Table II. Breast Cancer risks associated with the tag SNPs examined in this study.
| Gene and SNPs | MAF | OR (95% CI) (heterozygotes versus common homozygotes) |
OR (95% CI) (rare homozygotes versus common homozygotes) |
Heterogeneity, P-value (2df) |
Trend test, P-value (1 df) |
|---|---|---|---|---|---|
| CCND1 | |||||
| rs602652 (07) | 0.48 | 0.93 (0.81–1.07) | 0.97 (0.83–1.15) | 0.599 | 0.713 |
| rs3862792 (02)a | 0.03 | 1.07 (0.83–1.39) | 1.07 (0.07–17.14) | 0.871 | 0.600 |
| rs603965 (03) | 0.46 | 0.92 (0.80–1.06) | 0.90 (0.76–1.07) | 0.386 | 0.205 |
| rs3212879 (08) | 0.46 | 1.03 (0.90–1.18) | 1.09 (0.92–1.29) | 0.612 | 0.329 |
| rs3212891 (10) | 0.43 | 1.01 (0.88–1.15) | 1.09 (0.92–1.29) | 0.559 | 0.371 |
| rs678653 (04) | 0.35 | 1.06 (0.97–1.16) | 1.14 (0.99–1.30) | 0.136 | 0.046 |
| rs7178 (01)a | 0.07 | 0.99 (0.83–1.18) | 1.10 (0.49–2.45) | 0.969 | 0.994 |
| CCND2 | |||||
| rs3217795 (01) | 0.10 | 1.01 (0.87–1.17) | 1.21 (0.64–2.29) | 0.833 | 0.752 |
| rs3217805 (02) | 0.40 | 0.87 (0.77–1.00) | 0.93 (0.77–1.11) | 0.129 | 0.180 |
| rs3217820 (03) | 0.38 | 1.05 (0.92–1.19) | 0.90 (0.75–1.09) | 0.255 | 0.573 |
| rs3217852 (09) | 0.24 | 0.95 (0.84–1.08) | 0.91 (0.71–1.17) | 0.615 | 0.324 |
| rs3217862 (10) | 0.16 | 1.01 (0.89–1.16) | 1.28 (0.90–1.82) | 0.379 | 0.355 |
| rs3217863 (11) | 0.07 | 1.02 (0.86–1.20) | 1.17 (0.45–3.04) | 0.934 | 0.779 |
| rs3217869 (05) | 0.38 | 1.14 (1.00–1.29) | 1.08 (0.90–1.29) | 0.141 | 0.183 |
| rs3217901 (18) | 0.43 | 1.01 (0.89–1.15) | 0.90 (0.76–1.07) | 0.351 | 0.317 |
| rs3217906 (14) | 0.26 | 0.97 (0.85–1.10) | 0.93 (0.74–1.18) | 0.781 | 0.483 |
| rs3217916 (15) | 0.27 | 1.02 (0.90–1.15) | 1.02 (0.81–1.29) | 0.952 | 0.764 |
| rs3217925 (16) | 0.25 | 1.04 (0.92–1.18) | 1.00 (0.78–1.28) | 0.796 | 0.678 |
| rs3217926 (06) | 0.40 | 1.06 (0.94–1.21) | 0.89 (0.74–1.06) | 0.101 | 0.404 |
| rs3217933 (17) | 0.26 | 1.00 (0.88–1.13) | 0.91 (0.72–1.16) | 0.751 | 0.620 |
| rs3217936 (07) | 0.32 | 1.04 (0.92–1.18) | 1.11 (0.91–1.35) | 0.570 | 0.293 |
| CCND3 | |||||
| rs3218114 (08) | 0.17 | 1.07 (0.94–1.22) | 0.88 (0.60–1.27) | 0.445 | 0.673 |
| rs3218110 (07) | 0.25 | 1.08 (0.95–1.22) | 0.99 (0.78–1.26) | 0.488 | 0.488 |
| rs9529 (06) | 0.28 | 0.90 (0.79–1.01) | 0.98 (0.78–1.24) | 0.206 | 0.239 |
| rs1051130 (03)b | 0.45 | 0.93 (0.82–1.07) | 0.92 (0.78–1.08) | 0.507 | 0.282 |
| rs2479717 (02) | 0.27 | 0.90 (0.80–1.02) | 0.96 (0.76–1.22) | 0.264 | 0.217 |
| rs3218092 (04) | 0.17 | 1.02 (0.90–1.17) | 0.87 (0.61–1.25) | 0.690 | 0.914 |
| rs1410492 (01) | 0.27 | 0.97 (0.86–1.10) | 0.88 (0.70–1.11) | 0.554 | 0.321 |
| CCNE1 | |||||
| rs997669 (02) | 0.39 | 1.13 (1.03–1.24) | 1.18 (1.04–1.34) | 0.008 | 0.003 |
| rs3218036 (12) | 0.32 | 1.09 (0.96–1.23)) | 1.12 (0.92–1.36) | 0.326 | 0.150 |
| rs3218038 (05) | 0.04 | 0.96 (0.77–1.21) | 103.75 (0.00–37209) | 0.573 | 0.836 |
| rs3218076 (08)a | 0.27 | 1.06 (0.94–1.20) | 0.82 (0.65-1.05) | 0.112 | 0.647 |
| CDK2 | |||||
| rs2069408 (02) | 0.33 | 1.07 (0.94–1.21) | 0.96 (0.79-1.17) | 0.447 | 0.866 |
| rs1045435 (04) | 0.08 | 0.99 (0.84–1.17) | 1.30 (0.67–2.51) | 0.731 | 0.820 |
| CDK4 | |||||
| rs2270777 (01) | 0.43 | 1.14 (0.99–1.31) | 1.08 (0.91–1.29) | 0.169 | 0.233 |
| rs2069506 (02)b | 0.34 | 1.01 (0.88–1.15) | 0.86 (0.71–1.05) | 0.299 | 0.285 |
| CDK6 | |||||
| rs8179 (09)b | 0.20 | 1.13 (0.99–1.28) | 0.95 (0.71–1.26) | 0.156 | 0.294 |
| rs2285332 (12) | 0.25 | 0.91 (0.80–1.03) | 1.08 (0.84–1.37) | 0.216 | 0.580 |
| rs42046 (08) | 0.26 | 1.08 (0.96–1.22) | 1.03 (0.82–1.31) | 0.454 | 0.335 |
| rs3731348 (11) | 0.05 | 1.16 (0.96–1.40) | 0.79 (0.18–3.55) | 0.292 | 0.157 |
| rs2237570 (13) | 0.11 | 0.94 (0.85–1.05) | 0.92 (0.64–1.31) | 0.512 | 0.251 |
| rs3731343 (01) | 0.47 | 0.94 (0.82–1.08) | 0.94 (0.80–1.12) | 0.665 | 0.469 |
| rs3757823 (02) | 0.09 | 1.09 (0.98–1.22) | 1.24 (0.76–2.02) | 0.211 | 0.079 |
| rs2079147 (03) | 0.46 | 0.99 (0.87–1.14) | 1.04 (0.88–1.23) | 0.801 | 0.639 |
| rs2282991 (10) | 0.10 | 0.91 (0.81–1.02) | 0.90 (0.58–1.40) | 0.243 | 0.100 |
| rs4729049 (04) | 0.09 | 1.00 (0.85–1.17) | 0.73 (0.37–1.44) | 0.655 | 0.703 |
| rs8 (05)b | 0.21 | 0.92 (0.81–1.04) | 1.20 (0.88–1.65) | 0.168 | 0.719 |
| rs445 (06) | 0.10 | 1.04 (0.89–1.21) | 0.93 (0.54–1.62) | 0.861 | 0.758 |
| rs992519 (07) | 0.14 | 0.91 (0.80–1.05) | 1.31 (0.84–2.02) | 0.188 | 0.631 |
| CDKN1A | |||||
| rs762624 (07) | 0.27 | 1.02 (0.93–1.11) | 1.22 (1.04–1.44) | 0.051 | 0.063 |
| rs2395655 (06) | 0.39 | 0.99 (0.87–1.12) | 1.11 (0.93–1.32) | 0.393 | 0.372 |
| rs3176326 (17) | 0.21 | 0.98 (0.87–1.11) | 1.13 (0.83–1.53) | 0.676 | 0.811 |
| rs3176331 (11) | 0.13 | 0.97 (0.84–1.12) | 1.13 (0.70–1.81) | 0.807 | 0.927 |
| rs3176336 (12) | 0.39 | 1.01 (0.92–1.11) | 1.25 (1.11–1.42) | 0.00078 | 0.0026 |
| rs3176343 (14) | 0.05 | 1.09 (0.89–1.32) | 2.10 (0.72–6.16) | 0.283 | 0.217 |
| rs1801270 (01) | 0.06 | 1.08 (0.95–1.23) | 2.08 (1.18–3.68) | 0.021 | 0.040 |
| rs3176352 (02) | 0.26 | 1.04 (0.95–1.14) | 1.18 (1.00–1.40) | 0.124 | 0.063 |
| rs1059234 (03) | 0.06 | 1.09 (0.90–1.32) | 3.28 (1.39–7.73) | 0.011 | 0.039 |
| rs6457937 (04)a | 0.09 | 1.07 (0.91–1.25) | 1.56 (0.89–2.74) | 0.224 | 0.151 |
| CDKN1B | |||||
| rs3759216 (04) | 0.46 | 0.86 (0.75–0.99) | 0.96 (0.81–1.13) | 0.084 | 0.417 |
| rs3759217 (05) | 0.13 | 0.91 (0.79–1.05) | 1.02 (0.61–1.70) | 0.405 | 0.262 |
| rs34330 (01) | 0.24 | 1.08 (0.99–1.18) | 1.22 (1.02–1.47) | 0.044 | 0.013 |
| rs2066827 (02) | 0.24 | 0.98 (0.86–1.12) | 0.95 (0.72–1.25) | 0.908 | 0.668 |
| rs34329 (06) | 0.31 | 0.89 (0.79–1.01) | 1.12 (0.92–1.38) | 0.043 | 0.934 |
| rs3093736 (07) | 0.03 | 0.94 (0.73–1.21) | 2.08 (0.52–8.33) | 0.508 | 0.943 |
| rs7330 (03) a | 0.40 | 1.04 (0.94–1.14) | 1.10 (0.97–1.24) | 0.354 | 0.155 |
| rs1420023 (08) | 0.11 | 0.96 (0.82–1.12) | 0.93 (0.56–1.56) | 0.842 | 0.559 |
| CDKN2A/2B | |||||
| rs3731257 (2A–13) | 0.25 | 1.10 (0.97–1.25) | 0.95 (0.74–1.20) | 0.232 | 0.514 |
| rs3088440 (2A–11) | 0.09 | 0.93 (0.79–1.10) | 0.70 (0.36–1.35) | 0.409 | 0.234 |
| rs11515 (2A–10) | 0.14 | 1.03 (0.89–1.18) | 1.44 (0.94–2.21) | 0.227 | 0.246 |
| rs3731249 (2A–12)a | 0.03 | 0.96 (0.74–1.23) | 1.04 (0.15–7.41) | 0.939 | 0.742 |
| rs3731239 (2A–09) | 0.37 | 0.86 (0.79–0.94) | 0.90 (0.79–1.03) | 0.005 | 0.013 |
| rs4074785(2A–14)a | 0.10 | 0.94 (0.80–1.10) | 0.71 (0.38–1.35) | 0.442 | 0.256 |
| rs3731222 (2A–01)ab | 0.14 | 0.94 (0.82–1.08) | 1.52 (0.96–2.39) | 0.119 | 0.861 |
| rs3731211(2A–02)b | 0.28 | 1.00 (0.92–1.09) | 1.25 (1.07–1.47) | 0.018 | 0.059 |
| rs3731197 (2A–15) | 0.39 | 0.97 (0.85–1.10) | 1.08 (0.90–1.29) | 0.488 | 0.603 |
| rs3218020 (2A–03) | 0.34 | 0.98 (0.86–1.11) | 1.04 (0.86–1.26) | 0.823 | 0.855 |
| rs2811712(2A–04) | 0.10 | 1.06 (0.95–1.17) | 1.64 (1.11–2.42) | 0.030 | 0.045 |
| rs3218012(2B–04) | 0.44 | 0.92 (0.81–1.05) | 0.96 (0.81–1.14) | 0.492 | 0.505 |
| rs3218009 (2B–03) | 0.12 | 0.99 (0.86–1.14) | 1.24 (0.74–2.08) | 0.701 | 0.832 |
| rs3218005 (2A–05) | 0.09 | 1.11 (0.99–1.24) | 1.55 (1.02–2.37) | 0.027 | 0.013 |
| rs3217992 (2A–06) | 0.37 | 1.04 (0.91–1.18) | 1.00 (0.84–1.21) | 0.837 | 0.796 |
| rs1063192 (2B–02) | 0.45 | 0.93 (0.81–1.06) | 0.94 (0.80–1.12) | 0.538 | 0.421 |
| CDKN2C | |||||
| rs3176459 (02) | 0.33 | 1.02 (0.90–1.16) | 1.09 (0.89–1.32) | 0.698 | 0.431 |
| rs12855 (01) | 0.10 | 0.85 (0.73–0.99) | 1.19 (0.63–2.24) | 0.105 | 0.111 |
| CDKN2D | |||||
| rs3218222 (02) | 0.23 | 1.10 (0.98–1.25) | 1.00 (0.78–1.30) | 0.284 | 0.290 |
| rs1465701 (01) | 0.05 | 0.98 (0.81–1.20) | 1.46 (0.46–4.62) | 0.795 | 0.957 |
SNPs shaded grey were taken through into set 2. The results presented here refer to the combined data for set 1 and set 2.
a
Extra SNPs genotyped that were not part of the tagging set.
b
Controls are out of Hardy–Weinberg.