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We previously used a single nucleotide polymorphism (SNP) in the  CHRNA5-A3-B4  gene cluster associated with heaviness of smoking within smokers to confirm the causal effect of smoking in reducing body mass index (BMI) in a Mendelian randomisation analysis. While seeking to extend these findings in a larger sample we found that this SNP is associated with 0.74% lower body mass index (BMI) per minor allele in current smokers (95% CI -0.97 to -0.51,  P  = 2.00×10 −10 ), but also unexpectedly found that it was associated with 0.35%  higher  BMI in never smokers (95% CI +0.18 to +0.52,  P  = 6.38×10 −5 ). An interaction test confirmed that these estimates differed from each other ( P  = 4.95×10 −13 ). This difference in effects suggests the variant influences BMI both via pathways unrelated to smoking, and via the weight-reducing effects of smoking. It would therefore be essentially undetectable in an unstratified genome-wide association study of BMI, given the opposite association with BMI in never and current smokers. This demonstrates that novel associations may be obscured by hidden population sub-structure. Stratification on well-characterized environmental factors known to impact on health outcomes may therefore reveal novel genetic associations.

Stratification by Smoking Status Reveals an Association of CHRNA5-A3-B4 Genotype with Body Mass Index in Never Smokers