Stratified analyses by breast cancer subtype revealed that the association of rs12468790 (INHBB) with breast cancer was stronger for ER-negative (OR [95% CI] per minor allele increase = 0.93 [0.91–0.95], P = 1.5 × 10− 9) than ER-positive tumors (OR [95% CI] = 0.98 [0.96–0.99], P = 3.8 × 10− 3). Here, ESR1 is linked to breast cancer.