Alterations affecting SWI/SNF-encoding genes ARID1A, SMARCA4 and PBRM1 were more common in adenocarcinomas, whereas ESCCs contained more frequent alterations in histone-modifying factors KDM6A (UTX), KMT2D (MLL2) and KMT2C (MLL3). Here, KDM6A is linked to adenocarcinoma.