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Table 3 Genotype relative risk evaluated from genotype distribution of SNPs in PGM1.

From: Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses

  

Frequency

  

SNP

Genotype

Case

Control

Relative Risk

95% CI

SNP1

0

0.6513

0.6528

0.9977

(0.9573-1.0399)

 

1

0.3082

0.3076

1.0018

(0.9204-1.0905)

 

2

0.0405

0.0396

1.0229

(0.7757-1.3488)

SNP2

0

0.6493

0.6521

0.9957

(0.9552-1.0379)

 

1

0.3087

0.3079

1.0024

(0.9209-1.0910)

 

2

0.0420

0.0399

1.0519

(0.8006-1.3822)

SNP3

0

0.6153

0.6568

0.9368

(0.8972-0.9782)

 

1

0.3472

0.3056

1.1361

(1.0479-1.2316)

 

2

0.0375

0.0376

0.9974

(0.7490-1.3281)

SNP4

0

0.6638

0.6668

0.9956

(0.9564-1.0364)

 

1

0.2991

0.2969

1.0074

(0.9237-1.0988)

 

2

0.0370

0.0363

1.0202

(0.7636-1.3631)

(SNP1, SNP3)

0 0

0.6043

0.6448

0.9372

(0.8966-0.9796)

 

0 1

0.0470

0.0080

5.8858

(3.7730-9.1816)

 

1 0

0.0110

0.0120

0.9183

(0.5420-1.5561)

 

1 1

0.2961

0.2943

1.0064

(0.9222-1.0983)

 

1 2

0.0010

0.0013

0.7514

(0.1378-4.0984)

 

2 1

0.0040

0.0033

1.2022

(0.4753-3.0408)

 

2 2

0.0365

0.0363

1.0064

(0.7523-1.3463)

(SNP2, SNP3)

00

0.6038

0.6448

0.9364

(0.8958-0.9789)

 

01

0.0455

0.0073

6.2159

(3.9154-9.8681)

 

10

0.0115

0.0117

0.9875

(0.5853-1.6661)

 

11

0.2966

0.2949

1.0058

(0.9218-1.0975)

 

12

0.0005

0.0013

0.3757

(0.0420-3.3588)

 

21

0.0050

0.0033

1.5028

(0.6266-3.6038)

 

22

0.0370

0.0363

1.0202

(0.7636-1.3631)

(SNP3, SNP4)

00

0.6138

0.6551

0.9369

(0.8971-0.9785)

 

01

0.0015

0.0017

0.9017

(0.2157-3.7686)

 

10

0.0500

0.0117

4.2936

(2.9340-6.2831)

 

11

0.2971

0.2936

1.0121

(0.9274-1.1044)

 

21

0.0005

0.0017

0.3006

(0.0351-2.5706)

 

22

0.0370

0.0360

1.0297

(0.7702-1.3765)

  1. The relative risk is calculated from the ratio between the probability of a genotype of interest occurring in the case group and that of the same genotype occurring in the control group. Only the relative risks based on genotypic information from each SNP and SNP pairs identified by 2LOmb are considered. Characters 0, 1 and 2 represent different genotypes at each locus where 0 denotes a homozygous wild-type genotype, 1 denotes a heterozygous genotype and 2 denotes a homozygous variant or homozygous mutant genotype. The relative risk displayed in boldface is statistically significant. The major/minor alleles for rs2269241, rs2269239, rs3790857 and rs2269238 are T/C, G/C, C/T and G/T, respectively. The allelic information is extracted from the original T2D data. SNP1 = rs2269241, SNP2 = rs2269239, SNP3 = rs3790857 and SNP4 = rs2269238.
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BMC Bioinformatics

ISSN: 1471-2105

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