Hence, our study utilized large-scale genomic experiments such as ATAC-Seq and H3K27ac ChIP-Seq, as well as FOXA1 and GATA3 ChIP-Seq and Hi-C combined with RNA-Seq to construct a comprehensive molecular map of luminal and basal BLCA in both cell line models as well as patient tumors. Here, FOXA1 is linked to bladder transitional cell carcinoma.