Five of these were strong cross-tissue eQTLs in GTEx (for ATG10, ATP6AP1L, and RPS23, all associated with rs7707921, and C5orf35 (also known as SETD9) and rs889312; P < 1 × 10− 5 in at least 19 tissues with concordant directionality) and maintain their regulatory capacity in breast cancer cells. Here, SETD9 is linked to breast carcinoma.