For alcohol dependence, per one-unit increase in genetically predicted log odds of T1D as measured by the GLIS3 cis instrument, there was a 22% decrease in odds using the secondary weighted median method only (OR = 0.78; 95% CI = 0.65–0.78; P = 0.017); this association did not persist following adjustment for multiple testing (adjusted P = 0.068). Here, GLIS3 is linked to alcohol dependence.