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Table 7 Significant haplotype association (global P < 0.05) of 136 SCARB1 genotyped variants with HDL-C and ApoA-I

From: Genetic contribution of SCARB1 variants to lipid traits in African Blacks: a candidate gene association study

Wind #

SNP 1 - SNP 4

Chr12 Positionc

Location

Amino Acid Change

Major/ Minor Alleles

MAF

β

Single-site P

Haplotype #

Hap Seq

Hap Freq

Coef

SE

t.stat

Hap P

Global P

(SNP Namea-SNP IDb/Chr12 Posc)

HDL-C

               

39

p41632-rs6488943

125307888

Intron 1

 

A/C

0.2954

−0.2195

0.3244

h39.1

CCGG

0.0315

0.4305

0.6471

0.6654

0.5060

0.0207

39

p42467-rs11057830

125307053

Intron 1

 

C/T

0.1523

−0.2810

0.3015

h39.2

CCGA

0.2508

−0.5918

0.2725

−2.1713

0.0302

 

39

p45516-rs1902569

125304004

Intron 1

 

G/A

0.1544

0.5447

0.0386

h39.3

ATGA

0.1414

−0.6841

0.3192

−2.1433

0.0324

 

39

p45627-rs12297372

125303893

Intron 1

 

A/G

0.0487

−0.0483

0.9156

h39.4

ACAA

0.1514

0.1991

0.2963

0.6720

0.5018

 
         

h39.5

ACGG

0.0155

−1.7144

0.9080

−1.8880

0.0594

 
         

h39.6 (rare)

****

0.0148

2.5239

1.0902

2.3151

0.0209

 
         

hap.base39

ACGA

0.3946

NA

NA

NA

NA

 

44

p48969-rs2343394

125300551

Intron 2

 

C/T

0.1898

0.3165

0.1788

h44.1

TCWG

0.1855

0.5292

0.2523

2.0977

0.0363

0.0271

44

p49537-rs7305310

125299983

Intron 2

 

C/T

0.1007

−0.3396

0.2566

h44.2

CCDG

0.2244

0.4676

0.2429

1.9249

0.0546

 

44

p49570delC-rs145376237

125299950

Intron 2

 

W/D

0.2276

0.3121

0.1773

h44.3

CCWG

0.0446

1.0491

0.4882

2.1489

0.0320

 

44

p49690-rs4765615

125299830

Intron 2

 

G/A

0.4426

−0.4646

0.0130

h44.4

CTWG

0.1018

−0.1197

0.3121

−0.3835

0.7015

 
         

h44.5 (rare)

****

0.0089

−0.9887

1.0998

−0.8990

0.3689

 
         

hap.base44

CCWA

0.4348

NA

NA

NA

NA

 

45

p49537-rs7305310

125299983

Intron 2

 

C/T

0.1007

−0.3396

0.2566

h45.1

CDGC

0.2282

0.4661

0.2393

1.9473

0.0519

0.0155

45

p49570delC-rs145376237

125299950

Intron 2

 

W/D

0.2276

0.3121

0.1773

h45.2

CWGC

0.2302

0.6926

0.2376

2.9146

0.0037

 

45

p49690-rs4765615

125299830

Intron 2

 

G/A

0.4426

−0.4646

0.0130

h45.3

TWGC

0.1020

−0.0653

0.3085

−0.2115

0.8325

 

45

p49759-rs146272788

125299761

Intron 2

 

C/T

0.0020

2.5988

0.2219

h45.4 (rare)

****

0.0030

2.0667

2.0848

0.9913

0.3219

 
         

hap.base45

CWAC

0.4366

NA

NA

NA

NA

 

46

p49570delC-rs145376237

125299950

Intron 2

 

W/D

0.2276

0.3121

0.1773

h46.1

DGCG

0.2228

0.4373

0.2413

1.8123

0.0703

0.0278

46

p49690-rs4765615

125299830

Intron 2

 

G/A

0.4426

−0.4646

0.0130

h46.2

WGCG

0.3311

0.4910

0.2105

2.3326

0.0199

 

46

p49759-rs146272788

125299761

Intron 2

 

C/T

0.0020

2.5988

0.2219

h46.3 (rare)

****

0.0080

1.9089

1.0569

1.8061

0.0713

 

46

p49978-rs5891

125299542

Exon 3

Val135lle

G/A

0.0058

1.3374

0.2791

hap.base46

WACG

0.4381

NA

NA

NA

NA

 

47

p49690-rs4765615

125299830

Intron 2

 

G/A

0.4426

−0.4646

0.0130

h47.1

ACGG

0.4346

−0.4701

0.1824

−2.5777

0.0101

0.0079

47

p49759-rs146272788

125299761

Intron 2

 

C/T

0.0020

2.5988

0.2219

h47.2 (rare)

****

0.0101

1.4683

0.9441

1.5552

0.1203

 

47

p49978-rs5891

125299542

Exon 3

Val135lle

G/A

0.0058

1.3374

0.2791

hap.base47

GCGG

0.5553

NA

NA

NA

NA

 

47

p50024-rs368880622

125299496

Intron 3

 

G/T

0.0026

1.6506

0.4362

        

63

p53359-rs112371713

125296161

Intron 5

 

G/A

0.1243

0.4193

0.1651

h63.1

ACGA

0.1237

0.3273

0.3011

1.0871

0.2773

0.0394

63

p53372-rs115604379

125296148

Intron 5

 

C/T

0.0066

3.0372

0.0093

h63.2

GCGG

0.0427

−0.1630

0.4738

−0.3441

0.7309

 

63

p53790-rs4765614

125295730

Intron 5

 

G/A

0.2653

−0.3281

0.1218

h63.3

GCAA

0.2678

−0.2408

0.2194

−1.0975

0.2728

 

63

p54445-rs60910935

125295075

Intron 5

 

A/G

0.0418

−0.1247

0.7963

h63.4 (rare)

****

0.0068

2.9428

1.2559

2.3432

0.0194

 
         

hap.base63

GCGA

0.5591

NA

NA

NA

NA

 

72

p55923-rs838900

125293597

Intron 6

 

G/A

0.3921

0.2787

0.1549

h72.1

ACAG

0.2725

0.4039

0.2520

1.6024

0.1095

0.0315

72

p55963-rs7134858

125293557

Intron 6

 

C/T

0.1560

0.4418

0.0799

h72.2

ACGG

0.1086

−0.1763

0.3929

−0.4486

0.6538

 

72

p56845-rs838902

125292675

Intron 6

 

A/G

0.4249

−0.0786

0.6801

h72.3

GTAG

0.1284

0.3877

0.3170

1.2228

0.2218

 

72

p57004-rs187562853

125292516

Intron 6

 

G/A

0.0098

1.6474

0.0872

h72.4

GTGG

0.0297

0.8722

0.6546

1.3323

0.1832

 
         

h72.5

GCAG

0.1716

−0.4913

0.3344

−1.4690

0.1422

 
         

h72.6 (rare)

****

0.0101

1.7731

0.9506

1.8653

0.0625

 
         

hap.base72

GCGG

0.2791

NA

NA

NA

NA

 

111

p78747-rs2293440

125270773

Intron 11

T/C

0.4112

−0.1684

0.3806

h111.1

CCCG

0.0306

0.7458

0.5599

1.3321

0.1832

0.0040

111

p78791-rs75289200

125270729

Intron 11

T/C

0.0321

0.7037

0.2078

h111.2

CTGC

0.1534

−0.5556

0.2830

−1.9629

0.0500

 

111

p79721-rs838896

125269799

Intron 11

G/C

0.3104

0.3565

0.0817

h111.3

CTCG

0.2269

0.1234

0.2391

0.5162

0.6058

 

111

p79828-rs838895

125269692

Intron 11

C/G

0.3171

0.4961

0.0162

h111.4

TTGG

0.0180

2.3022

0.7617

3.0225

0.0026

 
         

h111.5

TTCG

0.0439

0.5755

0.5317

1.0823

0.2795

 
         

h111.6

TTCC

0.0145

0.9606

0.8068

1.1907

0.2342

 
         

h111.7 (rare)

****

0.0033

0.7755

2.1917

0.3538

0.7236

 
         

hap.base111

TTGC

0.5094

NA

NA

NA

NA

 

112

p78791-rs75289200

125270729

Intron 11

T/C

0.0321

0.7037

0.2078

h112.1

CCGA

0.0311

0.7440

0.5559

1.3384

0.1812

0.0055

112

p79721-rs838896

125269799

Intron 11

G/C

0.3104

0.3565

0.0817

h112.2

TGGA

0.0171

2.3734

0.7506

3.1621

0.0016

 

112

p79828-rs838895

125269692

Intron 11

C/G

0.3171

0.4961

0.0162

h112.3

TGCA

0.0112

−1.2672

0.9074

−1.3964

0.1630

 

112

p80045-rs838893

125269475

Intron 11

G/A

0.3244

0.3127

0.1224

h112.4

TCGA

0.2704

0.2488

0.2164

1.1501

0.2505

 
         

h112.5

TCCG

0.0139

1.1219

0.8186

1.3704

0.1710

 
         

h112.6 (rare)

****

0.0068

1.6244

1.2691

1.2800

0.2009

 
         

hap.base112

TGCG

0.6493

NA

NA

NA

NA

 

113

p79721-rs838896

125269799

Intron 11

G/C

0.3104

0.3565

0.0817

h113.1

GGAG

0.0171

2.3949

0.7509

3.1895

0.0015

0.0048

113

p79828-rs838895

125269692

Intron 11

C/G

0.3171

0.4961

0.0162

h113.2

GCAG

0.0120

−1.1963

0.8784

−1.3619

0.1736

 

113

p80045-rs838893

125269475

Intron 11

G/A

0.3244

0.3127

0.1224

h113.3

CGAG

0.2996

0.3071

0.2067

1.4861

0.1377

 

113

p81863-rs185445624

125267657

Intron 11

G/A

0.0020

−0.9612

0.6510

h113.4

CCGG

0.0139

1.1509

0.8168

1.4090

0.1592

 
         

h113.5 (rare)

****

0.0081

1.1622

1.0896

1.0666

0.2865

 
         

hap.base113

GCGG

0.6493

NA

NA

NA

NA

 

114

p79828-rs838895

125269692

Intron 11

C/G

0.3171

0.4961

0.0162

h114.1

GAGC

0.3173

0.3755

0.2023

1.8559

0.0639

0.0447

114

p80045-rs838893

125269475

Intron 11

G/A

0.3244

0.3127

0.1224

h114.2

CGGT

0.0306

−0.8840

0.5344

−1.6541

0.0985

 

114

p81863-rs185445624

125267657

Intron 11

G/A

0.0020

−0.9612

0.6510

h114.3

CAGC

0.0111

−1.2612

0.9170

−1.3754

0.1694

 

114

p82019-rs838890

125267501

Intron 11

C/T

0.0320

−1.0051

0.0618

h114.4 (rare)

****

0.0086

0.9073

1.0936

0.8296

0.4070

 
         

hap.base114

CGGC

0.6325

NA

NA

NA

NA

 

117

p82019-rs838890

125267501

Intron 11

C/T

0.0320

−1.0051

0.0618

h117.1

CCAG

0.0238

−1.0596

0.6275

−1.6884

0.0917

0.0433

117

p82264-rs141545424

125267256

Exon 12

Gly501Gly

C/A

0.0007

11.5850

0.0016

h117.2

TCGG

0.0311

−0.9657

0.5302

−1.8215

0.0689

 

117

p82340-rs77483223

125267180

Intron 12

G/A

0.0231

−1.0458

0.1012

h117.3 (rare)

****

0.0067

1.6191

1.2946

1.2507

0.2114

 

117

p82369-rs75446635

125267151

Intron 12

G/A

0.0059

0.5896

0.6322

hap.base117

CCGG

0.9383

NA

NA

NA

NA

 

118

p82264-rs141545424

125267256

Exon 12

Gly501Gly

C/A

0.0007

11.5850

0.0016

h118.1

CAGT

0.0238

−1.0621

0.6274

−1.6929

0.0909

0.0375

118

p82340-rs77483223

125267180

Intron 12

G/A

0.0231

−1.0458

0.1012

h118.2

CGGC

0.0307

−1.0134

0.5313

−1.9073

0.0569

 

118

p82369-rs75446635

125267151

Intron 12

G/A

0.0059

0.5896

0.6322

h118.3 (rare)

****

0.0067

1.6189

1.2762

1.2685

0.2050

 

118

p82434-rs838889

125267086

Intron 12

T/C

0.0315

−1.0389

0.0526

hap.base118

CGGT

0.9387

NA

NA

NA

NA

 

123

p83884-rs701106

125265636

Intron 12

C/T

0.2597

0.2471

0.2601

h123.1

TCCT

0.0256

−1.2114

0.6218

−1.9483

0.0518

0.0386

123

p86245-rs188375019

125263275

Intron 12

C/T

0.0341

0.7447

0.1639

h123.2

TCCG

0.2327

0.5306

0.2403

2.2085

0.0275

 

123

p86276-rs747155

125263244

Intron 12

C/T

0.1495

0.2793

0.2980

h123.3

CCTG

0.1476

0.3955

0.2811

1.4071

0.1598

 

123

p86316-rs701104

125263204

Intron 12

G/T

0.0487

−0.9838

0.0286

h123.4

CCCT

0.0233

−0.2329

0.7038

−0.3309

0.7408

 
         

h123.5

CTCG

0.0330

0.8888

0.5458

1.6283

0.1039

 
         

h123.6 (rare)

****

0.0029

1.1191

3.2961

0.3395

0.7343

 
         

hap.base123

CCCG

0.5348

NA

NA

NA

NA

 

124

p86245-rs188375019

125263275

Intron 12

C/T

0.0341

0.7447

0.1639

h124.1

CTGA

0.1476

0.1530

0.2692

0.5683

0.5700

0.0368

124

p86276-rs747155

125263244

Intron 12

C/T

0.1495

0.2793

0.2980

h124.2

CCTG

0.0465

−1.1879

0.4699

−2.5281

0.0117

 

124

p86316-rs701104

125263204

Intron 12

G/T

0.0487

−0.9838

0.0286

h124.3

CCGA

0.0915

0.1086

0.3376

0.3218

0.7477

 

124

p86481-rs701103

125263039

Exon 13-3' UTR

Gly499Arg (isoform 2)

G/A

0.2451

0.1642

0.4492

h124.4

TCGG

0.0337

0.7348

0.5362

1.3702

0.1710

 
         

h124.5 (rare)

****

0.0045

4.0859

2.1131

1.9336

0.0535

 
         

hap.base124

CCGG

0.6761

NA

NA

NA

NA

 

125

p86276-rs747155

125263244

Intron 12

C/T

0.1495

0.2793

0.2980

h125.1

TGAA

0.1476

0.1543

0.2689

0.5737

0.5664

0.0307

125

p86316-rs701104

125263204

Intron 12

G/T

0.0487

−0.9838

0.0286

h125.2

CTGA

0.0465

−1.1980

0.4691

−2.5535

0.0109

 

125

p86481-rs701103

125263039

Exon 13-l3' UTR

Gly499Arg (isoform 2)

G/A

0.2451

0.1642

0.4492

h125.3

CGAA

0.0915

0.1139

0.3375

0.3375

0.7359

 

125

p86967-rs187492239

125262553

Exon 13-3' UTR

 

A/G

0.0355

0.7743

0.1412

h125.4

CGGG

0.0352

0.7974

0.5241

1.5216

0.1285

 
         

h125.5 (rare)

****

0.0045

4.0989

2.1134

1.9394

0.0528

 
         

hap.base125

CGGA

0.6747

NA

NA

NA

NA

 

ApoA-I

               

47

p49690-rs4765615

125299830

Intron 2

 

G/A

0.4426

−0.9139

0.0480

h47.1

ACGG

0.4351

−0.8907

0.4584

−1.9432

0.0524

0.0343

47

p49759-rs146272788

125299761

Intron 2

 

C/T

0.0020

1.5883

0.7630

h47.2 (rare)

****

0.0106

3.5858

2.2998

1.5592

0.1194

 

47

p49978-rs5891

125299542

Exon 3

Val135lle

G/A

0.0058

5.6762

0.0628

hap.base47

GCGG

0.5543

NA

NA

NA

NA

 

47

p50024-rs368880622

125299496

Intron 3

 

G/T

0.0026

1.6012

0.7255

        

48

p49759-rs146272788

125299761

Intron 2

 

C/T

0.0020

1.5883

0.7630

h48.1

CGGT

0.0206

3.3555

1.6564

2.0258

0.0431

0.0293

48

p49978-rs5891

125299542

Exon 3

Val135lle

G/A

0.0058

5.6762

0.0628

h48.2 (rare)

****

0.0106

4.0750

2.3644

1.7235

0.0852

 

48

p50024-rs368880622

125299496

Intron 3

 

G/T

0.0026

1.6012

0.7255

hap.base48

CGGC

0.9688

NA

NA

NA

NA

 

48

p50118-rs58710319

125299402

Intron 3

 

C/T

0.0208

3.1376

0.0571

        

49

p49978-rs5891

125299542

Exon 3

Val135lle

G/A

0.0058

5.6762

0.0628

h49.1

GGTT

0.0213

3.3792

1.6416

2.0584

0.0399

0.0289

49

p50024-rs368880622

125299496

Intron 3

 

G/T

0.0026

1.6012

0.7255

h49.2

GGCC

0.1928

0.8864

0.5841

1.5176

0.1295

 

49

p50118-rs58710319

125299402

Intron 3

 

C/T

0.0208

3.1376

0.0571

h49.3 (rare)

****

0.0086

4.7388

3.1873

1.4868

0.1375

 

49

p50151-rs2278986

125299369

Intron 3

 

T/C

0.1933

0.8568

0.1419

hap.base49

GGCT

0.7774

NA

NA

NA

NA

 

70

p54627-chr12_125294893

125294893

Intron 5

 

G/C

0.0020

3.6910

0.4850

h70.1

GCAC

0.3873

0.8579

0.5090

1.6854

0.0923

0.0140

70

p54856-chr12_125294664

125294664

Intron 6

 

C/T

0.0007

−24.0757

0.0082

h70.2

GCGT

0.1568

2.0940

0.6700

3.1254

0.0018

 

70

p55923-rs838900

125293597

Intron 6

 

G/A

0.3921

0.3606

0.4549

h70.3 (rare)

****

0.0027

−2.5567

5.2200

−0.4898

0.6244

 

70

p55963-rs7134858

125293557

Intron 6

 

C/T

0.1560

1.7537

0.0052

hap.base70

GCGC

0.4532

NA

NA

NA

NA

 

71

p54856-chr12_125294664

125294664

Intron 6

 

C/T

0.0007

−24.0757

0.0082

h71.1

CACA

0.2736

0.7883

0.6210

1.2694

0.2047

0.0488

71

p55923-rs838900

125293597

Intron 6

 

G/A

0.3921

0.3606

0.4549

h71.2

CACG

0.1134

1.1284

0.9724

1.1604

0.2462

 

71

p55963-rs7134858

125293557

Intron 6

 

C/T

0.1560

1.7537

0.0052

h71.3

CGTA

0.1296

2.1103

0.7906

2.6691

0.0078

 

71

p56845-rs838902

125292675

Intron 6

 

A/G

0.4249

−0.3052

0.5129

h71.4

CGTG

0.0300

2.1358

1.6772

1.2734

0.2032

 
         

h71.5

CGCA

0.1706

−0.1013

0.8355

−0.1212

0.9035

 
         

hap.base71

CGCG

0.2822

NA

NA

NA

NA

 

72

p55923-rs838900

125293597

Intron 6

 

G/A

0.3921

0.3606

0.4549

h72.1

ACAG

0.2733

0.7471

0.6218

1.2016

0.2299

0.0463

72

p55963-rs7134858

125293557

Intron 6

 

C/T

0.1560

1.7537

0.0052

h72.2

ACGG

0.1057

0.7094

0.9850

0.7202

0.4716

 

72

p56845-rs838902

125292675

Intron 6

 

A/G

0.4249

−0.3052

0.5129

h72.3

GTAG

0.1297

2.0304

0.7898

2.5707

0.0103

 

72

p57004-rs187562853

125292516

Intron 6

 

G/A

0.0098

3.2853

0.1690

h72.4

GTGG

0.0299

2.1741

1.6857

1.2897

0.1975

 
         

h72.5

GCAG

0.1712

−0.3122

0.8263

−0.3778

0.7057

 
         

h72.6 (rare)

****

0.0100

3.9105

2.4373

1.6044

0.1090

 
         

hap.base72

GCGG

0.2801

NA

NA

NA

NA

 

78

p57592-rs838903

125291928

Intron 7

 

G/A

0.3763

−0.7661

0.1109

h78.1

GCAC

0.0559

1.8913

1.0469

1.8067

0.0712

0.0326

78

p58514-rs838905

125291006

Intron 7

 

T/C

0.4329

−0.4213

0.3646

h78.2

GTAC

0.0367

1.0784

1.2814

0.8415

0.4003

 

78

p58664-rs865716

125290856

Intron 7

 

A/T

0.2708

0.5369

0.3008

h78.3

GTAT

0.2557

0.3365

0.6035

0.5576

0.5773

 

78

p60255-rs3782287

125289265

Intron 7

 

C/T

0.2831

0.3715

0.4856

h78.4

GTTC

0.2463

0.4962

0.5864

0.8462

0.3977

 
         

h78.5

GTTT

0.0238

5.5715

1.6643

3.3477

0.0009

 
         

h78.6 (rare)

****

0.0075

0.6333

2.9303

0.2161

0.8289

 
         

hap.base78

ACAC

0.3740

NA

NA

NA

NA

 

79

p58514-rs838905

125291006

Intron 7

 

T/C

0.4329

−0.4213

0.3646

h79.1

CACT

0.1270

0.3290

0.8318

0.3955

0.6926

0.0256

79

p58664-rs865716

125290856

Intron 7

 

A/T

0.2708

0.5369

0.3008

h79.2

TACC

0.0379

0.6384

1.2921

0.4941

0.6214

 

79

p60255-rs3782287

125289265

Intron 7

 

C/T

0.2831

0.3715

0.4856

h79.3

TATC

0.2563

0.1851

0.6336

0.2921

0.7703

 

79

p61872-rs838909

125287648

Intron 7

 

C/T

0.2199

0.9232

0.1056

h79.4

TTCC

0.1587

−0.6020

0.7769

−0.7749

0.4386

 
         

h79.5

TTCT

0.0880

1.8902

0.8856

2.1342

0.0331

 
         

h79.6

TTTC

0.0238

5.1755

1.6851

3.0714

0.0022

 
         

h79.7 (rare)

****

0.0059

1.2466

3.1079

0.4011

0.6885

 
         

hap.base79

CACC

0.3024

NA

NA

NA

NA

 

80

p58664-rs865716

125290856

Intron 7

 

A/T

0.2708

0.5369

0.3008

h80.1

ACCG

0.0389

−0.3521

1.2793

−0.2753

0.7832

0.0030

80

p60255-rs3782287

125289265

Intron 7

 

C/T

0.2831

0.3715

0.4856

h80.2

ACTG

0.1274

−0.1816

0.7909

−0.2297

0.8184

 

80

p61872-rs838909

125287648

Intron 7

 

C/T

0.2199

0.9232

0.1056

h80.3

ATCG

0.2611

−0.1400

0.6323

−0.2213

0.8249

 

80

p62140-rs838910

125287380

Intron 7

 

G/T

0.3047

−0.0755

0.8821

h80.4

TCCG

0.1549

−1.3614

0.7489

−1.8178

0.0695

 
         

h80.5

TCTG

0.0901

2.0511

0.8921

2.2992

0.0218

 
         

h80.6

TTCG

0.0224

4.7307

1.8842

2.5107

0.0123

 
         

h80.7 (rare)

****

0.0083

3.1429

3.4362

0.9147

0.3607

 
         

hap.base80

ACCT

0.2970

NA

NA

NA

NA

 

81

p60255-rs3782287

125289265

Intron 7

 

C/T

0.2831

0.3715

0.4856

h81.1

CCGC

0.1740

−1.5355

0.7276

−2.1103

0.0352

0.0050

81

p61872-rs838909

125287648

Intron 7

 

C/T

0.2199

0.9232

0.1056

h81.2

CCGT

0.0215

−0.5623

1.6155

−0.3481

0.7279

 

81

p62140-rs838910

125287380

Intron 7

 

G/T

0.3047

−0.0755

0.8821

h81.3

CCTC

0.0352

3.6130

1.4518

2.4886

0.0130

 

81

p62409-rs838911

125287111

Intron 7

 

C/T

0.4211

−0.6245

0.1888

h81.4

CCTT

0.2683

−0.7498

0.6337

−1.1832

0.2371

 
         

h81.5

CTGC

0.0886

1.4787

0.9259

1.5970

0.1107

 
         

h81.6

CTGT

0.1287

−0.2477

0.7967

−0.3109

0.7560

 
         

h81.7 (rare)

****

0.0017

4.9120

8.4190

0.5834

0.5598

 
         

hap.base81

TCGC

0.2819

NA

NA

NA

NA

 

82

p61872-rs838909

125287648

Intron 7

 

C/T

0.2199

0.9232

0.1056

h82.1

CGTT

0.0214

0.3707

1.6055

0.2309

0.8175

0.0137

82

p62140-rs838910

125287380

Intron 7

 

G/T

0.3047

−0.0755

0.8821

h82.2

CTCT

0.0364

3.8641

1.3703

2.8199

0.0049

 

82

p62409-rs838911

125287111

Intron 7

 

C/T

0.4211

−0.6245

0.1888

h82.3

CTTT

0.2692

−0.2007

0.5674

−0.3537

0.7237

 

82

p62615-rs7138386

125286905

Intron 7

 

T/C

0.1137

−0.6495

0.3851

h82.4

TGCT

0.0869

2.1488

0.8777

2.4481

0.0146

 
         

h82.5

TGTT

0.0179

3.0085

1.9599

1.5351

0.1252

 
         

h82.6

TGTC

0.1116

−0.1961

0.7815

−0.2510

0.8019

 
         

h82.7 (rare)

****

0.0020

−4.7635

9.0097

−0.5287

0.5972

 
         

hap.base82

CGCT

0.4546

NA

NA

NA

NA

 

83

p62140-rs838910

125287380

Intron 7

 

G/T

0.3047

−0.0755

0.8821

h83.1

GCTA

0.0854

2.0624

0.8886

2.3211

0.0205

0.0187

83

p62409-rs838911

125287111

Intron 7

 

C/T

0.4211

−0.6245

0.1888

h83.2

GTTG

0.0389

1.3667

1.2527

1.0910

0.2756

 

83

p62615-rs7138386

125286905

Intron 7

 

T/C

0.1137

−0.6495

0.3851

h83.3

GTCG

0.1129

−0.3143

0.7855

−0.4002

0.6891

 

83

p63483-rs838912

125286037

Intron 7

 

G/A

0.0867

1.8700

0.0234

h83.4

TCTG

0.0368

3.8488

1.3757

2.7977

0.0053

 
         

h83.5

TTTG

0.2675

−0.1681

0.5759

−0.2918

0.7705

 
         

h83.6 (rare)

****

0.0031

−0.5696

5.5038

−0.1035

0.9176

 
         

hap.base83

GCTG

0.4554

NA

NA

NA

NA

 

86

p63483-rs838912

125286037

Intron 7

 

G/A

0.0867

1.8700

0.0234

h86.1

ATCG

0.0871

2.5431

0.8550

2.9743

0.0030

0.0290

86

p64772-rs5888

125284748

Exon 8

Ala350Ala

C/T

0.0961

2.0962

0.0080

h86.2

GCAG

0.1457

0.3613

0.6957

0.5194

0.6037

 

86

p64923-rs838915

125284597

Intron 8

 

C/A

0.1435

−0.3684

0.5766

h86.3

GCCA

0.2814

1.0972

0.5782

1.8976

0.0581

 

86

p65999-rs12819677

125283521

Intron 8

 

G/A

0.2813

0.6769

0.2052

h86.4

GTCG

0.0116

1.6563

2.1240

0.7798

0.4357

 
         

hap.base86

GCCG

0.4736

NA

NA

NA

NA

 

95

p71867-rs7954022

125277653

Intron 9

 

C/T

0.1323

0.8502

0.2241

h95.1

TACT

0.1311

0.8202

0.7688

1.0669

0.2864

0.0131

95

p72197-rs838861

125277323

Intron 9

 

A/G

0.3777

−0.1507

0.7464

h95.2

CACC

0.0507

0.3188

1.2809

0.2489

0.8035

 

95

p72777-rs838862

125276743

Intron 9

 

C/T

0.0887

0.7012

0.3938

h95.3

CGCT

0.1846

−0.7832

0.6960

−1.1253

0.2608

 

95

p75766-rs838866

125273754

Intron 9

 

T/C

0.2116

−0.0497

0.9306

h95.4

CGCC

0.1022

0.7176

0.8581

0.8362

0.4033

 
         

h95.5

CGTT

0.0324

4.7525

1.5071

3.1534

0.0017

 
         

h95.6

CGTC

0.0582

−1.3987

1.0854

−1.2887

0.1979

 
         

h95.7 (rare)

****

0.0009

18.2723

NA

NA

NA

 
         

hap.base95

CACT

0.4399

NA

NA

NA

NA

 

96

p72197-rs838861

125277323

Intron 9

 

A/G

0.3777

−0.1507

0.7464

h96.1

ACCT

0.0443

1.0796

1.2832

0.8413

0.4004

0.0484

96

p72777-rs838862

125276743

Intron 9

 

C/T

0.0887

0.7012

0.3938

h96.2

GCTC

0.1849

−0.7979

0.6554

−1.2176

0.2238

 

96

p75766-rs838866

125273754

Intron 9

 

T/C

0.2116

−0.0497

0.9306

h96.3

GCCT

0.0727

−0.3866

0.9478

−0.4079

0.6835

 

96

p75778-rs7301120

125273742

Intron 9

 

C/T

0.1135

0.3767

0.6174

h96.4

GCCC

0.0282

1.9372

1.6107

1.2027

0.2295

 
         

h96.5

GTTC

0.0319

4.2363

1.4400

2.9419

0.0034

 
         

h96.6

GTCC

0.0595

−1.3421

1.0101

−1.3286

0.1844

 
         

h96.7 (rare)

****

0.0058

−3.2342

3.8265

−0.8452

0.3983

 
         

hap.base96

ACTC

0.5728

NA

NA

NA

NA

 

97

p72777-rs838862

125276743

Intron 9

 

C/T

0.0887

0.7012

0.3938

h97.1

CTCT

0.1997

−1.0781

0.6237

−1.7287

0.0843

0.0098

97

p75766-rs838866

125273754

Intron 9

 

T/C

0.2116

−0.0497

0.9306

h97.2

CCTT

0.1141

0.2005

0.7597

0.2639

0.7919

 

97

p75778-rs7301120

125273742

Intron 9

 

C/T

0.1135

0.3767

0.6174

h97.3

CCCT

0.0336

0.7963

1.3894

0.5731

0.5667

 

97

p76757-rs9919713

125272763

Intron 9

 

A/T

0.4390

−0.1860

0.6921

h97.4

TTCT

0.0301

4.3773

1.4494

3.0201

0.0026

 
         

h97.5

TCCT

0.0588

−1.4125

1.0117

−1.3961

0.1631

 
         

h97.6 (rare)

****

0.0050

−6.5869

3.6167

−1.8213

0.0690

 
         

hap.base97

CTCA

0.5587

NA

NA

NA

NA

 

109

p78402-rs838898

125271118

Intron 10

G/A

0.0714

−0.9806

0.2889

h109.1

AGCT

0.0288

−1.4134

1.6436

−0.8600

0.3901

0.0195

109

p78430-rs838897

125271090

Intron 10

C/G

0.3830

−0.1887

0.6887

h109.2

AGTT

0.0451

−1.5093

1.2496

−1.2078

0.2275

 

109

p78747-rs2293440

125270773

Intron 11

T/C

0.4112

−0.2984

0.5352

h109.3

GGCC

0.0317

3.0784

1.3763

2.2366

0.0256

 

109

p78791-rs75289200

125270729

Intron 11

T/C

0.0321

3.6568

0.0086

h109.4

GGCT

0.1633

−0.4126

0.6911

−0.5971

0.5506

 
         

h109.5

GGTT

0.1088

−1.6537

0.8639

−1.9142

0.0560

 
         

h109.6

GCCT

0.1851

−1.8104

0.7168

−2.5256

0.0118

 
         

hap.base109

GCTT

0.4363

NA

NA

NA

NA

 

110

p78430-rs838897

125271090

Intron 10

C/G

0.3830

−0.1887

0.6887

h110.1

GCCC

0.0305

3.0357

1.4224

2.1342

0.0331

0.0012

110

p78747-rs2293440

125270773

Intron 11

T/C

0.4112

−0.2984

0.5352

h110.2

GCTG

0.0189

−3.0973

2.2833

−1.3565

0.1753

 

110

p78791-rs75289200

125270729

Intron 11

T/C

0.0321

3.6568

0.0086

h110.3

GCTC

0.1696

−0.0290

0.6830

−0.0424

0.9662

 

110

p79721-rs838896

125269799

Intron 11

G/C

0.3104

1.1147

0.0278

h110.4

GTTG

0.1400

−2.3158

0.7741

−2.9914

0.0029

 
         

h110.5

GTTC

0.0189

1.3536

2.3385

0.5788

0.5629

 
         

h110.6

CCTG

0.1379

−2.4014

0.7888

−3.0443

0.0024

 
         

h110.7

CCTC

0.0514

−0.8677

1.2628

−0.6871

0.4922

 
         

h110.8

CTTC

0.0398

−0.1892

1.4963

−0.1264

0.8994

 
         

h110.9 (rare)

****

0.0012

7.8235

8.0313

0.9741

0.3303

 
         

hap.base110

CTTG

0.3918

NA

NA

NA

NA

 

111

p78747-rs2293440

125270773

Intron 11

T/C

0.4112

−0.2984

0.5352

h111.1

CCCG

0.0305

3.5704

1.4077

2.5364

0.0114

0.0038

111

p78791-rs75289200

125270729

Intron 11

T/C

0.0321

3.6568

0.0086

h111.2

CTGC

0.1514

−2.1697

0.7058

−3.0742

0.0022

 

111

p79721-rs838896

125269799

Intron 11

G/C

0.3104

1.1147

0.0278

h111.3

CTCG

0.2233

0.3086

0.5985

0.5157

0.6062

 

111

p79828-rs838895

125269692

Intron 11

C/G

0.3171

1.2206

0.0164

h111.4

TTGG

0.0173

1.0502

1.9388

0.5417

0.5882

 
         

h111.5

TTGC

0.0431

0.3464

1.3140

0.2637

0.7921

 
         

h111.6

TTCC

0.0150

0.6429

1.9745

0.3256

0.7448

 
         

h111.7 (rare)

****

0.0047

3.8853

4.0634

0.9562

0.3393

 
         

hap.base111

TTGC

0.5147

NA

NA

NA

NA

 

112

p78791-rs75289200

125270729

Intron 11

T/C

0.0321

3.6568

0.0086

h112.1

CCGA

0.0309

3.7315

1.3947

2.6755

0.0076

0.0412

112

p79721-rs838896

125269799

Intron 11

G/C

0.3104

1.1147

0.0278

h112.2

TGGA

0.0179

1.8646

1.8467

1.0097

0.3130

 

112

p79828-rs838895

125269692

Intron 11

C/G

0.3171

1.2206

0.0164

h112.3

TGCA

0.0109

−3.3720

2.3180

−1.4547

0.1462

 

112

p80045-rs838893

125269475

Intron 11

G/A

0.3244

0.8859

0.0774

h112.4

TCGA

0.2661

0.7087

0.5428

1.3056

0.1921

 
         

h112.5

TCCG

0.0144

1.0316

2.0147

0.5120

0.6088

 
         

h112.6 (rare)

****

0.0068

2.8715

3.2105

0.8944

0.3714

 
         

hap.base112

TGCG

0.6530

NA

NA

NA

NA

 

123

p83884-rs701106

125265636

Intron 12

C/T

0.2597

1.2967

0.0156

h123.1

TCCT

0.0235

−1.7638

1.7393

−1.0141

0.3109

0.0468

123

p86245-rs188375019

125263275

Intron 12

C/T

0.0341

1.8399

0.1674

h123.2

TCCG

0.2351

1.8726

0.6006

3.1179

0.0019

 

123

p86276-rs747155

125263244

Intron 12

C/T

0.1495

−0.2164

0.7433

h123.3

CCTG

0.1485

0.3912

0.6981

0.5604

0.5754

 

123

p86316-rs701104

125263204

Intron 12

G/T

0.0487

−0.6627

0.5579

h123.4

CCCT

0.0238

1.6476

1.7546

0.9390

0.3480

 
         

h123.5

CTCG

0.0328

2.3144

1.3655

1.6949

0.0905

 
         

h123.6 (rare)

****

0.0024

1.2704

8.8153

0.1441

0.8855

 
         

hap.base123

CCCG

0.5340

NA

NA

NA

NA

 
  1. ApoA-I apolipoprotein A-I, Coef coefficient, del/D deletion, HDL-C high-density lipoprotein cholesterol, MAF minor allele frequency, NA not analyzed, SE standard error, SNP single nucleotide polymorphism, UTR untranslated region, W wild type allele for deletion on RefSeq
  2. All alleles on the reverse strand. HDL-C and ApoA-I variables were in mg/dL and Box-Cox transformed
  3. Results were adjusted for covariates: sex, age, waist, current smoking (yes/no), and minutes of daily walking or biking to work (jobmin) for HDL-C; sex and age for ApoA-I
  4. SNP 1-SNP 4 for each window are shown as “SNP name-SNP ID/Chromosome 12 Position (for novel variants)”. All 10 novel variants identified in this study have been submitted to dbSNP database (batch ID: SCARB1_AB): http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/SNP/snp_viewTable.cgi?handle=KAMBOH.
  5. Nominally significant P-values (P < 0.05) for SNPs with MAF ≥5 % in single-site analysis are shown in bold
  6. Haplotype sequences corresponding to SNP 1-SNP 4 in the 5′ to 3′ direction, respectively
  7. Haplotype association results for all haplotype windows are shown in Additional file 16: Table S11, see haplotype association plots in Fig. 3
  8. a, cRefSeq of SCARB1: hg19, NM_005505 (CHIP Bioinformatics)
  9. bdbSNP build 139: GRCh37.p10