To elucidate 3D genome structure alteration and its possible consequences in EGFR-amplified glioblastoma, in this study, we performed a comparative analysis of Hi-C, RNA-seq, and whole-genome sequencing (WGS) on EGFR-amplified glioblastoma-derived A172 and normal astrocytes (HA1800 cell line). The gene discussed is EGFR; the disease is glioblastoma.