1317286 (primary p = 0.00034, OR = 1.28) is in the same LD bin and highly correlated (r2 = 0.975) with the slightly more significant rs16969968 (p = 0.00013, OR = 1.30), confirming that these findings coincide. We believe that rs16969968 is the best functional candidate among the correlated SNPs representing this locus, and further work to test this is underway. The second SNP rs6495308 is correlated (r2 = 0.76) with our separate significant finding at rs578776. This suggests that the signal at rs6495308 (p = 0.0019, OR = 1.29) may be an attenuation of the stronger association at rs578776 (p = 0.00011, OR = 1.34). The correlation between rs16969968 and rs6495308 is low (r2 = 0.15), again indicating that these represent two different signals.
