Hypomethylation of CpG sites annotated to TNNT3 was associated with MDD case status in both cohorts (Fig. 2, cg08337959, b = − 0.52, p = 2.37 × 10–4 in cohort 1 and b = − 0.71, p = 6.46 × 10–8 in cohort 2; Supplementary Fig. 3, cg01821149 b = − 0.24, p = 7.15 × 10–4 in cohort 1 and b = − 0.27, p = 1.02 × 10–7 in cohort 2, Table 1) and these associations remained unchanged after correcting the CpG probe cg05575921 annotated to AHRR, which serves as a surrogate for smoking status. This evidence concerns the gene AHRR and major depressive disorder.