Rs16969968 is non-synonymous, functional, and a strong candidate to be a causal allele. It remains unclear what biologically causal variant might explain a potential “second” distinct locus, and we are unable to fully exclude the possibility that a single causal variant underlies all observed signals. Interestingly, our evidence for multiple common nicotine dependence risk alleles in the same gene region is similar to other recent examples of multiple independent loci for other common diseases [37, 38].