Table 2.
MMP-2 SNPs and Breast Cancer Risk, The Shanghai Breast Cancer Study
| SNP | Alleles * | Region | Method † | Study Phase † | MAF (%) ‡ | Breast Cancer Risk § |
||
|---|---|---|---|---|---|---|---|---|
| AB OR (95% CI) | BB OR (95% CI) | p-value | ||||||
| rs1005912 | T/A | promoter | Affy 6.0 | 1 & 2 | 45.3 | 1.2 (1.0–1.3) | 1.1 (0.9–1.3) | 0.207 |
| rs1116195 | A/T | promoter | Targeted | 1 & 2 | 44.6 | 1.0 (0.9–1.2) | 1.2 (1.0–1.4) | 0.075 |
| rs11644561 | G/A | promoter | Affy 6.0 | 1 & 2 | 13.0 | 0.9 (0.8–1.1) | 0.6 (0.3–1.0) | 0.098 |
| rs243867 | A/G | promoter | Affy 6.0 | 1 & 2 | 40.4 | 1.1 (0.9–1.2) | 1.1 (0.9–1.3) | 0.403 |
| rs11643630 | T/G | promoter | Affy 6.0 | 1 & 2 | 42.9 | 1.0 (0.8–1.1) | 0.8 (0.7–1.0) | 0.046 |
| rs243866 | G/A | promoter | Affy 6.0 | 1 & 2 | 11.0 | 1.0 (0.9–1.2) | 1.2 (0.7–2.1) | 0.602 |
| rs243865 | C/T | promoter | Targeted | 1 & 2 | 11.5 | 0.9 (0.8–1.1) | 1.4 (0.9–2.4) | 0.776 |
| rs243864 | T/G | promoter | Affy 6.0 | 1 & 2 | 10.7 | 1.0 (0.9–1.2) | 1.1 (0.6–2.0) | 0.782 |
| rs2285053 | C/T | promoter | Targeted | Phase 2 | 23.4 | 1.2 (1.0–1.4) | 0.9 (0.6–1.2) | 0.436 |
| rs1477017 | A/G | intron 2 | Both | 1 & 2 | 27.4 | 1.0 (0.9–1.2) | 1.0 (0.8–1.2) | 0.833 |
| rs865094 | A/G | intron 2 | Both | 1 & 2 | 29.1 | 0.9 (0.8–1.0) | 1.1 (0.9–1.4) | 0.838 |
| rs11646643 | A/G | intron 3 | Affy 6.0 | 1 & 2 | 15.5 | 1.0 (0.8–1.1) | 1.1 (0.7–1.6) | 0.726 |
| rs1053605 | C/T | exon 5 | Both | 1 & 2 | 13.0 | 1.1 (0.9–1.2) | 0.8 (0.4–1.3) | 0.862 |
| rs9302671 | G/T | intron 5 | Affy 6.0 | 1 & 2 | 15.3 | 1.0 (0.8–1.1) | 1.1 (0.8–1.6) | 0.936 |
| rs2241145 | G/C | intron 5 | Targeted | Phase 1 | 48.9 | 1.0 (0.8–1.2) | 0.9 (0.8–1.2) | 0.613 |
| rs2241146 | G/A | intron 5 | Targeted | Phase 1 | 21.8 | 1.1 (0.9–1.3) | 1.0 (0.7–1.5) | 0.632 |
| rs243849 | C/T | exon 7 | Affy 6.0 | 1 & 2 | 18.8 | 0.9 (0.8–1.1) | 1.1 (0.8–1.6) | 0.816 |
| rs12599775 | G/C | intron 7 | Targeted | Phase 1 | 11.2 | 1.1 (0.9–1.4) | 0.9 (0.4–1.9) | 0.453 |
| rs243847 | T/C | intron 7 | Both | 1 & 2 | 42.3 | 1.1 (0.9–1.2) | 1.0 (0.8–1.2) | 0.881 |
| rs2192852 | A/G | intron 7 | Targeted | Phase 1 | 38.1 | 1.0 (0.8–1.2) | 0.9 (0.7–1.2) | 0.546 |
| rs12923011 | C/T | intron 7 | Targeted | Phase 1 | 16.4 | 0.9 (0.7–1.1) | 0.7 (0.4–1.3) | 0.118 |
| rs243845 | G/A | intron 8 | Affy 6.0 | 1 & 2 | 31.1 | 1.0 (0.9–1.2) | 1.0 (0.8–1.2) | 0.945 |
| rs243844 | G/A | intron 8 | Targeted | Phase 1 | 30.7 | 1.0 (0.8–1.2) | 1.1 (0.8–1.5) | 0.604 |
| rs2287074 | G/A | exon 9 | Targeted | Phase 1 | 27.4 | 1.0 (0.8–1.2) | 0.8 (0.5–1.1) | 0.276 |
| rs243842 | T/C | intron 9 | Affy 6.0 | 1 & 2 | 31.9 | 1.0 (0.9–1.2) | 1.0 (0.8–1.2) | 0.882 |
| rs183112 | G/A | intron 9 | Targeted | Phase 1 | 18.7 | 1.0 (0.8–1.2) | 0.9 (0.6–1.5) | 0.874 |
| rs243839 | A/G | intron 9 | Both | 1 & 2 | 41.1 | 1.0 (0.9–1.1) | 1.0 (0.8–1.2) | 0.924 |
| rs9923304 | C/T | intron 9 | Affy 6.0 | 1 & 2 | 27.1 | 1.0 (0.9–1.2) | 0.9 (0.7–1.2) | 0.983 |
| rs11639960 | A/G | intron 10 | Both | 1 & 2 | 28.8 | 1.0 (0.9–1.1) | 1.1 (0.8–1.3) | 0.889 |
| rs243831 | T/G | 3′ FR || | Targeted | Phase 1 | 13.6 | 0.8 (0.7–1.0) | 0.8 (0.4–1.6) | 0.113 |
| rs12930259 | T/C | 3′ FR || | Targeted | Phase 1 | 33.6 | 1.0 (0.9–1.2) | 1.0 (0.7–1.3) | 0.899 |
| rs2192853 | A/G | 3′ FR || | Targeted | Phase 1 | 35.8 | 0.9 (0.8–1.1) | 1.0 (0.7–1.3) | 0.607 |
| rs1583587 | G/C | 3′ FR || | Affy 6.0 | 1 & 2 | 35.7 | 1.0 (0.9–1.2) | 1.0 (0.8–1.2) | 0.796 |
| rs8053806 | C/A | 3′ FR || | Affy 6.0 | 1 & 2 | 23.4 | 1.1 (1.0–1.3) | 1.1 (0.9–1.5) | 0.139 |
| rs12708952 | G/C | 3′ FR || | Affy 6.0 | 1 & 2 | 36.0 | 1.0 (0.9–1.2) | 1.0 (0.8–1.2) | 0.874 |
| rs1583585 | G/A | 3′ FR || | Affy 6.0 | 1 & 2 | 23.1 | 1.1 (0.9–1.2) | 1.1 (0.9–1.5) | 0.192 |
Major/minor alleles as determined by allele frequency among genotyped controls
Genotyping Method and SBCS Study Phase: Affymetrix Targeted Genotyping among 1,062 cases and 1,069 controls from SBCS Phase 1 and/or Sequenom Targeted Genotyping among 1,495 cases and 1,437 controls from SBCS Phase 2 (Targeted), or Affymetrix 6.0 genotyping among 1,104 cases and 1,109 controls from Phase 1, and 965 cases and 971 controls from SBCS Phase 2 (Affy 6.0), or genotyped by both methods (Both); study phases 1&2 show pooled estimates
Minor allele freqency among all genotyped controls
Risk of breast cancer, adjusted for age, education, and Study Phase (when appropriate); AA major allele homozygotes (reference group), AB heterozygotes, BB minor allele homozygotes; p-value for trend from additive models
3′ FR: downstream flanking region, 3′ of the MMP-2 gene
Bold values considered to be significant at p≤0.05