Supplementary Table S2 contains summary statistics from TWAS analyses. For dense area, one variant on chromosome 12 (rs1877183750) maps to PRIM1 gene in dense area GWAS and is associated with expression of CD63 (p = 1.9 × 10−6, Z = −4.75, Figure 3a). For area percent density, one variant on chromosome 19 (chr19:35115879) is associated with expression of FXYD3 (p = 7.8 × 10−7, Z = −4.93, Figure 3b). CD63 [35,36,37,38,39], PRIM1 [34], and FXYD3 [40,41] have been previously implicated in breast cancer. Here, PRIM1 is linked to breast cancer.