Table 5.
CpG sites associated with breast cancer risk, passing the false discovery rate of 0.05 in the main analysis of normal breast tissue and replicated in the same direction in both secondary analyses (normal breast tissue and blood samples).
| CpG | Chr | Gene | Gene Region | CpG Island Region | logFC | p-Value | q-Value |
|---|---|---|---|---|---|---|---|
| cg09434832 | chr19 | ZNF616 | 5′UTR | N_Shore | 0.148 | 1.98 × 10−5 | 0.01 |
| cg16927253 | chr6 | POM121L2 | TSS1500 | Island | −0.215 | 0.0001 | 0.02 |
| cg13585675 | chr7 | NPTX2 | Body | S_Shelf | 0.289 | 0.0002 | 0.02 |
| cg27639104 | chr11 | KCNQ1 | 1stExon;5′UTR;Body | OpenSea | 0.181 | 0.0002 | 0.02 |
| cg20754261 | chr2 | - | - | Island | −0.456 | 0.0006 | 0.04 |
| cg03938369 | chr12 | CLEC4C * | Body | OpenSea | 0.197 | 0.0006 | 0.04 |
In bold: genes enriched in breast cancer (CGAP); * genes enriched in the normal epithelium (CGAP); CGAP—Cancer Genome Anatomy Project; Chr—chromosome.