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Table 3 Significant SNPs for T-cell subpopulations

From: Genome-wide association study for T lymphocyte subpopulations in swine

Trait

No. SNPs

SNP Name

SSC.

Position

Significance levelb

Nearest gene

Distance (bp)

    

(bp)a

   

CD4-CD8- T%

3

ALGA0006170

SSC1

147676962

A

SELS

101263

  

ALGA0027442

SSC4

106255554

A

LOC100515138

15207

  

MARC0035862

SSC17

26683704

A

FLRT3

999166

CD4+CD8+ T%

15

ASGA0000475

SSC1

5393161

A

QKI

197563

  

MARC0090836

SSC5

18263549

A

LOC100523435

8399

  

H3GA0016197

SSC5

30846602

A

LOC100514286

within

  

DRGA0005876

SSC5

52631994

A

LOC100153016

7905

  

ASGA0093882

SSC8

27821389

A

LOC100515221

68339

  

MARC0103793

SSC9

117134341

A

NCF2

within

  

ALGA0061180

SSC11

18408471

A

LOC100518860

within

  

ALGA0062506

SSC11

55628913

A

RNF219

152990

  

DRGA0012994

SSC13

116721928

A

LOC100518275

Within

  

ASGA0059251

SSC13

116794774

A

LOC100518275

within

  

H3GA0037561

SSC13

117065279

A

LOC100518275

within

  

MARC0024545

SSC13

117511306

A

LOC100739759

within

  

H3GA0037568

SSC13

117963270

A

CLDN11

within

  

ALGA0072642

SSC13

118134975

A

SLC7A14

22223

  

ASGA0077977

SSC17

59215829

A

CBLN4

within

CD4+CD8- T%

31

SIRI0000967

SSC1

65386385

A

MAP3K7

93369

  

ALGA0109882

SSC1

65402776

A

MAP3K7

76978

  

ALGA0003935

SSC1

67256904

A

LOC100152346

within

  

MARC0008049

SSC6

74003688

A

LOC100738715

within

  

ALGA0105115

SSC9

127202082

A

CD46

12474

  

MARC0076632

SSC9

127394064

B

LOC100514786

within

  

ASGA0046812

SSC10

16205420

A

LOC100513811

within

  

ALGA0057450

SSC10

16220722

A

LOC100513811

within

  

ALGA0061535

SSC11

23576083

A

TRNAE-UUC

42913

  

M1GA0015162

SSC11

61231196

A

LOC100154696

within

  

ASGA0051093

SSC11

61450492

A

LOC100154696

112456

  

ALGA0108362

SSC12

6596691

A

LOC100518214

225784

  

MARC0009109

SSC12

6637944

A

SOX9

229926

  

ALGA0106073

SSC12

6663787

A

SOX9

204083

  

ASGA0052986

SSC12

6791202

A

SOX9

76668

  

ASGA0052974

SSC12

6826155

A

SOX9

41715

  

ALGA0064738

SSC12

6891741

A

SOX9

20500

  

H3GA0033370

SSC12

6976387

B

LOC100518393

21514

  

ASGA0053002

SSC12

7105246

A

LOC100519105

55408

  

ASGA0104370

SSC12

7185885

A

LOC100519105

136047

  

ALGA0064767

SSC12

7400177

A

LOC100519105

350339

  

ALGA0078815

SSC14

76804400

A

LOC100521406

85124

  

H3GA0041012

SSC14

77946383

A

PSAP

within

  

ASGA0065687

SSC14

107127514

A

HTR7

260753

  

ALGA0087956

SSC15

123078022

A

LOC100516232

22744

  

INRA0055474

SSC18

21991584

A

LOC100622672

28674

  

ALGA0097499

SSC18

22003396

A

LOC100513190

3075

  

ASGA0079256

SSC18

22055859

A

LOC100525548

1899

  

ALGA0098112

SSC18

38463920

A

BMPER

113622

  

MARC0089391

SSC18

38488630

A

BMPER

88912

  

MARC0024065

SSC18

50965324

A

LOC100622432

within

CD4-CD8+ T%

3

ASGA0022812

SSC4

126976845

A

LOC100737939

107579

  

H3GA0041012

SSC14

77946383

A

PSAP

within

  

ALGA0103427

SSC15

127742340

A

IKZF2

within

CD4+ T%

6

ASGA0023262

SSC4

130826499

A

LOC100151966

174827

  

ALGA0030335

SSC5

7606208

A

LOC100512654

6682

  

ALGA0122248

SSC16

73417692

A

LOC100518939

70693

  

INRA0055474

SSC18

21991584

A

LOC100513190

within

  

ASGA0079256

SSC18

22055859

A

LOC100525548

1899

  

ASGA0080319

SSC18

49513089

A

LOC100516656

43287

CD8+ T%

1

ALGA0006170

SSC1

147676962

B

SELS

101263

CD4+:CD8+

5

H3GA0041012

SSC14

77946383

A

PSAP

within

  

ALGA0117513

SSC15

123215784

A

LOC100518938

11678

  

ALGA0122248

SSC16

73417692

A

LOC100738933

403285

  

ALGA0098112

SSC18

38463920

A

BMPER

113622

  

MARC0089391

SSC18

38488630

A

BMPER

88912

  1. a: Derived from the recent porcine genome sequence assembly (Sscrofa9.2) (http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9823&build=previous).
  2. b: A means chromosome-wise significance level, B means genome-wise significance level.