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. 2020 Oct 23;12(11):3088. doi: 10.3390/cancers12113088

Table 3.

CpG sites associated with breast cancer risk in the main analysis of normal breast tissue and passing strict Bonferroni correction (p-value < 1.22 × 10−7).

CpG Chr Gene Gene Region CpG Island Region logFC p-Value
cg03835987 chr4 ELOVL6 * TSS1500 S_Shore −0.546 1.61 × 10−11
cg19462193 chr12 VPS33A TSS200 Island 0.288 9.98 × 10−11
cg11051893 chr13 MPHOSPH8 TSS200 Island 0.337 2.45 × 10−10
cg08716396 chr1 SDHC TSS1500 Island 0.299 4.01 × 10−9
cg09155575 chr17 ORMDL3 TSS200 Island 0.247 4.47 × 10−9
cg27160524 chr2 PXDN * Body OpenSea −0.314 9.57 × 10−9
cg00982919 chr9 LHX2 Body Island −0.618 1.13 × 10−9
cg15295166 chr21 CLIC6 TSS1500 N_Shore −0.291 1.39 × 10−9
cg13401911 chr1 CAMK2N1 1stExon;5′UTR Island 0.334 1.64 × 10−9
cg14291745 chr10 - - N_Shore −0.379 3.14 × 10−9
cg24410535 chr4 FAT1 TSS200 Island −0.459 3.96 × 10−9
cg19066273 chr17 - - Island −0.516 4.08 × 10−9
cg11031869 chr7 - - OpenSea −0.298 4.28 × 10−9
cg14910241 chr3 TGFBR2 Body Island −0.221 5.98 × 10−9
cg13492692 chr9 LHX2 Body Island −0.378 7.30 × 10−9
cg13322131 chr6 TFAP2B 3′UTR S_Shore −0.537 7.91 × 10−9
cg13170891 chr6 PPP1R10 3′UTR OpenSea 0.322 7.92 × 10−9
cg00705992 chr7 HOXA11 Body;TSS1500 N_Shore −0.308 1.13 × 10−8
cg05992226 chr14 SMEK1 Body Island −0.254 1.21 × 10−8
cg23695222 chr8 - - OpenSea −0.329 1.22 × 10−8
cg06562570 chr14 VRK1 TSS200 Island 0.232 1.86 × 10−8
cg05508048 chr13 INTS6 TSS200 Island 0.306 2.15 × 10−8
cg11170179 chr19 KLK10 * 5′UTR Island 0.362 2.26 × 10−8
cg00954771 chr11 TOLLIP Body Island 0.307 3.04 × 10−8
cg01868405 chr1 - - Island −0.427 3.10 × 10−8
cg14011789 chr17 SEPT9 * Body;5′UTR OpenSea 0.486 3.43 × 10−8
cg10332787 chr14 C14orf106 TSS200 Island 0.205 3.54 × 10−8
cg16724588 chr4 JAKMIP1 Body Island −0.585 3.62 × 10−8
cg07557790 chr3 CAND2 * TSS1500 N_Shore −0.391 3.78 × 10−8
cg05559558 chr6 KIAA1244 1stExon;5′UTR Island 0.204 4.08 × 10−8
cg20430816 chr4 STBD1 Body Island −0.259 4.16 × 10−8
cg10092770 chr20 NCRNA00029 TSS200 S_Shore 0.365 4.40 × 10−8
cg05335186 chr13 - - N_Shore 0.285 4.48 × 10−8
cg14255751 chr15 PTPLAD1 TSS200 N_Shore 0.252 4.83 × 10−8
cg03171770 chr10 - - Island −0.476 4.86 × 10−8
cg24354933 chr19 PODNL1 Body;TSS200 OpenSea 0.414 4.93 × 10−8
cg02457207 chr16 SPG7 Body N_Shelf −0.315 4.97 × 10−8
cg14047370 chr7 HECW1 Body OpenSea −0.461 5.23 × 10−8
cg01764116 chr1 VPS45 5′UTR;1stExon Island 0.276 5.40 × 10−8
cg22606205 chr1 PKP1 5′UTR;1stExon Island −0.316 5.79 × 10−8
cg23535449 chr17 AATK TSS200;Body N_Shelf 0.250 6.17 × 10−8
cg21352943 chr12 C12orf41 TSS200 Island −0.261 6.25 × 10−8
cg06380356 chr2 - - Island −0.371 7.02 × 10−8
cg24014538 chr13 FARP1 * Body OpenSea −0.405 7.15 × 10−8
cg10938586 chr10 - - Island 0.336 7.60 × 10−8
cg14319655 chr19 AKAP8 TSS200 Island 0.217 7.88 × 10−8
cg09103187 chr6 TRERF1 * Body OpenSea −0.250 8.69 × 10−8
cg17939432 chr22 ZC3H7B Body S_Shore 0.311 8.82 × 10−8
cg12241297 chr5 HNRNPA0 * TSS1500 Island 0.239 1.08 × 10−7
cg05295557 chr14 NKX2-1 Body;1stExon Island −0.249 1.14 × 10−7
cg20877313 chr12 GLS2 1stExon Island −0.326 1.21 × 10−7
cg00253204 chr17 NCOR1 * 1stExon;5′UTR Island −0.212 1.21 × 10−7

In bold: genes enriched in breast cancer (CGAP); * genes enriched in the normal epithelium (CGAP); CGAP—Cancer Genome Anatomy Project; Chr—chromosome.