Table 2 |
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|
Significant SNPs after Bonferroni correction by gene (Padj) |
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|
Pathway |
Gene |
SNP |
Genomic position |
Minor Allele |
MAF (%) Controls |
MAF (%) Cases |
OR† |
95% CI |
P |
Padj |
Model or Test§ |
Gene P |
|
|
|
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|
DNA repair |
FANCM |
rs1367580 |
Chr14: 44714339 |
Ex14+316 (V878L) |
T |
10.4 |
16.7 |
1.97 |
(1.26-3.08) |
0.0031 |
0.034 |
Dominant |
0.019 |
|
rs11845507 |
Chr14: 44721715 |
IVS16-1012 |
A |
10.5 |
16.7 |
1.96 |
(1.25-3.06) |
0.0033 |
0.037 |
Dominant |
|||
|
rs4900664 |
Chr14: 44732264 |
IVS20-2861 |
T |
9.3 |
15.3 |
2.00 |
(1.25-3.17) |
0.0035 |
0.038 |
Dominant |
|||
|
rs7141145 |
Chr14: 44733578 |
IVS20-1547 |
A |
10.3 |
16.5 |
1.95 |
(1.24-3.07) |
0.0039 |
0.043 |
Dominant |
|||
|
MDM2 |
rs1690916 |
Chr12: 67521673 |
downstream, no gene |
A |
42.5 |
31.3 |
0.62 |
(0.45-0.85) |
0.0029 |
0.026 |
Additive |
0.016 |
|
|
MPG |
rs216614 |
Chr16: 60334 |
upstream, in RHBDF1 |
A |
0.7 |
3.1 |
4.80 |
-- |
0.0036 |
0.047 |
Fisher's |
0.027 |
|
|
|
|||||||||||||
|
Growth and hormone |
FGF2 |
rs11737764 |
Chr4: 124046230 |
downstream, in NUDT6 |
T |
8.1 |
14.1 |
2.12 |
(1.33-3.39) |
0.0016 |
0.036 |
Dominant |
0.020 |
|
FGFR3 |
rs6599400 |
Chr4: 1754823 |
upstream, no gene |
A |
33.0 |
42.6 |
1.51 |
(1.12-2.03) |
0.0069 |
0.021 |
Additive |
0.017 |
|
|
GH1 |
rs11079515 |
Chr17: 59359377 |
downstream, no gene |
G |
37.9 |
49.5 |
1.61 |
(1.20-2.16) |
0.0016 |
0.005 |
Additive |
0.002 |
|
|
rs7921 |
Chr17: 59359991 |
downstream, in CD79B |
A |
27.2 |
16.1 |
0.52 |
(0.35-0.76) |
0.0009 |
0.003 |
Additive |
|||
|
GNRH2 |
rs3761243 |
Chr20: 2971022 |
upstream, no gene |
C |
29.7 |
40.5 |
1.60 |
(1.19-2.16) |
0.0020 |
0.031 |
Additive |
0.021 |
|
|
IGF1 |
rs7956547 |
Chr12: 101382946 |
IVS2+10605 |
C |
26.3 |
15.8 |
0.53 |
(0.36-0.79) |
0.0019 |
0.040 |
Additive |
0.021 |
|
|
|
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|
MAF = minor allele frequency; † Odds ratios were estimated using logistic regression models with the most common allele or genotype as the referent, adjusted for gender; § Results are shown for the model or test chosen to deal with rare variants in the sequence of logistic regression on the additive trend model, logistic regression on the dominant model, or the Fisher's Exact Test. |
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|
Mirabello et al. BMC Cancer 2011 11:209 doi:10.1186/1471-2407-11-209 |
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