SNPs in pairwise LD at FGFR2, and in pairwise LD at ENO4, are consistently associated with breast cancer
SNP | Locus | Variant | Study | OR (95% CI) | P |
---|---|---|---|---|---|
rs1219648 | 10q26.13 | G | NBC | 1.25 (1.08–1.44) | 0.0025 |
123,346,190 bp | CGEMS | 1.33 (1.19–1.50) | 1.49 × 10−6 | ||
FGFR2 | CBCS | 1.23 (1.10–1.38) | 3.57 × 10−4 | ||
rs11200014 | 10q26.13 | T | NBC | 1.25 (1.08–1.44) | 0.0024 |
123,334,930 bp | CGEMS | 1.31 (1.17–1.48) | 4.41 × 10−6 | ||
FGFR2 | CBCS | 1.20 (1.07–1.34) | 0.0018 | ||
rs2420946 | 10q26.13 | T | NBC | 1.24 (1.07–1.43) | 0.0042 |
123,351,324 bp | CGEMS | 1.34 (1.19–1.51) | 1.18 × 10−6 | ||
FGFR2 | CBCS | 1.19 (1.06–1.33) | 0.0024 | ||
rs2981579 | 10q26.13 | T | NBC | 1.25 (1.08–1.44) | 0.0024 |
123,337,335 bp | CGEMS | 1.31 (1.17–1.48) | 4.41 × 10−6 | ||
FGFR2 | CBCS | 1.20 (1.07–1.34) | 0.0018 | ||
rs1626678 | 10q25.3 | G | NBC | 1.19 (1.03–1.37) | 0.016 |
118,576,146 bp | CGEMS | 1.19 (1.06–1.33) | 0.0036 | ||
ENO4 | CBCS | 1.15 (1.03–1.29) | 0.013 | ||
rs1681723 | 10q25.3 | A | NBC | 1.17 (1.02–1.34) | 0.030 |
118,591,615 bp | CGEMS | 1.17 (1.04–1.31) | 0.0090 | ||
ENO4 | CBCS | 1.12 (1.00–1.25) | 0.049 | ||
rs740363 | 10q25.3 | C | NBC | 1.18 (1.02–1.36) | 0.022 |
118,575,606 bp | CGEMS | 1.17 (1.05–1.32) | 0.0065 | ||
ENO4 | CBCS | 1.14 (1.02–1.28) | 0.021 |
The four SNPs in the second intron of FGFR2 have pairwise LD values ≥ 0.84, whereas those near ENO4 have pairwise LD values ≥ 0.90. FGFR2 and ENO4 are 4.7 MB apart, not in linkage disequilibrium with each other. SNP nucleotide positions are given for human genome build GRCh37/hg19.