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Table 2 Genotype distributions of all tag SNPS in case-control set 1 and the eligible ones in sets 1 and 2 combined

From: Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk

    Set 1 Sets 1 and 2
SNP MAF Base change Controls Cases Odds ratio (95 percent CI) HWE p value Genotype frequency p value Trend test p value Controls Cases Odds ratio (95 percent CI) Trend test p value
ATM
   GG 1,881 1,808 1a        
   ATM-04 0.09 GT 378 364 1.00 [0.86–1.17] 0.84 0.84 0.79     
   rs4987876   TT 18 21 1.21 [0.64–2.29]        
   AA 707 694 1a        
   ATM-05 0.44 AG 1,146 1,069 0.95 [0.83–1.09] 0.24 0.52 0.84     
   rs189037   GG 420 427 1.04 [0.87–1.23]        
   AA 2,103 1,992 1a        
   ATM-06 0.04 AG 169 183 1.14 [0.92–1.42] 0.19 0.47 0.29     
   rs2234996   GG 6 5 0.88 [0.27–2.89]        
   AA 727 713 1a        
   ATM-07 0.43 AG 1,147 1,058 0.94 [0.82–1.07] 0.14 0.37 0.80     
   rs599164   GG 398 409 1.05 [0.88–1.24]        
   AA 1,627 1,611 1a     3,280 3,223 1a  
   ATM-08 0.15 AG 606 553 0.92 [0.81–1.05] 0.03 0.09 0.06 1,193 1,081 0.92 [0.84–1.01] 0.10
   rs3092991   GG 44 27 0.62 [0.38–1.01]     82 74 0.92 [0.67–1.26]  
   GG 1,052 990 1a        
   ATM-09 0.32 GA 1,000 971 1.03 [0.91–1.17] 0.48 0.70 0.41     
   rs665293   AA 222 227 1.09 [0.89–1.33]        
   TT 712 688 1a        
   ATM-10 0.43 TA 1,110 1,036 0.97 [0.84–1.11] 0.45 0.34 0.45     
   rs582157   AA 405 426 1.09 [0.92–1.29]        
   CC 2,043 1,990 1a        
   ATM-11 0.05 CT 214 183 0.88 [0.71–1.08] 0.01 0.35 0.15     
   rs1800889   TT 13 9 0.71 [0.30–1.67]        
   GG 1,945 1,872 1a        
   ATM-12 0.08 GA 310 300 1.01 [0.85–1.19] 0.02 0.48 0.64     
   rs611018   AA 22 14 0.66 [0.34–1.30]        
BRCA1
   P871l   TT 1,001 939 1a        
   BRCA1-01 0.33 TC 1,031 996 1.03 [0.91–1.17] 0.19 0.40 0.22     
   rs1799917   CC 234 252 1.15 [0.94–1.40]        
   Q356R   TT 2,004 1,955 1a     4,013 3,879 1a  
   BRCA1-02 0.06 TC 256 221 0.89 [0.73–1.07] 0.13 0.15 0.08 511 469 0.95 [0.83–1.08] 0.23
   rs1799950   CC 13 6 0.47 [0.18–1.25]     23 14 0.63 [0.32–1.23]  
   TT 1,673 1,580 1a        
   BRCA1-05 0.14 TC 553 568 1.09 [0.95–1.25] 0.87 0.45 0.38     
   rs8176166   CC 47 42 0.95 [0.62–1.44]        
   TT 1,281 1,208 1a        
   BRCA1-06 0.25 TG 857 851 1.05 [0.93–1.19] 0.69 0.68 0.65     
   rs8176199   GG 137 127 0.95 [0.76–1.27]        
   GG 1,893 1,834 1a        
   BRCA1-07 0.09 GA 362 337 0.96 [0.82–1.13] 0.31 0.53 0.38     
   rs3737559   AA 22 15 0.70 [0.36–1.36]        
BRCA2
   TT 715 688 1a        
   BRCA2-01 0.45 TC 1,083 1,057 1.01 [0.89–1.16] 0.08 0.72 0.62     
   rs206115   CC 475 435 0.95 [0.81–1.13]        
   GG 870 813 1a     1,676 1,621 1a  
   BRCA2-02 0.39 GA 1020 1,010 1.06 [0.93–1.21] 0.39 0.63 0.79 2,145 2,028 0.98 [0.89–1.07] 0.95
   rs206116   AA 380 355 1.00 [0.84–1.19]     724 705 1.01 [0.89–1.14]  
   GG 1,576 1,504 1a        
   BRCA2-03 0.17 GA 628 601 1.00 [0.88–1.15] 0.96 0.64 0.58     
   rs3092989   AA 63 71 1.18 [0.83–1.67]        
   AA 1,515 1,506 1a     3,046 2,943 1a  
   BRCA2-04 0.19 GA 667 616 0.93 [0.81–1.06] 0.07 0.02 0.02 1,328 1,287 1.00 [0.92–1.10] 0.29
   rs206118   GG 91 57 0.63 [0.45–0.88]     172 132 0.79 [0.63–1.00]  
   AA 1,353 1,241 1a     2,691 2,502 1a  
   BRCA2-05 0.22 GA 763 719 1.03 [0.90–1.17] 0.09 0.75 0.98 1,594 1,486 1.00 [0.92–1.10] 0.40
   rs206119   GG 102 86 0.92 [0.68–1.24]     203 216 1.14 [0.94–1.40]  
   GG 1,263 1,189 1a        
   BRCA2-07 0.25 GT 875 828 1.01 [0.89–1.14] 0.31 0.21 0.23     
   rs9567552   TT 135 158 1.24 [0.98–1.59]        
   GG 612 626 1a     1,228 1,200 1a  
   BRCA2-09 0.48 GA 1,137 1,082 0.93 [0.81–1.07] 0.46 0.22 0.08 2,317 2,189 0.97 [0.88–1.07] 0.60
   rs9534174   AA 523 461 0.86 [0.72–1.02]     1,006 954 0.97 [0.86–1.09]  
   CC 1,487 1,453 1a        
   BRCA2-10 0.18 CT 669 620 0.95 [0.83–1.08] 0.62 0.63 0.73     
   rs2126042   TT 70 74 1.08 [0.77–1.51]        
   AA 1,824 1,701 1a     3,609 3,434 1a  
   BRCA2-11 0.10 AC 428 450 1.13 [0.97–1.31] 0.40 0.10 0.04 893 876 1.03 [0.92–1.14] 0.28
   rs11571686   CC 25 35 1.50 [0.89–2.52]     52 63 1.27 [0.88–1.84]  
   AA 1,422 1,290 1a     2,812 2,672 1a  
   BRCA2-13 0.21 AG 761 776 1.12 [0.99–1.27] 0.70 0.03 0.01 1,548 1,491 1.01 [0.93–1.11] 0.48
   rs1799955   GG 92 115 1.38 [1.04–1.83]     194 201 1.09 [0.89–1.34]  
   GG 1,204 1,205 1a        
   BRCA2-14 0.27 GA 907 833 0.92 [0.81–1.04] 0.83 0.26 0.10     
   rs1151742   AA 167 145 0.87 [0.68–1.10]        
   AA 1,733 1,603 1a        
   BRCA2-16 0.12 AG 484 414 0.92 [0.80–1.07] 0.33 0.56 0.43     
   rs4942485   GG 34 33 1.05 [0.65–1.70]        
   CC 2,020 1,910 1a        
   BRCA2-18 0.06 CA 235 253 1.14 [0.94–1.38] 6 × 10-5 0.27 0.11     
   rs11571789   AA 19 24 1.34 [0.73–2.45]        
   AA 1,247 1,186 1a        
   BRCA2-19 0.26 AG 829 820 1.04 [0.92–1.18] 0.11 0.83 0.63     
   rs542551   GG 164 159 1.02 [0.81–1.29]        
   AA 1,383 1,370 1a     2,791 2,668 1a  
   BRCA2-21 0.22 AG 769 720 0.94 [0.83–1.07] 0.39 0.15 0.08 1,527 1,465 1.00 [0.92–1.10] 0.54
   rs206343   GG 119 90 0.76 [0.57–1.01]     225 192 0.89 [0.73–1.09]  
   N372H   AA 1,149 1,109 1a     2,306 2,182 1a  
   BRCA2-22 0.28 AC 942 896 0.98 [0.87–1.11] 0.07 0.96 0.78 1,892 1,824 1.02 [0.93–1.11] 0.58
   rs144848   CC 171 161 0.97 [0.77–1.23]     339 333 1.04 [0.88–1.22]  
CHEK2
   AA 914 857 1a        
   CHEK2-05 0.37 AT 1,045 1,019 1.04 [0.92–1.18] 0.55 0.82 0.60     
   rs5762760   TT 315 306 1.04 [0.86–1.24]        
   AA 1,296 1,243 1a        
   CHEK2-06 0.25 AG 813 789 1.01 [0.89–1.15] 0.11 0.72 0.72     
   rs2073327   GG 152 133 0.91 [0.71–1.17]        
   GG 1,554 1,548 1a        
   CHEK2-07 0.17 GC 633 558 0.88 [0.77–1.01] 0.87 0.20 0.12     
   rs2347443   CC 66 62 0.94 [0.66–1.34]        
   GG 1,150 1,130 1a        
   CHEK2-08 0.29 GA 938 868 0.94 [0.83–1.07] 0.63 0.64 0.50     
   rs738722   AA 182 175 0.98 [0.78–1.22]        
   GG 1,718 1,598 1a     3,439 3,199 1a  
   CHEK2-09 0.13 GA 510 553 1.17 [1.02–1.34] 0.31 0.04 0.18 1,021 1,087 1.14 [1.04–1.26] 0.07
   rs2236141   AA 41 29 0.76 [0.47–1.23]     86 69 0.86 [0.63–1.19]  
   GG 1,235 1,198 1a        
   CHEK2-10 0.26 GA 872 834 0.99 [0.87–1.12] 0.55 0.76 0.54     
   rs4035540   AA 144 127 0.91 [0.71–1.17]        
   AA 1,914 1,885 1a     3,866 3,770 1a  
   CHEK2-11 0.08 AT 331 281 0.86 [0.73–1.02] 0.71 0.22 0.10 633 563 0.91 [0.81–1.03] 0.11
   rs1076807   TT 17 15 0.90 [0.45–1.80]     28 23 0.84 [0.48–1.46]  
   GG 1,150 1,130 1a        
   CHEK2-12 0.29 GA 928 851 0.93 [0.82–1.06] 0.87 0.54 0.47     
   rs1807609   AA 184 178 0.98 [0.79–1.23]        
   GG 1,992 1,886 1a        
   CHEK2-13 0.06 GA 270 2,866 1.12 [0.94–1.34] 0.19 0.38 0.17     
   rs17508019   AA 5 7 1.48 [0.47–4.67]        
   CC 694 626 1a     1,410 1,249 1a  
   CHEK2-14 0.45 CG 1,114 1,057 1.05 [0.92–1.21] 0.09 0.18 0.07 2,188 2,123 1.10 [0.99–1.21] 0.02
   rs9608698   GG 463 488 1.17 [0.99–1.38]     940 956 1.15 [1.02–1.29]  
   1100delCb 0.02 CC      0.90   2,887 2,671 1a 0.002
   delC        14 34 2.63 [1.41–4.90]  
TP53
   R72P   GG 1,177 1,107 1a        
   TP53-01 0.27 GC 854 768 0.96 [0.84–1.09] 0.52 0.75 0.48     
   rs1042522   CC 166 148 0.95 [0.75–1.20]        
   CC 1,622 1,545 1a        
   TP53-02 0.14 CT 520 449 0.91 [0.79–1.05] 0.09 0.39 0.20     
   rs1625895   TT 55 48 0.92 [0.62–1.36]        
   CC 1,797 1,699 1a        
   TP53-03 0.11 CG 438 453 1.09 [0.94–1.27] 0.04 0.45 0.41     
   rs2287499   GG 39 34 0.92 [0.58–1.47]        
   AA 2,053 1,971 1a        
   TP53-06 0.05 AG 217 204 0.98 [0.80–1.20] 0.77 0.91 0.94     
   rs17887200   GG 5 6 1.25 [0.38–4.10]        
   CC 2,067 1,986 1a        
   TP53-07 0.05 CT 204 198 1.01 [0.82–1.24] 0.99 0.81 0.76     
   rs17886760   TT 5 7 1.46 [0.46–4.60]        
   CC 865 833 1a        
   TP53-08 0.39 CT 1,069 1,022 0.99 [0.87–1.13] 0.69 0.95 0.89     
   rs9893249   TT 342 336 1.02 [0.84–1.22]        
  1. Values in the minor allele frequency (MAF) and Hardy-Weinberg equilibrium (HWE) p value columns refer to controls only. aReference group. bAttempted in only 61% of subjects. CI, confidence interval.