Smokers with low FKBP5 mRNA expression had lower cortisol levels than those with high FKBP5 expression (main effect for group: F(1,118)=9.46; P<0.005 and group-by-time interaction:F(1,184)=2.9; P<0.05). Consistent with these findings, FKBP5 mRNA expression was associated with cortisol at baseline before the initiation of nicotine administration (r2= 0.20, p =0.001), but not at the end of the study (Figure 3). The cortisol effects were independent of genotype, array number, cigarette pack-years, and RNA Integrity Number, which were entered into the models in post-hoc analyses. FKBP5 genotype was not associated with cortisol levels. The RNA-cortisol relationship was confirmed by RT-PCR (Supplementary Figure S1).