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Table 2 The rare allele frequencies of 51 single nucleotide polymorphisms (SNPs) in breast cancer patients and control subjects and their association with risk of breast cancer, The Singapore Chinese Health Study, 1993 to 1998

From: Breast cancer risk assessment using genetic variants and risk factors in a Singapore Chinese population

Chr Genes in or near region SNP Effect allele RAF in controls RAF in cases Per-allele OR (95% CI) SE Pvalue* Pooled OR FDR-correctedPhet
1 PEX14 rs616488 G 0.348 0.361 1.06 (0.89, 1.26) 0.09 0.510 0.94 0.790
1 PTPN22/BCL2L15/AP4B1/DCLRE1B/HIPK1 rs11552449 A 0.596 0.556 0.85 (0.72, 0.99) 0.08 0.040 1.06 0.068
1 FCGR1B rs11249433 G 0.029 0.026 0.85 (0.52, 1.39) 0.25 0.517 1.09 0.371
2 INHBB- rs4849887 A 0.259 0.269 1.05 (0.87, 1.25) 0.09 0.634 0.92 0.561
2 METAP1D/DLX1/DLX2 rs2016394 A 0.195 0.191 0.96 (0.79, 1.18) 0.10 0.727 0.95 0.790
2 TNP1 rs13387042 G 0.907 0.883 0.77 (0.60, 0.99) 0.13 0.045 0.93 0.062
2 DIRC3 rs16857609 C 0.376 0.367 1.07 (0.90, 1.27) 0.09 0.462 1.08 0.977
3 ITPR1/EGOT rs6762644 G 0.098 0.096 0.97 (0.73, 1.29) 0.14 0.841 1.07 0.790
3 SLC4A7 rs4973768 A 0.190 0.186 0.97 (0.80, 1.18) 0.10 0.757 1.11 0.473
3 TGFBR2 rs12493607 G 0.278 0.262 0.91 (0.76, 1.09) 0.09 0.290 1.06 0.619
4 TET2 rs9790517 A 0.613 0.635 1.09 (0.93, 1.29) 0.08 0.293 1.05 0.440
4 ADAM29 rs6828523 A 0.275 0.271 0.99 (0.82, 1.18) 0.09 0.879 0.90 0.729
5 5p12 (intergenic) rs4415084 C 0.441 0.434 0.96 (0.82, 1.14) 0.08 0.668 1.15 0.087
5 MRPS30 rs10941679 G 0.499 0.519 1.09 (0.93, 1.29) 0.08 0.289 1.12 0.409
5 MAP3K1 rs889312 C 0.589 0.577 0.96 (0.82, 1.14) 0.08 0.666 1.05 0.727
5 RAB3C rs10472076 G 0.247 0.260 1.07 (0.89, 1.28) 0.09 0.465 1.04 0.500
5 EBF1 rs1432679 G 0.631 0.642 1.05 (0.89, 1.24) 0.08 0.558 1.07 0.931
6 FOXQ1 rs11242675 A 0.597 0.633 1.15 (0.98, 1.35) 0.08 0.088 - -
6 ECHDC1/RNF146 rs2180341 G 0.181 0.198 1.09 (0.90, 1.33) 0.10 0.365 1.31 0.100
6 RANBP9 rs204247 G 0.588 0.611 1.10 (0.94, 1.29) 0.08 0.248 1.05 0.911
6 FAM46A rs17529111 G 0.218 0.206 0.92 (0.75, 1.12) 0.10 0.404 1.06 0.675
6 ESR1 rs3757318 A 0.276 0.316 1.20 (1.01, 1.42) 0.09 0.039 1.04 0.790
6 ESR1 rs2046210 A 0.380 0.434 1.25 (1.06, 1.46) 0.08 0.008 1.27 0.970
7 ARHGEF5 rs720475 A 0.046 0.041 0.90 (0.61, 1.33) 0.20 0.596 0.94 0.941
8 RPL17P33 rs9693444 A 0.282 0.288 1.04 (0.87, 1.24) 0.09 0.691 1.07 0.977
8 8q24 rs13281615 G 0.502 0.500 0.99 (0.84, 1.16) 0.08 0.872 1.07 0.215
8 8q24 rs1562430 C 0.181 0.184 1.03 (0.83, 1.27) 0.11 0.820 0.87 0.273
9 CDKN2A rs1011970 A 0.096 0.095 0.98 (0.75, 1.28) 0.14 0.875 1.07 0.639
9 KLF4 rs10759243 A 0.431 0.476 1.20 (1.02, 1.41) 0.08 0.027 1.06 0.790
9 KLF4 rs865686 C 0.057 0.067 1.19 (0.87, 1.64) 0.16 0.275 0.90 0.150
10 ZNF365 rs10822013 T 0.500 0.517 1.07 (0.91, 1.25) 0.08 0.409 1.08 0.387
10 ZNF365 rs10995190 A 0.012 0.013 1.14 (0.57, 2.30) 0.36 0.713 1.06 0.350
10 ZMIZ1 rs704010 A 0.369 0.397 1.12 (0.95, 1.33) 0.08 0.169 1.08 0.473
10 FGFR2 rs1219648 G 0.404 0.427 1.08 (0.92, 1.27) 0.08 0.343 1.14 0.560
10 FGFR2 rs2981582 A 0.338 0.370 1.14 (0.96, 1.34) 0.08 0.128 1.26 0.451
11 LSP1 rs3817198 G 0.095 0.108 1.14 (0.89, 1.46) 0.13 0.311 1.07 0.931
11 DKFZp761E198/OVOL1/SNX32/CFL1 rs3903072 A 0.210 0.175 0.81 (0.66, 0.99) 0.10 0.039 0.95 0.268
11 BARX2 rs11820646 A 0.489 0.509 1.09 (0.93, 1.28) 0.08 0.278 0.95 0.574
12 ATF7IP rs12422552 C 0.273 0.325 1.29 (1.08, 1.53) 0.09 0.004 1.06 0.128
12 PTHLH rs10771399 G 0.192 0.173 0.88 (0.71, 1.08) 0.11 0.221 0.86 0.729
12 NTN4 rs17356907 G 0.253 0.247 0.98 (0.82, 1.18) 0.09 0.839 0.91 0.604
14 PAX9/SLC25A21 rs2236007 A 0.297 0.255 0.83 (0.69, 0.98) 0.09 0.031 0.92 0.469
14 CCDC88C rs941764 G 0.126 0.140 1.13 (0.90, 1.42) 0.12 0.308 1.06 0.931
16 TOX3 rs4784227 T 0.245 0.274 1.17 (0.97, 1.41) 0.09 0.098 1.23 0.574
16 TOX3 rs3112612 G 0.228 0.210 0.90 (0.74, 1.10) 0.10 0.300 1.13 0.066
16 CDYL2 rs13329835 G 0.053 0.054 1.02 (0.70, 1.46) 0.18 0.938 1.09 0.351
16 MIR1972-2/FTO rs17817449 C 0.140 0.118 0.83 (0.66, 1.06) 0.12 0.134 0.93 0.079
18 AQP4 rs527616 G 0.267 0.266 0.99 (0.83, 1.19) 0.09 0.951 0.98 0.805
18 CHST9 rs1436904 C 0.486 0.509 1.09 (0.93, 1.28) 0.08 0.287 0.96 0.225
19 C19orf61:KCNN4:LYPD5:ZNF283 rs3760982 A 0.136 0.148 1.10 (0.87, 1.38) 0.12 0.437 1.06 0.994
21 NRIP1 rs2823093 A 0.035 0.032 0.90 (0.57, 1.40) 0.23 0.631 0.92 0.994
  1. A pooled odds ratio (pOR) was not obtained for rs11242675 due to significant heterogeneity with other published studies; a pOR with the Asian studies was obtained due to heterogeneity with the results of European studies.*P value was derived from conditional logistic regression analysis. Chr, chromosome; RAF, risk allele frequency; FDR, false discovery rate.