Sample sizes for the four smoking phenotype analyses (i.e., with complete genotype and phenotype data) were n=32 389 for SI, n=16 877 for AOI, n=15 547 for CPD and n=16 215 for SC. Manhattan plots for the four smoking phenotypes after double-GC scaling are shown in Figure 1. In the entire analysis, only one SNP, rs2036527, achieved genome-wide significance for one trait, CPD (β=0.04, s.e.=0.007, P=1.84 × 10−8, I2=41.6%, Table 2; study-specific results are show in Supplementary Table 3). This variant is located 6246 bp 5′ of the CHRNA5 gene on chromosome 15q25.1. We observed multiple SNPs with P-values of 10−7 associated with CPD: rs3101457, located in intron 2 (IVS2) of C1orf100 on 1q44, and rs547843, located 63 kb 5′ of a non-coding RNA sequence (LOC503519) on 15q12. Three highly correlated SNPs (r2>0.95, YRI) in the SPOCK2 gene on 10q22.1 exhibited a P-value of 10−7 with AOI (Table 2). The most significant associations for SI and SC were observed at rs566973 (∼20 kb 3′ of CRCT1 on 1q21.3) and rs3813637 (in the 3′-untranslated region of C1orf49 on 1q25.2), respectively (data not shown).
