Table 2

Significant SNPs after Bonferroni correction by gene (Padj)

Pathway

Gene

SNP

Genomic position

Minor Allele

MAF (%) Controls

MAF (%) Cases

OR

95% CI

P

Padj

Model or Test§

Gene P


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


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.

Mirabello et al. BMC Cancer 2011 11:209   doi:10.1186/1471-2407-11-209

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