Association testing was done in stages. First, we conducted genome-wide association meta-analysis. Variants with p-values less than the genome-wide significance threshold of 5×10 −8 were deemed statistically significant. Loci were defined as 1 million basepair windows surrounding a “sentinel” (most significant) variant in the locus. Overlapping or adjacent loci were combined into a single locus. Conditional analysis and fine mapping was then performed within each locus. We attempted to replicate one very rare variant (rs36015615 in STARD3 associated with CigDay; see results and Table 1) that was available in two other exome chip consortia. These were the CHD Exome+ Consortium (N=17,789) and the Consortium for Genetics of Smoking Behaviour (N=28,583). Both consortia defined their phenotypes, including cigarettes per day similarly, as the usual number of cigarettes smoked in a day corrected for sex, age, principal components (and/or genetic relatedness, as appropriate), and inverse-normalized prior to association analysis.
