By the analysis of H3K27ac enrichment in hormone-deprived MCF-7 cells, we defined a set of Super Enhancers (SEs) occupied by apoERa, including one mapped in proximity of the DSCAM-AS1 lncRNA gene.This represents a paradigm of apoERa activity since its expression is largely unaffected by estrogenic treatment,despite the fact that E2 increases ERa binding on DSCAM-AS1 promoter. We validated the enrichment of apoERa, p300, GATA3, FoxM1 and CTCF at both DSCAM-AS1 TSS and at its associated SE by ChIP-qPCR. Furthermore, by analyzing MCF-7 ChIA-PET data and by 3C assays, we confirmed long range chromatin interaction between the SE and the DSCAM-AS1 TSS. Interestingly, CTCF and p300 binding showed an enrichment in hormone-depleted medium and in the presence of ERa, elucidating the dynamics of the estrogen-independent regulation of DSCAM-AS1 expression.The most significant down-regulated lncRNAs were RP11-68L18.1, MIR9-3HG, and LINC01016, whereas NKILA, AC144831.1, and LINC00657 were the most significant up-regulated lncRNAs