Smoking behaviors, including amount smoked, smoking cessation, and tobacco-related diseases, are altered by the rate of nicotine clearance. Nicotine clearance can be estimated using the nicotine metabolite ratio (NMR) (ratio of 3’hydroxycotinine/cotinine), but only in current smokers. Advancing the genomics of this highly heritable biomarker of CYP2A6, the main metabolic enzyme for nicotine, will also enable investigation of never- and former- smokers. We performed the largest genome-wide association study (GWAS) to date of the NMR in European ancestry current smokers (n=5185), found 1255 genome-wide significant variants, and replicated the chromosome 19 locus. Fine-mapping of chromosome 19 revealed 13 putatively causal variants, with nine of these being highly putatively causal and mapping to
CYP2A6
,
MAP3K10
,
ADCK4
, and
CYP2B6
. We also identified a putatively causal variant on chromosome 4 mapping to
TMPRSS11E
and demonstrated an association between
TMPRSS11E
variation and a UGT2B17 activity phenotype. Together the 14 putatively causal SNPs explained ~38% of NMR variation, a substantial increase from the ~20–30% previously explained. Our additional GWASs of nicotine intake biomarkers showed that cotinine and smoking intensity (cotinine/cigarettes per day (CPD)) shared chromosome 19 and 4 loci with the NMR, and that cotinine and a more accurate biomarker, cotinine+3’hydroxycotinine, shared a chromosome 15 locus near
CHRNA5
with CPD and Pack-Years (i.e. cumulative exposure). Understanding the genetic factors influencing smoking-related traits facilitates epidemiological studies of smoking and disease, as well as assists in optimizing smoking cessation support, which in turn will reduce the enormous personal and societal costs associated with smoking.