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

From: Investigating the complex genetic architecture of ankle-brachial index, a measure of peripheral arterial disease, in non-Hispanic whites

Main Effects (2)

 

SNP

Subset 1 p-value

Subset 2 p-value

Full Sample p-value

R2

CV R2

  

NOS3_rs891512

0.0003

0.0458

0.0005

0.0151

0.0096

  

NOS3_rs1808593

0.0006

0.0333

0.0001

0.0178

0.0105

SNP-Covariate Interactions (3)

SNP

Covariate

   

R 2

CV R 2

 

ADRB2_rs1042713

Lp(a)

0.0847

0.0407

0.0006

0.0176

0.0089

 

SLC4A5_rs828853

DIABETES

0.0564

0.0462

0.0004

0.0143

0.0095

 

SLC4A5_rs12991424

DIABETES

0.0350

0.0278

0.0005

0.0106

0.0085

SNP-SNP Interactions (25)

SNP1

SNP2

   

R 2

CV R 2

 

TTRAP_rs1129644

HLA-DOA_rs2581

0.0535

0.0608

0.0001

0.0198

0.0116

 

ADD2_rs2110981

TGFB3_rs2268622

0.0355

0.0134

0.0004

0.0171

0.0115

 

ADD2_rs2110981

TGFB3_rs2284791

0.0439

0.0049

0.0001

0.0200

0.0156

 

ADD2_rs2270042

AGT_rs5049

0.0085

0.0765

0.0003

0.0171

0.0127

 

ADRB2_rs1042713

PRL_rs1205960

0.0066

0.0885

0.0003

0.0175

0.0119

 

ATP6V1B1_rs11681642

IL1B_rs3917356

0.0223

0.0105

0.0002

0.0195

0.0130

 

ATP6V1B1_rs1024764

ACCN4_rs3755065

0.0395

0.0005

0.0002

0.0189

0.0152

 

ATP6V1B1_rs2239484

ACCN4_rs3755065

0.0550

0.0005

0.0005

0.0161

0.0121

 

ATP6V1B1_rs2239487

ACCN4_rs3755065

0.0238

0.0013

0.0004

0.0175

0.0123

 

AUP1_rs10779958

SLC2A2_rs5400

0.0041

0.0868

0.0003

0.0155

0.0149

 

SCN7A_rs1406275

TGFB3_rs3917195

0.0283

0.0004

0.0001

0.0180

0.0137

 

FGB_rs4220

KCNE4_rs3795884

8.98E-05

0.0584

3.45E-05

0.0208

0.0163

 

GPC6_rs1924115

IL6_rs2069827

0.0203

0.0338

0.0007

0.0145

0.0124

 

ICAM1_rs5030352

SLC19A3_rs12185721

0.0869

0.0028

0.0001

0.0172

0.0073

 

MMP3_rs683878

VCAM1_rs1041163

0.0644

0.0407

0.0003

0.0172

0.0085

 

MMP9_rs20544

SLC12A3_rs2304483

0.0157

0.0876

0.0002

0.0180

0.0132

 

SLC4A5_rs702462

TGFB3_rs3917187

0.0734

0.0010

0.0004

0.0176

0.0088

 

SLC4A5_rs702462

TGFB3_rs3917201

0.0456

0.0010

7.65E-05

0.0207

0.0147

 

SLC4A5_rs702462

TGFB3_rs3917210

0.0329

0.0009

4.62E-05

0.0222

0.0156

 

SLC4A5_rs702462

TGFB3_rs3917211

0.0358

0.0015

5.91E-05

0.0212

0.0097

 

PRKAR2B_rs257376

SLC17A2_rs1540273

0.0075

0.0036

0.0005

0.0174

0.0134

 

PRKAR2B_rs257376

SLC17A2_rs2071299

0.0161

0.0020

0.0002

0.0182

0.0103

 

PLIN_rs1052700

TGFB3_rs3917195

0.0126

0.0015

0.0006

0.0146

0.0054

 

SELE_rs5368

SLC22A3_rs668871

0.0004

0.0954

0.0005

0.0167

0.0127

 

SELE_rs5356

SLC22A3_rs668871

0.0009

0.0932

0.0006

0.0157

0.0124

  1. All associations adjusted for age, gender, body mass index, smoking, diabetes, and hypertension.
  2. ACCN4 amiloride-sensitive cation channel 4, pituitary; ADD2 adducin 2 (beta); ADRB2 *b2-adrenergic receptor; AGT angiotensinogen (serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 8); ATP6V1B1 ATPase, H+ transporting, lysosomal 56/58 kDa, V1 subunit B, isoform 1 (Renal tubular acidosis with deafness); AUP1 ancient ubiquitous protein 1; FGB fibrinogen, B beta polypeptide; GPC6 glypican 6; HLA-DOA human leukocyte antigen; ICAM1 intercellular adhesion molecule 1 (CD54), human rhinovirus receptor; ILB1 interleukin 1, beta; IL6 interleukin 6 (interferon, beta 2); KCNE4 potassium voltage-gated channel, Isk-related family, member 4; MMP3 matrix metalloproteinase 3 (stromelysin 1, progelatinase); MMP9 matrix metalloproteinase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase); NOS3 nitric oxide synthase 3 (endothelial cell); PLIN perilipin; PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta; PRL prolactin; SCN7A sodium channel, voltage-gated, type VII, alpha; SELE selectin E (endothelial adhesion molecule 1); SLC2A2 solute carrier family 2 (facilitated glucose transporter), member 2; SLC2A5 solute carrier family 4, sodium bicarbonate cotransporter, member 5; SLC12A3 solute carrier family 12 (sodium/chloride transporters), member 3; SLC17A2 solute carrier family 17 (sodium phosphate), member 2; SLC19A3 solute carrier family 19, member 3; SLC22A3 solute carrier family 22 (extraneuronal monoamine transporter), member 3; TGFB3 transforming growth factor, beta 3; TTRAP TRAF and TNF receptor associated protein; VCAM1 vascular cell adhesion molecule 1.
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BMC Medical Genomics

ISSN: 1755-8794

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