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Table 4 Haplotype 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

Allele and Haplotype

Case

Control

Relative Risk

95% CI

SNP1

0

0.8054

0.8066

0.9985

(0.9791-1.0183)

 

1

0.1946

0.1934

1.0061

(0.9274-1.0916)

SNP2

0

0.8037

0.8061

0.9970

(0.9775-1.0168)

 

1

0.1963

0.1939

1.0126

(0.9336-1.0982)

SNP3

0

0.7889

0.8096

0.9744

(0.9550-0.9943)

 

1

0.2111

0.1904

1.1087

(1.0240-1.2003)

SNP4

0

0.8134

0.8152

0.9977

(0.9789-1.0170)

 

1

0.1866

0.1848

1.0100

(0.9288-1.0982)

(SNP1, SNP3)

0 0

0.7812

0.8019

0.9742

(0.9543-0.9945)

 

0 1

0.0242

0.0047

5.1533

(3.3946-7.8231)

 

1 0

0.0077

0.0077

1.0000

(0.6349-1.5752)

 

1 1

0.1869

0.1857

1.0064

(0.9257-1.0941)

(SNP2, SNP3)

00

0.7804

0.8017

0.9734

(0.9535-0.9938)

 

01

0.0232

0.0044

5.3216

(3.4557-8.1949)

 

10

0.0085

0.0079

1.0758

(0.6930-1.6701)

 

11

0.1879

0.1861

1.0099

(0.9291-1.0977)

(SNP3, SNP4)

00

0.7881

0.8086

0.9747

(0.9552-0.9946)

 

01

0.0008

0.0010

0.7661

(0.1943-3.0205)

 

10

0.0253

0.0067

3.7936

(2.6367-5.4582)

 

11

0.1858

0.1837

1.0113

(0.9298-1.0999)

  1. The relative risk is calculated from the ratio between the probability of a haplotype of interest occurring in the case group and that of the same haplotype occurring in the control group. Haplotype inference is carried out using an expectation-maximisation method. Only the relative risks based on genotypic information from each SNP and SNP pairs identified by 2LOmb are considered. Characters 0 and 1 represent different alleles at each locus where 0 and 1 denote major and minor alleles, respectively. The relative risk displayed in boldface is statistically significant. The allelic information for each SNP is given in Table 3. SNP1 = rs2269241, SNP2 = rs2269239, SNP3 = rs3790857 and SNP4 = rs2269238.
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BMC Bioinformatics

ISSN: 1471-2105

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