Using saliva and blood samples for DNA methylation analysis, low SES at age 11–15 years was found to be predictive of increased methylation of SLC6A4 at age 13–18 years, which was predictive of increased amygdala reactivity to a fearful stimulus (detected by fMRI) over the same period, and which in turn was associated with increased risk of depression at age 14–19 years for adolescents with a positive family history of depression. Here, SLC6A4 is linked to depressive disorder.