To test whether additional loci contribute to dichotomous smoking quantity over and above the effect of rs16969968, we included both locus 1 and each of the other loci in the logistic regression models adjusting for sex and age, with and without a SNP×SNP interaction term. For lung cancer and COPD the models also included categorical cigarettes-per-day as an unordered covariate. These results were then meta-analyzed as described above. The SNP×SNP interaction term was never significant in the meta-analysis (p>0.3), so we report results from the joint models without interactions. To allow comparison between single-SNP and joint results on comparable data, for each locus pair we also repeated the univariate single-SNP meta-analyses on the subset of datasets that had genotypes available at both loci. For dichotomous smoking quantity we also tabulated pair-wise joint genotype by case status counts for locus 1 (rs16969968) versus each of the other three loci across the contributing datasets that had both loci.
