Table 1.

SNPs in pairwise LD at FGFR2, and in pairwise LD at ENO4, are consistently associated with breast cancer

SNPLocusVariantStudyOR (95% CI)P
rs121964810q26.13GNBC1.25 (1.08–1.44)0.0025
123,346,190 bpCGEMS1.33 (1.19–1.50)1.49 × 10−6
FGFR2CBCS1.23 (1.10–1.38)3.57 × 10−4
rs1120001410q26.13TNBC1.25 (1.08–1.44)0.0024
123,334,930 bpCGEMS1.31 (1.17–1.48)4.41 × 10−6
FGFR2CBCS1.20 (1.07–1.34)0.0018
rs242094610q26.13TNBC1.24 (1.07–1.43)0.0042
123,351,324 bpCGEMS1.34 (1.19–1.51)1.18 × 10−6
FGFR2CBCS1.19 (1.06–1.33)0.0024
rs298157910q26.13TNBC1.25 (1.08–1.44)0.0024
123,337,335 bpCGEMS1.31 (1.17–1.48)4.41 × 10−6
FGFR2CBCS1.20 (1.07–1.34)0.0018
rs162667810q25.3GNBC1.19 (1.03–1.37)0.016
118,576,146 bpCGEMS1.19 (1.06–1.33)0.0036
ENO4CBCS1.15 (1.03–1.29)0.013
rs168172310q25.3ANBC1.17 (1.02–1.34)0.030
118,591,615 bpCGEMS1.17 (1.04–1.31)0.0090
ENO4CBCS1.12 (1.00–1.25)0.049
rs74036310q25.3CNBC1.18 (1.02–1.36)0.022
118,575,606 bpCGEMS1.17 (1.05–1.32)0.0065
ENO4CBCS1.14 (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.