Table 2

SNP-pairs with large epistatic effects validated with WTCCC data

Chr1

SNP1

Location1

Gene1

Marg. Rank1a

Chr1

SNP1

Location1

Gene1

Marg. Rank2a

p-Value


6

rs2244579

31544618

HCP5

2933

6

rs206015

32290737

NOTCH4

623

1.39 × 10-5

6

rs4394275

31426156

HLA-B

4705

6

rs9276440

32822761

HLA-DQA2

3042

5.33 × 10-5

6

rs4394275

31426156

HLA-B

4705

6

rs9276432

32820362

HLA-DQA2

2165

1.06 × 10-4

6

rs4394275

31426156

HLA-B

4705

6

rs9276429

32820082

HLA-DQA2

2386

1.08 × 10-4

6

rs2248880

31341489

HLA-C

130792

6

rs9273363

32734250

HLA-DQB1

709

1.14 × 10-4

6

rs4394275

31426156

HLA-B

4705

6

rs9276431

32820225

HLA-DQA2

2484

1.40 × 10-4

6

rs9263794

31237998

TCF19

4325

6

rs438475

32294223

NOTCH4

1243

7.56 × 10-4

6

rs1265074

31221193

CCHCR1

20388

6

rs438475

32294223

NOTCH4

1243

2.20 × 10-3

6

rs2244579

31544618

HCP5

2933

6

rs438475

32294223

NOTCH4

1243

2.27 × 10-3

6

rs4394275

31426156

HLA-B

4705

6

rs9273363

32734250

HLA-DQB1

709

3.49 × 10-3

6

rs2844615

31350938

HLA-C

10590

6

rs2596477

31435702

HLA-B

76640

2.36 × 10-2

6

rs4394275

31426156

HLA-B

4705

6

rs2227127

32819760

HLA-DQA2

585

3.16 × 10-2

6

rs2736172

31698877

BAT2

406

6

rs438475

32294223

NOTCH4

1243

3.37 × 10-2

6

rs1063635

31487910

MICA

897

6

rs206015

32290737

NOTCH4

623

3.41 × 10-2


Each row gives the annotations of SNP-pairs with validated epistatic effects.

aMarg. Rank 1 and 2 give the ranks of single-marker association strengths of the SNPs 1 and 2 in the WTCCC data. The rank > 1015 corresponds to the Bonferroni p-value > 0.1 in a single-marker study.

Wu et al. BMC Proceedings 2009 3(Suppl 7):S29  

Open Data