Table 2. Genetic variants known to influence risk of breast cancer.
| Variant | Nearest Gene | Chromf | Position (build 37g) | Breast cancer risk allele | Published odds ratioa | RAPPER risk allele frequency | RAPPER imputation r2c |
|---|---|---|---|---|---|---|---|
| rs616488 | PEX14 | 1 | 10566215 | A | 1.06 | 0.67 | 1 |
| rs11552449 | PTPN22-BCL2L15-AP4B1-DCLRE1B-HIPK1 | 1 | 114448389 | T | 1.08 | 0.20 | 0.98 |
| rs11249433 | None | 1 | 121280613 | G | 1.10 | 0.38 | 0.67 |
| rs12405132 | RNF115 | 1 | 145644984 | C | 1.05b | 0.64 | 1 |
| rs12048493 | OTUD7B | 1 | 149927034 | C | 1.07b | 0.39 | 0.66 |
| rs6678914 | LGR6 | 1 | 202187176 | G | 1.01 | 0.59 | 0.99 |
| rs4245739 | MDM4 | 1 | 204518842 | C | 1.03 | 0.28 | 0.99 |
| rs72755295 | EXO1 | 1 | 242034263 | G | 1.15b | 0.03 | 0.69 |
| rs12710696 | OSR1 | 2 | 19320803 | A | 1.04 | 0.38 | 0.99 |
| rs4849887 | INHBB | 2 | 121245122 | C | 1.09 | 0.90 | 0.99 |
| rs2016394 | METAP1D-DLX1-DLX2 | 2 | 172972971 | G | 1.05 | 0.54 | 1 |
| rs1550623 | CDCA7 | 2 | 174212894 | A | 1.06 | 0.83 | 0.98 |
| rs1045485 | CASP8 d | 2 | 202149589 | G | 1.04 | 0.86 | 0.98 |
| rs13387042 | IGFBP5d | 2 | 217905832 | A | 1.14 | 0.55 | 1 |
| rs16857609 | DIRC3 | 2 | 218296508 | T | 1.07 | 0.29 | 0.98 |
| rs6762644 | ITPR1-EGOT | 3 | 4742276 | G | 1.07 | 0.40 | 0.99 |
| rs4973768 | SLC4A7 | 3 | 27416013 | T | 1.09 | 0.50 | 1 |
| rs12493607 | TGFBR2 | 3 | 30682939 | C | 1.05 | 0.33 | 0.99 |
| rs6796502 | PRSS42 | 3 | 46866866 | G | 1.09b | 0.90 | 0.96 |
| rs1053338 | ATXN7 | 3 | 63967900 | G | 1.08b | 0.15 | 0.98 |
| rs9790517 | TET2 | 4 | 106084778 | T | 1.05 | 0.20 | 0.99 |
| rs6828523 | ADAM29 | 4 | 175846426 | C | 1.10 | 0.89 | 0.99 |
| rs10069690 | TERT d | 5 | 1279790 | T | 1.02 | 0.27 | 1 |
| rs7726159 | TERT d | 5 | 1282319 | A | 1.04 | 0.33 | 0.85 |
| rs2736108 | TERT d | 5 | 1297488 | C | 1.07 | 0.72 | 0.90 |
| rs13162653 | MARCH11 | 5 | 16187528 | G | 1.05b | 0.55 | 0.89 |
| rs2012709 | SUB1 | 5 | 32567732 | T | 1.05b | 0.49 | 1 |
| rs10941679 | None | 5 | 44706498 | G | 1.12 | 0.30 | 0.98 |
| rs889312 | MAP3K1 d | 5 | 56031884 | C | 1.12 | 0.31 | 0.99 |
| rs10472076 | RAB3C | 5 | 58184061 | C | 1.04 | 0.39 | 0.96 |
| rs1353747 | PDE4D | 5 | 58337481 | T | 1.09 | 0.90 | 0.98 |
| rs7707921 | ATG10 | 5 | 81538046 | A | 1.08b | 0.76 | 0.99 |
| rs1432679 | EBF1 | 5 | 158244083 | G | 1.07 | 0.46 | 0.99 |
| rs11242675 | FOXQ1 | 6 | 1318878 | T | 1.06 | 0.63 | 0.94 |
| rs204247 | RANBP9 | 6 | 13722523 | G | 1.05 | 0.45 | 0.99 |
| rs9257408 | None | 6 | 28926220 | C | 1.05b | 0.39 | 0.99 |
| rs17529111 | None | 6 | 82128386 | G | 1.05 | 0.21 | 0.99 |
| rs12662670 | ESR1 e | 6 | 151918856 | G | 1.14 | 0.09 | 0.99 |
| rs2046210 | ESR1 e | 6 | 151948366 | A | 1.05 | 0.37 | 0.99 |
| rs6964587 | AKAP9 | 7 | 91630620 | T | 1.05b | 0.40 | 0.98 |
| rs4593472 | LINC-PINT | 7 | 130667121 | C | 1.05b | 0.66 | 0.92 |
| rs720475 | ARHGEF5-NOBOX | 7 | 144074929 | G | 1.06 | 0.74 | 0.95 |
| rs9693444 | None | 8 | 29509616 | A | 1.07 | 0.34 | 0.99 |
| rs13365225 | KCNU1 | 8 | 36858483 | A | 1.05b | 0.85 | 0.98 |
| rs6472903 | CASC9 | 8 | 76230301 | T | 1.10 | 0.84 | 0.94 |
| rs2943559 | HNF4G | 8 | 76417937 | G | 1.13 | 0.09 | 0.98 |
| rs13267382 | None | 8 | 117209548 | A | 1.05b | 0.36 | 0.96 |
| rs13281615 | MYC d | 8 | 128355618 | G | 1.10 | 0.44 | 0.99 |
| rs11780156 | MYC d | 8 | 129194641 | T | 1.07 | 0.17 | 0.99 |
| rs1011970 | CDKN2A/B | 9 | 22062134 | T | 1.05 | 0.18 | 1 |
| rs10759243 | KLF4 d | 9 | 110306115 | A | 1.05 | 0.29 | 0.75 |
| rs865686 | KLF4 d | 9 | 110888478 | T | 1.11 | 0.62 | 0.99 |
| rs2380205 | ANKRD16 | 10 | 5886734 | C | 1.02 | 0.59 | 0.99 |
| rs7072776 | MLLT10-DNAJC1 | 10 | 22032942 | A | 1.06 | 0.27 | 0.91 |
| rs11814448 | DNAJC1 | 10 | 22315843 | C | 1.22 | 0.02 | 0.84 |
| rs10995190 | NRBF2 d | 10 | 64278682 | G | 1.17 | 0.87 | 0.99 |
| rs704010 | ZMIZ1 | 10 | 80841148 | T | 1.07 | 0.43 | 0.97 |
| rs7904519 | TCF7L2 | 10 | 114773927 | G | 1.06 | 0.48 | 0.99 |
| rs11199914 | FGFR2 d | 10 | 123093901 | C | 1.06 | 0.70 | 0.73 |
| rs2981579 | FGFR2 d | 10 | 123337335 | A | 1.25 | 0.47 | 0.99 |
| rs3817198 | LSP1 | 11 | 1909006 | C | 1.07 | 0.33 | 0.92 |
| rs3903072 | DKFZp761e198-OVOLI-SNX32-CFL1-MUS81 | 11 | 65583066 | G | 1.06 | 0.55 | 0.99 |
| rs78540526 | CCND1 d | 11 | 69331418 | T | 1.18 | 0.08 | 0.95 |
| rs554219 | CCND1 d | 11 | 69331642 | G | 1.12 | - | - |
| rs75915166 | CCND1 d | 11 | 69379161 | A | 1.024 | 0.06 | 0.86 |
| rs11820646 | BARX2 | 11 | 129461171 | C | 1.05 | 0.60 | 0.98 |
| rs12422552 | None | 12 | 14413931 | C | 1.03 | - | - |
| rs10771399 | PTHLH | 12 | 28155080 | A | 1.16 | - | - |
| rs17356907 | NTN4 | 12 | 96027759 | A | 1.10 | - | - |
| rs1292011 | None | 12 | 115836522 | A | 1.08 | 0.59 | 1 |
| rs11571833 | BRCA2-N4BP2LI-N4BP2L2 | 13 | 32972626 | T | 1.26 | 0.01 | 0.87 |
| rs2236007 | PAX9-SLO25A21 | 14 | 37132769 | G | 1.09 | 0.82 | 1 |
| rs2588809 | RAD51L1 | 14 | 68660428 | T | 1.07 | 0.17 | 0.97 |
| rs999737 | RAD51L1 | 14 | 69034682 | C | 1.08 | 0.77 | 0.97 |
| rs941764 | CCDC88C | 14 | 91841069 | G | 1.06 | 0.36 | 0.95 |
| rs11627032 | RIN3 | 14 | 93104072 | T | 1.06b | 0.74 | 0.93 |
| rs3803662 | TOX3 | 16 | 52586341 | A | 1.23 | 0.29 | 1 |
| rs17817449 | MIRI972-2-FTO | 16 | 53813367 | T | 1.08 | 0.60 | 0.99 |
| rs11075995 | FTO | 16 | 53855291 | T | 1.04 | 0.76 | 0.99 |
| rs13329835 | CDYL2 | 16 | 80650805 | G | 1.08 | 0.24 | 0.98 |
| rs146699004 | TEFM | 17 | 29230520 | GGT | 1.08b | 0.74 | 0.99 |
| rs6504950 | COX11 e | 17 | 53056471 | G | 1.07 | 0.72 | 0.97 |
| rs745570 | CBX8 | 17 | 77781725 | A | 1.05b | 0.50 | 0.97 |
| rs527616 | None | 18 | 24337424 | G | 1.04 | 0.66 | 0.98 |
| rs1436904 | CHST9 | 18 | 24570667 | T | 1.06 | 0.63 | 0.99 |
| rs6507583 | SETBP1 | 18 | 42399590 | A | 1.10b | 0.93 | 0.99 |
| rs8170 | ABHD8/ANKLE1 e | 19 | 17389704 | A | 1.03 | 0.20 | 0.99 |
| rs2363956 | ABHD8/ANKLE1 e | 19 | 17394124 | T | 1.03 | 0.51 | 0.98 |
| rs4808801 | SSBP4-ISYNA1-ELL | 19 | 18571141 | A | 1.07 | 0.67 | 0.99 |
| rs3760982 | C19orf61-KCNN4-LYPD5-ZNF283 | 19 | 44286513 | A | 1.06 | 0.49 | 1 |
| rs2823093 | NRIP1 | 21 | 16520832 | G | 1.08 | 0.75 | 0.96 |
| rs17879961 | CHEK2 | 22 | 29121087 | G | 1.36 | 0.001 | 0.69 |
| rs132390 | EMID1-RHBDD3-EWSR1 | 22 | 29621477 | C | 1.11 | 0.04 | 1 |
| rs6001930 | MKL1 | 22 | 40876234 | C | 1.13 | 0.11 | 0.99 |
a
adjusted odds ratios from Mavaddat et al. 2015
b
unadjusted odds ratios from Michailidou et al. 2013 or Michailidou et al. 2015
c
imputation r2 calculated by the mean info score from IMPUTE2. The info score represents the certainty with which the SNP has been imputed and lies between 0 (no certainty) and 1 (high certainty; r2=1 for genotyped SNPs)
d
published target gene
e
known target gene, not yet published
f
chromosome
g
human genome build 37 (GRCh37) by the Genome Reference Consortium, released 3 March 2009. Available from: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/