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Table 3 Genetic effects that replicated internally, cross-validated, and passed FDR criterion

From: Complexity in the genetic architecture of leukoaraiosis in hypertensive sibships from the GENOA Study

Main Effects (4)

 

SNP

Subset 1 p-value

Subset 2 p-value

Full Sample p-value

R2 × 100

CV R2 × 100

  

F3_rs3917643

0.0477

0.0270

0.0021

1.58

1.05

  

KITLG_rs995029

0.0001

0.0921

0.0001

2.33

0.96

  

CAPN10_rs7571442

0.0856

0.0318

0.0021

1.70

0.59

  

MMP2_rs9928731

0.0161

0.0383

0.0032

1.48

0.56

SNP-Covariate Interactions (12)

SNP

Covariate

Subset 1 p-value

Subset 2 p-value

Full Sample p-value

R 2 × 100

CV R 2 × 100

 

KITLG_rs1492347

Log homocysteine

0.0002

0.0640

0.0003

4.37

1.57

 

ITGB3_rs3851806

Height

0.0286

0.0101

0.0010

2.54

1.51

 

TGFB3_rs2284791

Log C-reactive protein

0.0073

0.0173

0.0003

2.92

1.51

 

TGFB3_rs2284791

Physical activity

0.0885

0.0015

0.0007

2.69

1.46

 

TGFB3_rs2268622

Log C-reactive protein

0.0026

0.0360

0.0003

2.86

1.42

 

KITLG_rs995029

Log homocysteine

0.0002

0.0621

0.0003

4.42

1.40

 

IL28RA_rs11587500

LDL particle size

0.0026

0.0014

0.0004

2.79

1.26

 

ACCN4_rs1872858

Fibrinogen

0.0494

0.0339

0.0010

2.59

1.24

 

LTA4H_rs17025079

Log homocysteine

0.0006

0.0709

0.0001

3.41

1.16

 

PCSK9_rs10888896

Log homocysteine

0.0239

0.0567

0.0009

2.33

1.13

 

IL22RA1_rs3795299

CHD

0.0859

0.0138

0.0009

2.41

0.70

 

SERPINE1_rs2227672

Body mass index

0.0113

0.0219

0.0003

2.69

0.54

SNP-SNP Interactions (20 of 173)

SNP1

SNP2

Subset 1 p-value

Subset 2 p-value

Full Sample p-value

R 2 × 100

CV R 2 × 100

 

RHAG_rs11759060

GLS_rs1921913

0.0032

0.0225

8.0 E-06

5.49

2.61

 

F8 _rs7053448

MPO_rs34704261

0.0354

0.0279

0.0001

4.10

2.58

 

RHAG_rs11759060

GLS_rs3771316

0.0032

0.0225

8.0 E-06

5.49

2.55

 

MPO_rs34704261

F8_rs1800291

0.0362

0.0279

0.0001

4.10

2.44

 

SLC20A1_rs10758

IL22RA1_rs12093987

0.0439

0.0085

4.0 E-05

5.44

2.35

 

SLC20A1_rs3827758

IL22RA1_rs12093987

0.0315

0.0915

0.0004

3.88

2.27

 

KITLG_rs995029

TLR4_rs1927911

0.0035

0.0586

5.0 E-05

5.58

2.27

 

SLC20A1_rs1053652

IL22RA1_rs12093987

0.0237

0.0045

5.0 E-05

5.07

2.22

 

MPO_rs34704261

F8_rs4898399

0.0433

0.0315

0.0002

4.18

2.11

 

RHAG_rs2518100

GLS_rs1921913

0.0029

0.0534

0.0001

4.50

2.11

 

MMP2_rs243834

IL28RA_rs4330872

0.0136

0.0856

0.0002

4.46

2.09

 

RHAG_rs2518100

GLS_rs3771316

0.0029

0.0534

0.0001

4.50

1.95

 

MPO_rs8077532

F8_rs1800291

0.0417

0.0802

0.0003

3.93

1.93

 

NMUR1_rs10933376

GPR55_rs2969126

0.0945

0.0022

4.3 E-05

5.03

1.90

 

ACCN4_rs3770234

TNFSF10_rs3136596

0.0246

0.0007

0.0001

4.65

1.84

 

PRKAR2B_rs257376

PKRAR2B_rs3729877

0.0085

0.0027

4.8 E-05

3.55

1.84

 

CX3CR1_rs2853712

F2_rs3136435

0.0153

0.0480

0.0010

3.31

1.82

 

KITLG_rs1492347

TLR4_rs10116253

0.0049

0.0577

0.0001

5.44

1.81

 

F8_rs7053448

MPO_rs8077532

0.0417

0.0802

0.0003

3.93

1.81

 

MPO_rs8077532

F8_rs4898399

0.0515

0.0822

0.0006

4.04

1.81

  1. For all associations, the outcome was leukoaraiosis volume transformed using the natural logarithm and adjusted for age, sex, and total brain volume.
  2. P-value refers to the model p-value (SNP main effects) or the partial F-test p-value of the interaction terms (SNP-Covariate interactions and SNP-SNP interactions).
  3. For SNP-Covariate and SNP-SNP interaction models, CV R2 × 100 refers to the difference in CV R2 × 100 between the full model (including interaction terms) and the reduced model (including main effects only).
  4. ACCN4 amiloride-sensitive cation channel neuronal 4;CAPN10 calpain 10 (cysteine protease); CX3CR1 chemokine, CX3C motif, receptor 1; F2 coagulation factor 2; F3 coagulation factor 3; F8 coagulation factor 8; GLS glutaminase, phosphate activated; GPR55 G protein-coupled receptor 55;IL22RA1 interleukin 22 receptor, alpha-1;IL28RA interleukin 28 receptor; ITGB3 integrin, beta-3; KITLG KIT tyrosine kinase receptor ligand; LTA4H leukotriene A4 hydroxylase; MMP2 matrix metalloproteinase 2 (72 kDa type IV collagenase); MPO myeloperoxidase; NMUR1 neuromedin U receptor 1 (G protein-coupled receptor 66);PCSK9 proprotein convertase, subtilisin/kexin-type, 9;PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta; RHAG rhesus blood group-associated glycoprotein; SERPINE1 plasminogen activator inhibitor 1; SLC20A1 solute carrier family 20 (phosphate transporters), member 1; TGFB3 transforming growth factor, beta 3; TLR4 toll-like receptor 4; TNFSF10 tumor necrosis factor ligand superfamily, member 10
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BMC Medical Genomics

ISSN: 1755-8794

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