The Genomic Atlas of Breast Cancer — the non-coding theme

Update News

  • GABC update 2020.06.15
  • GABC update 2019.03.20
  • GABC online 2018.08.09
  • Data collection 2018.04.09

About Us

  • Steven Xi Chen:
    steven.chen@miami.edu
  • Yunpeng Zhang:
    YXZ1418@med.miami.edu
  • Peng Wang:
    wpgqy@163.com
  • Shangwei Ning:
    ningsw@ems.hrbmu.edu.cn
  • Xia Li:
    lixia@hrbmu.edu.cn

Breast cancer associated SNPs

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Chr Position SNPID Disease/Trait name pvalue PMID
20 32582871 rs1007090 Breast cancer (Estrogen receptor negative breast cancer) 5.19E-07 22976474
20 57350302 rs1022697 Breast cancer 3.92E-05 20872241
20 6009174 rs1028410 Gene expression of CRLS1 (probeID ILMN_1737685) in breast tumors 1.17E-14 22522925
20 61472596 rs1046789 Gene expression of TCFL5 (probeID ILMN_1814247) in breast tumors 5.13E-36 22522925
20 41797929 rs10485698 Gene expression of UBE2C (probeID ILMN_1742958) in breast tumors 6.18E-04 22522925
20 7962128 rs1058007 Gene expression of TXNDC13 (probeID ILMN_1702759) in breast tumors 8.95E-16 22522925
20 11303203 rs1119133 Breast cancer risk (in BRCA1 mutation carriers) 3.70E-05 20852631
20 34312713 rs11699044 Gene expression of CPNE1 (probeID ILMN_1670841) in breast tumors 4.75E-12 22522925
20 8725737 rs117230765 Breast size (bra cup size in women) 3.10E-05 22747683
20 18122912 rs117280420 Breast cancer 4.50E-04 23555315
20 37341437 rs13036407 Breast size (bra cup size in women) 6.87E-05 22747683
20 17682084 rs142858573 Breast size (bra cup size in women) 4.02E-05 22747683
20 50048783 rs145231526 Breast cancer (Estrogen receptor negative breast cancer) 7.40E-05 23555315
20 25457055 rs146288604 Breast cancer (Estrogen receptor positive breast cancer) 9.50E-06 23555315
20 25457055 rs146288604 Breast cancer 8.10E-05 23555315
20 1551621 rs147405398 Breast cancer 3.10E-04 23555315
20 62838961 rs148972645 Breast cancer 5.30E-04 23555315
20 32610401 rs1555075 Breast cancer (Estrogen receptor negative breast cancer) 1.03E-06 22976474
20 12898764 rs165557 Breast cancer risk (in BRCA1 mutation carriers) 1.21E-04 20852631
20 33435161 rs17092148 Breast cancer (Estrogen receptor negative breast cancer) 2.61E-05 22976474
20 34318911 rs17093026 Gene expression of CPNE1 (probeID ILMN_2307025) in breast tumors 9.71E-04 22522925
20 33872215 rs1802241 Breast cancer (Estrogen receptor negative breast cancer) 6.40E-05 23555315
20 30541443 rs1883507 Gene expression of SGCG (probeID ILMN_1659649) in breast tumors 4.66E-04 22522925
20 33342439 rs1884432 Breast cancer (Estrogen receptor negative breast cancer) 6.66E-05 22976474
20 23030102 rs191884040 Breast cancer 2.90E-04 23555315
20 3673557 rs199636258 Breast cancer (Estrogen receptor negative breast cancer) 5.40E-05 23555315
20 60892077 rs199776859 Breast cancer 3.00E-04 23555315
20 45158450 rs202370 Gene expression of ZNF334 (probeID ILMN_1672743) in breast tumors 2.54E-09 22522925
20 21302885 rs202835 Gene expression of XRN2 (probeID ILMN_2196479) in breast tumors 4.99E-152 22522925
20 49870811 rs2073124 Breast cancer 4.30E-04 21908515
20 56331777 rs2180690 Gene expression of HS.25555 (probeID ILMN_1892511) in breast tumors 7.59E-04 22522925
20 32709444 rs2223553 Breast cancer (Estrogen receptor negative breast cancer) 4.30E-06 22976474
20 36989391 rs2232597 Breast cancer 9.40E-04 23555315
20 33523840 rs2236271 Gene expression of GGTL3 (probeID ILMN_1786186) in breast tumors 1.19E-07 22522925
20 61387404 rs2249938 Breast cancer 1.52E-04 pha002853
20 25270339 rs2257991 Gene expression of ABHD12 (probeID ILMN_1745116) in breast tumors 2.65E-75 22522925
20 32596750 rs2268079 Breast cancer (Estrogen receptor negative breast cancer) 1.04E-05 22976474
20 32631388 rs2268084 Breast cancer (Estrogen receptor negative breast cancer) 4.03E-05 22976474
20 32648738 rs2268086 Breast cancer (Estrogen receptor negative breast cancer) 7.37E-06 22976474
20 32667298 rs2268089 Breast cancer (Estrogen receptor negative breast cancer) 1.81E-05 22976474
20 32588095 rs2284378 Breast cancer 1.00E-08 22976474
20 32588095 rs2284378 Breast cancer 1.10E-08 22976474
20 32588095 rs2284378 Breast cancer (Estrogen receptor negative breast cancer) 6.46E-07 22976474
20 32655741 rs2284388 Breast cancer (Estrogen receptor negative breast cancer) 5.57E-07 22976474
20 32714728 rs2378078 Breast cancer (Estrogen receptor negative breast cancer) 9.23E-08 22976474
20 44402869 rs2664529 Gene expression of WFDC3 (probeID ILMN_2308903) in breast tumors 2.67E-65 22522925
20 3520496 rs2853218 Breast cancer (hormonal receptor positive breast cancer) 9.67E-06 22951594
20 48930661 rs2869980 Breast size (bra cup size in women) 4.23E-05 22747683
20 62217589 rs311499 Breast cancer (BRCA2-positive) 3.48E-05 21060860
20 52192637 rs34323943 Breast cancer 8.00E-05 23555315
20 37342810 rs34490853 Breast size (bra cup size in women) 6.53E-05 22747683
20 60348084 rs34937312 Breast cancer 5.70E-05 23555315
20 33337751 rs3787220 Breast cancer (Estrogen receptor negative breast cancer) 6.31E-05 22976474
20 22447954 rs3935234 Breast cancer 8.64E-04 21424380
20 32553047 rs4012234 Breast cancer (Estrogen receptor negative breast cancer) 7.92E-06 22976474
20 23702419 rs4072312 Gene expression of CST1 (probeID ILMN_1753449) in breast tumors 3.24E-10 22522925
20 48930936 rs4239659 Breast size (bra cup size in women) 4.83E-05 22747683
20 25467359 rs446649 Gene expression of ABHD12 (probeID ILMN_2318685) in breast tumors 2.56E-17 22522925
20 61470725 rs4809261 Gene expression of TCFL5 (probeID ILMN_1814247) in breast tumors 5.66E-05 22522925
20 56449176 rs4810108 Breast cancer risk (in BRCA1 mutation carriers) 9.03E-05 20852631
20 48932992 rs4811027 Breast size (bra cup size in women) 7.52E-05 22747683
20 32615223 rs4911145 Breast cancer (Estrogen receptor negative breast cancer) 9.43E-06 22976474
20 32535305 rs4911379 Breast cancer (Estrogen receptor negative breast cancer) 7.69E-06 22976474
20 32555807 rs4911384 Breast cancer (Estrogen receptor negative breast cancer) 6.53E-06 22976474
20 32700566 rs4911408 Breast cancer (Estrogen receptor negative breast cancer) 5.54E-07 22976474
20 32729444 rs4911414 Breast cancer (Estrogen receptor negative breast cancer) 5.70E-07 22976474
20 44462924 rs57799507 Breast cancer 2.90E-04 23555315
20 62337406 rs6011040 Gene expression of ZGPAT (probeID ILMN_1794643) in breast tumors 4.70E-04 22522925
20 48931682 rs6012901 Breast size (bra cup size in women) 4.63E-05 22747683
20 48931020 rs6020436 Breast size (bra cup size in women) 4.33E-05 22747683
20 55364185 rs6025161 Gene expression of DTX2 (probeID ILMN_2275098) in breast tumors 2.03E-06 22522925
20 55749781 rs6025422 Gene expression of BMP7 (probeID ILMN_1741566) in breast tumors 2.09E-05 22522925
20 40704059 rs6029958 Breast size (bra cup size in women) 4.17E-05 22747683
20 44413410 rs6032532 Gene expression of WFDC3 (probeID ILMN_1740415) in breast tumors 5.32E-54 22522925
20 44420280 rs6032541 Gene expression of WFDC3 (probeID ILMN_2308903) in breast tumors 7.78E-13 22522925
20 44420280 rs6032541 Gene expression of WFDC3 (probeID ILMN_1740415) in breast tumors 5.30E-07 22522925
20 11297353 rs6033101 Breast cancer risk (in BRCA1 mutation carriers) 9.38E-05 20852631
20 22807870 rs6036227 Breast cancer (hormonal receptor positive breast cancer) 8.28E-05 22951594
20 11661444 rs6040836 Breast cancer (hormonal receptor positive breast cancer) 6.86E-05 22951594
20 23727145 rs6049064 Gene expression of CST1 (probeID ILMN_1753449) in breast tumors 6.68E-61 22522925
20 25366065 rs6050573 Gene expression of ABHD12 (probeID ILMN_1745116) in breast tumors 2.57E-19 22522925
20 33194257 rs6058089 Breast cancer (Estrogen receptor negative breast cancer) 6.64E-05 22976474
20 32457158 rs6059504 Breast cancer risk (in BRCA1 mutation carriers) 5.97E-05 20852631
20 32643877 rs6059649 Breast cancer (Estrogen receptor negative breast cancer) 5.91E-07 22976474
20 33340313 rs6060030 Breast cancer (Estrogen receptor negative breast cancer) 5.28E-05 22976474
20 33351864 rs6060034 Breast cancer (Estrogen receptor negative breast cancer) 9.95E-05 22976474
20 33364584 rs6060043 Breast cancer (Estrogen receptor negative breast cancer) 8.46E-05 22976474
20 34305445 rs6060578 Gene expression of CPNE1 (probeID ILMN_1670841) in breast tumors 9.12E-54 22522925
20 34305445 rs6060578 Gene expression of CPNE1 (probeID ILMN_2307025) in breast tumors 3.06E-50 22522925
20 30400657 rs6060964 Gene expression of MYLK2 (probeID ILMN_2050183) in breast tumors 2.14E-08 22522925
20 52193088 rs6063966 Breast cancer 5.60E-05 23555315
20 1340945 rs6074514 Gene expression of FKBP1A (probeID ILMN_1702237) in breast tumors 2.01E-08 22522925
20 8704552 rs6077414 Estradiol plasma levels (breast cancer) 1.00E-06 23518928
20 8704552 rs6077414 Plasma estradiol concentration in women with breast cancer 1.41E-06 23518928
20 11058072 rs6078047 Breast cancer early age of onset 4.70E-04 18463975
20 20008581 rs6081840 Gene expression of CRNKL1 (probeID ILMN_1768640) in breast tumors 3.04E-08 22522925
20 4071305 rs6084610 Gene expression of GPR52 (probeID ILMN_1671929) in breast tumors 5.60E-04 22522925
20 33197489 rs6087607 Breast cancer (Estrogen receptor negative breast cancer) 1.86E-05 22976474
20 33626216 rs6087664 Gene expression of TRPC4AP (probeID ILMN_2402805) in breast tumors 2.09E-12 22522925
20 60815446 rs6089701 Gene expression of OSBPL2 (probeID ILMN_2349124) in breast tumors 2.75E-21 22522925
20 58725838 rs6100755 Breast cancer 4.20E-04 20585626
20 59591960 rs6101183 Breast cancer 2.00E-04 17903305
20 10834078 rs6108719 Breast cancer risk (in BRCA1 mutation carriers) 3.99E-05 20852631
20 12861103 rs6109595 Breast cancer 1.47E-04 pha002853
20 23777130 rs6114296 Gene expression of CST2 (probeID ILMN_1673843) in breast tumors 1.19E-19 22522925
20 759315 rs6117615 Adverse response to chemotherapy in breast cancer (alopecia) (docetaxel) 7.00E-06 24025145
20 32675636 rs6120513 Breast cancer (Estrogen receptor negative breast cancer) 3.20E-06 22976474
20 33644358 rs6120816 Gene expression of TRPC4AP (probeID ILMN_2402805) in breast tumors 1.20E-133 22522925
20 12908451 rs6134722 Breast cancer risk (in BRCA1 mutation carriers) 1.01E-06 20852631
20 32527128 rs6142050 Breast cancer (Estrogen receptor negative breast cancer) 7.40E-06 22976474
20 16532878 rs6514689 Gene expression of KIF16B (probeID ILMN_1772786) in breast tumors 1.21E-05 22522925
20 17760632 rs7264107 Gene expression of GRB7 (probeID ILMN_1740762) in breast tumors 8.11E-18 22522925
20 17760632 rs7264107 Gene expression of GRB7 (probeID ILMN_2405254) in breast tumors 1.22E-17 22522925
20 17760632 rs7264107 Gene expression of ERBB2 (probeID ILMN_2352131) in breast tumors 1.43E-16 22522925
20 17760632 rs7264107 Gene expression of PERLD1 (probeID ILMN_1805636) in breast tumors 8.77E-16 22522925
20 17760632 rs7264107 Gene expression of GSDMB (probeID ILMN_1666206) in breast tumors 9.18E-16 22522925
20 17760632 rs7264107 Gene expression of C17ORF37 (probeID ILMN_1727078) in breast tumors 1.87E-15 22522925
20 17760632 rs7264107 Gene expression of STARD3 (probeID ILMN_1657095) in breast tumors 2.15E-15 22522925
20 17760632 rs7264107 Gene expression of ORMDL3 (probeID ILMN_1662174) in breast tumors 4.78E-15 22522925
20 17760632 rs7264107 Gene expression of GSDMB (probeID ILMN_2347193) in breast tumors 7.46E-15 22522925
20 17760632 rs7264107 Gene expression of GRB7 (probeID ILMN_1798582) in breast tumors 3.30E-13 22522925
20 17760632 rs7264107 Gene expression of PSMD3 (probeID ILMN_1796430) in breast tumors 8.99E-12 22522925
20 17760632 rs7264107 Gene expression of MED24 (probeID ILMN_1711853) in breast tumors 6.98E-11 22522925
20 17760632 rs7264107 Gene expression of MED24 (probeID ILMN_2388272) in breast tumors 1.22E-09 22522925
20 17760632 rs7264107 Gene expression of ERBB2 (probeID ILMN_1728761) in breast tumors 3.42E-06 22522925
20 17760632 rs7264107 Gene expression of PPARBP (probeID ILMN_1721729) in breast tumors 8.61E-06 22522925
20 17760632 rs7264107 Gene expression of RARA (probeID ILMN_1659206) in breast tumors 3.44E-05 22522925
20 17760632 rs7264107 Gene expression of TCAP (probeID ILMN_1804316) in breast tumors 5.43E-05 22522925
20 17760632 rs7264107 Gene expression of TMEM132A (probeID ILMN_2317923) in breast tumors 6.35E-05 22522925
20 17760632 rs7264107 Gene expression of PNMT (probeID ILMN_1710027) in breast tumors 1.53E-04 22522925
20 17760632 rs7264107 Gene expression of ARHGAP8 (probeID ILMN_2412475) in breast tumors 7.74E-04 22522925
20 33525407 rs7265992 Breast cancer (Estrogen receptor negative breast cancer) 2.27E-05 22976474
20 25298087 rs7267979 Gene expression of ABHD12 (probeID ILMN_1745116) in breast tumors 2.92E-15 22522925
20 33397303 rs7271289 Breast cancer (Estrogen receptor negative breast cancer) 6.80E-05 22976474
20 5145681 rs7271989 Breast cancer recurrence 5.40E-06 22232737
20 38289026 rs74632082 Breast size (bra cup size in women) 8.01E-05 22747683
20 32519988 rs761238 Breast cancer (Estrogen receptor negative breast cancer) 8.07E-06 22976474
20 38287890 rs77119337 Breast size (bra cup size in women) 7.81E-05 22747683
20 33874600 rs78127944 Breast cancer (Estrogen receptor negative breast cancer) 9.50E-05 23555315
20 11317483 rs8122608 Breast cancer risk (in BRCA1 mutation carriers) 1.43E-05 20852631
20 45142619 rs847055 Gene expression of ZNF334 (probeID ILMN_1672743) in breast tumors 4.26E-38 22522925
20 61385787 rs856937 Breast cancer 2.09E-04 pha002853
20 33764554 rs867186 Gene expression of PROCR (probeID ILMN_1717262) in breast tumors 1.95E-07 22522925
20 33333208 rs910871 Breast cancer (Estrogen receptor negative breast cancer) 4.69E-05 22976474
20 48934778 rs928072 Breast size (bra cup size in women) 2.88E-05 22747683
20 1420336 rs932524 Gene expression of NSFL1C (probeID ILMN_2366719) in breast tumors 6.92E-10 22522925
20 1420336 rs932524 Gene expression of NSFL1C (probeID ILMN_1657624) in breast tumors 1.27E-09 22522925
20 1420336 rs932524 Gene expression of HS.371006 (probeID ILMN_1841622) in breast tumors 1.27E-06 22522925
Chr Position SNPID Disease/Trait name pvalue PMID

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