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Table 4 Frequency and effect of gamete, allele-genotype or genotype-genotype combination in each epistasis effect with statistical significance of suggestive linkage.

From: Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham Heart Study data

Trait

SNP1

Chr1

SNP2

Chr2

          
     

Gamete

A-T

G-G

G-T

A-G

     
 

rs4437278

4

rs705169

10

Frequency

0.0785

0.413

0.434

0.0742

     

TC

    

Effect

0.103

0.0195

-0.0186

-0.108

     
     

Allele-genotype

A-GG

G-GT

A-TT

G-TT

A-GT

G-GG

   
 

rs4738150

8

rs16918936

9

Frequency

0.0015

0.0284

0.557

0.374

0.0387

0.001

   
     

Effect

0.961

0.0917

0.00219

-0.00313

-0.0636

-1.42

   
     

Gamete

A-C

G-T

G-C

A-T

     
 

rs10476539

5

rs2392885

8

Frequency

0.0538

0.593

0.226

0.127

     
     

Effect

0.15

0.0137

-0.0359

-0.0635

     
     

Genotype-genotype

GT-GG

GG-AG

GT-AA

TT-AG

TT-AA

TT-GG

GT-AG

GG-AA

GG-GG

 

rs4706271

6

rs6581219

12

Frequency

0.0817

0.0887

0.161

0.169

0.112

0.0619

0.24

0.055

0.0298

     

Effect

0.137

0.127

0.0694

0.066

-0.0495

-0.0908

-0.0932

-0.103

-0.189

     

Gamete

G-G

T-A

G-A

T-G

     

HDL-C

rs2787520

6

rs7236739

18

Frequency

0.106

0.448

0.241

0.206

     
     

Effect

0.0946

0.0224

-0.0416

-0.0488

     
     

Gamete

C-A

T-G

T-A

C-G

     
 

rs2842169

10

rs4756344

11

Frequency

0.0751

0.237

0.661

0.0272

     
     

Effect

0.0801

0.0253

-0.00908

-0.221

     
     

Genotype

CC-AG

CT-AA

CT-GG

TT-AG

TT-GG

TT-AA

CT-AG

CC-GG

CC-AA

 

rs12596869

16

rs6506699

18

Frequency

0.0501

0.103

0.115

0.208

0.131

0.115

0.215

0.0344

0.0279

     

Effect

0.223

0.109

0.0979

0.0535

-0.0433

-0.0494

-0.103

-0.167

-0.197