Table 3.
Results of association analysis of candidate genes with nominal p values ≤0.05. SNP: single nucleotide polymorphism. Major allele: most frequent in sample. Minor allele: least frequent in sample. OR: odds ratio. χ2: chi square statistic. P: nominal p value. EMP: empirical p value after permutation analysis.
| Gene (band) | SNP (position) | Role | Major Allele |
Minor Allele |
Minor Allele Relative Frequency Cases |
Minor Allele Relative Frequency Controls |
Genotype Count Cases |
Genotype Count Controls |
OR | χ2 | P | EMP |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IRF6 (1q32.2) | rs2235372 (208027059) | Near-gene-3 | G | A | 0.25 | 0.12 | 2/15/21 | 0/15/48 | 2.47 | 5.81 | 0.02 | 0.06 |
| rs742215 (208027646) | Near-gene-3 | A | T | 0.25 | 0.12 | 2/15/21 | 0/15/48 | 2.47 | 5.81 | 0.02 | 0.06 | |
| rs17317411 (208027937) | Untranslated-3 | T | C | 0.22 | 0.08 | 2/13/23 | 0/11/52 | 3.01 | 7.39 | 0.007 | 0.03 | |
| rs17015218 (208034538) | Intron | A | G | 0.24 | 0.10 | 2/14/22 | 0/13/50 | 2.70 | 6.52 | 0.01 | 0.04 | |
| rs17015226 (208036719) | Intron | C | G | 0.24 | 0.10 | 2/14/22 | 0/13/50 | 2.70 | 6.52 | 0.01 | 0.04 | |
| rs6540560 (208048696) | Unknown | C | T | 0.24 | 0.10 | 2/14/22 | 0/13/50 | 2.70 | 6.52 | 0.01 | 0.04 | |
| rs6696825 (208048995) | Unknown | A | G | 0.25 | 0.12 | 2/15/21 | 0/15/48 | 2.47 | 5.81 | 0.02 | 0.06 | |
| TGFA (2p13.3) | rs432203 (70618196) | Intron | G | T | 0.54 | 0.37 | 11/18/8 | 12/23/28 | 1.98 | 5.32 | 0.02 | 0.29 |
| rs377122 (70620533) | Intron | C | T | 0.53 | 0.37 | 11/18/9 | 12/23/28 | 1.87 | 4.54 | 0.03 | 0.47 | |
| SATB2 (2q33.1) | rs4673309 (199855654) | Intron | A | G | 0.21 | 0.08 | 1/14/23 | 0/10/53 | 3.10 | 7.27 | 0.007 | 0.04 |
| rs10497832 (199875181) | Intron | G | C | 0.21 | 0.08 | 1/14/23 | 0/10/53 | 3.10 | 7.27 | 0.007 | 0.04 | |
| rs1374361 (199878979) | Intron | C | T | 0.18 | 0.08 | 1/12/25 | 0/10/53 | 2.62 | 4.98 | 0.03 | 0.14 | |
| rs4675475 (199884288) | Intron | G | T | 0.30 | 0.18 | 2/19/17 | 1/21/41 | 1.94 | 3.89 | 0.05 | 0.28 | |
| rs7569519 (199888067) | Intron | A | C | 0.30 | 0.18 | 2/19/17 | 1/21/41 | 1.94 | 3.89 | 0.05 | 0.28 | |
| rs930616 (199894160) | Intron | A | G | 0.30 | 0.18 | 2/19/17 | 1/21/41 | 1.94 | 3.89 | 0.05 | 0.28 | |
| rs17197938 (199908430) | Intron | C | T | 0.12 | 0.25 | 0/9/29 | 2/28/33 | 0.39 | 5.38 | 0.02 | 0.12 | |
| rs16831370 (199939292) | Intron | C | G | 0.01 | 0.07 | 0/1/37 | 0/10/53 | 0.15 | 4.04 | 0.04 | 0.26 | |
| rs10497836 (199996963) | Intron | T | C | 0.39 | 0.24 | 4/22/12 | 2/26/35 | 2.09 | 5.57 | 0.02 | 0.12 | |
| rs895882 (200011260) | Intron | A | G | 0.39 | 0.24 | 4/22/12 | 2/26/35 | 2.09 | 5.57 | 0.02 | 0.12 | |
| rs13392032 (200017738) | Intron | C | G | 0.29 | 0.17 | 1/20/17 | 3/15/45 | 2.04 | 4.27 | 0.04 | 0.21 | |
| MTRR (5p15.31) | rs17184211 (7919106) | Intron | A | T | 0.14 | 0.27 | 3/5/30 | 3/28/31 | 0.45 | 4.53 | 0.03 | 0.23 |
| FGF10 (5p12) | rs17234541 (44344655) | Intron | G | T | 0.01 | 0.11 | 0/1/37 | 2/10/51 | 6.62 | 0.11 | 0.01 | 0.08 |
| rs17234079 (4497961) | Intron | C | T | 0.28 | 0.10 | 2/17/19 | 1/11/51 | 3.32 | 10.15 | 0.001 | 0.01 | |
| rs10512852 (44429326) | Unknown | T | C | 0.01 | 0.17 | 0/1/37 | 3/16/44 | 0.06 | 12.25 | 0.0005 | 0.005 | |
| ESR1 (6q25.1) | rs1543403 (152470397) | Unknown | G | C | 0.59 | 0.44 | 12/21/5 | 10/36/17 | 1.82 | 4.14 | 0.04 | 0.63 |
| FGFR2 (10q26.13) | rs1649202 (123230615) | Intron | C | T | 0.50 | 0.31 | 11/16/11 | 6/26/30 | 2.26 | 7.49 | 0.006 | 0.06 |
| rs2278202 (123233187) | Intron | A | G | 0.46 | 0.26 | 8/19/11 | 4/25/34 | 2.41 | 8.38 | 0.004 | 0.04 | |
| FGF3 (11q13.3) | rs12577891 (69332822) | Near-gene-3 | G | T | 0.29 | 0.17 | 7/8/23 | 2/17/44 | 2.04 | 4.27 | 0.04 | 0.20 |
| rs10908228 (69336099) | Intron | C | T | 0.29 | 0.17 | 7/8/23 | 2/17/44 | 2.04 | 4.27 | 0.04 | 0.20 | |
| PVRL1 (11q23.3) | rs10790332 (119058888) | Intron | T | C | 0.36 | 0.50 | 5/17/16 | 13/37/13 | 0.55 | 4.02 | 0.05 | 0.19 |
| rs4936492 (119065659) | Intron | G | A | 0.36 | 0.52 | 5/17/16 | 15/35/13 | 0.52 | 4.93 | 0.03 | 0.12 | |
| rs7950059 (119070705) | Intron | C | T | 0.38 | 0.54 | 6/17/15 | 15/38/10 | 0.53 | 4.75 | 0.03 | 0.13 | |
| rs1467051 (119073511) | Intron | G | A | 0.35 | 0.53 | 5/16/16 | 13/39/9 | 0.48 | 6.10 | 0.01 | 0.07 | |
| rs7945395 (119074947) | Intron | A | G | 0.34 | 0.53 | 6/14/18 | 14/39/10 | 0.46 | 6.87 | 0.009 | 0.04 | |
| rs7945424 (119075012) | Intron | G | T | 0.33 | 0.54 | 5/14/17 | 14/40/9 | 0.43 | 7.84 | 0.005 | 0.02 | |
| rs715849 (119080934) | Intron | G | A | 0.34 | 0.52 | 6/14/18 | 13/40/10 | 0.47 | 6.31 | 0.01 | 0.06 | |
| CBS (21q22.3) | rs2839631 (43343155) | Unknown | C | T | 0.46 | 0.33 | 7/21/10 | 5/31/27 | 1.77 | 3.69 | 0.05 | 0.22 |
| rs9325622 (43352770) | Intron | G | A | 0.46 | 0.32 | 7/21/10 | 5/30/28 | 1.84 | 4.16 | 0.04 | 0.19 | |
| rs1789953 (43356005) | Intron | T | C | 0.07 | 0.18 | 0/5/33 | 2/19/42 | 0.32 | 5.41 | 0.02 | 0.10 |