For the initial candidate gene study, SNPs were chosen to cover physical regions as uniformly as possible, while denser coverage was used for SNPs within exons and near candidate gene promoter regions. Quality control measures are described elsewhere (Saccone et al. 2007; Saccone et al. 2009) and include reliability of genotype-calls, Hardy-Weinberg equilibrium > 0.01, and 95% genotyping call-rate. Because of the additional statistical power-requirements for gene-environment analyses, we eliminated SNPs from analysis if they exhibited a minor allele frequency (MAF) of 4% or less. This resulted in a total of 3369 SNPs tested in this report. These SNPs cover a total of 348 genes.
