Gene-based collapsing tests using MAF < 0.01 variants, did not identify any associated genes at the pre-specified P < 8 × 10−7 threshold. Of the top four gene associations, three were novel (CHRNA2, MMP17, and CRCP) and one was known (CHRNA5), and had P < 7 × 10−4, with CPD and/or pack-years (Supp. Table 6). Analyses conditional on the variant with the smallest P-value in the gene, revealed the associations at CHRNA2, MMP17 and CRCP were due to more than one rare variant (conditional P < 0.05; Supp. Table 6). In contrast, the CHRNA5 gene association was attributable to a single variant (rs2229961).
