Fig. 6

Case studies for genetic variants related to breast cancer. The possible effects of SNPs on the expression of A MAP3K1, B FGFR2, and C CDYL2 genes are presented in the context of the 3D genome structure. Red stars are SNPs highly associated with a disease at a p-value of ≤5 × 10^− 8 affecting regulatory elements through long-range physical interactions according to dashed black arrows. Dashed gray arrows link regulatory elements, including transcription factors (blue teardrops) and their binding sites (BS, green sectors), and enhancers (orange rounded rectangles) to target genes (purple ovals). Chromatin fragments from the Hi-C data (gray double helices) annotated with their start and end coordinates are connected by solid black lines showing their order in the linear genome