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Table 1 Summary statistics, based on Replicates 1 through 200, for 12 polygenic SNPs and SNPs near the major causal SNP rs2294207 (shown in red) in chromosome 22.

From: Comparison between single-marker analysis using Merlin and multi-marker analysis using LASSO for Framingham simulated data

   

p-value from Merlin

entry number from LASSO

Markers

Loc (Mb)

LDa

E(p)b

rank E(p)c

E rank(p)d

Min.p

Max.pe

E(e)

rank E(e)

E rank(e)

Min.e

Max.e

Outf

rs131464

23.3948

0

0.075

94

439.6

1.1 × 10-4

0.67

1228

205

954.5

56

8702

0

rs133252

24.137

0

0.27

525

1345

7.9 × 10-4

0.98

1690

466

1170

32

10001

4

rs5752309

25.0701

0

0.066

74

390.3

6.6 × 10-6

0.99

1570

398

915.6

31

10001

11

rs1543335

33.5136

0

0.64

4457

3007.5

5.2 × 10-2

1

6452

3757

3113.3

445

10001

82

rs17002034

39.3263

0

0.026

36

184.2

3.3 × 10-6

0.48

5127

3167

2499.2

192

10001

71

rs6519313

40.8828

0

0.14

198

743.2

2.8 × 10-4

0.95

3431

2009

2021.8

23

10001

20

rs7364152

41.6466

0

0.15

212

785.2

1.2 × 10-4

0.85

6747

3873

3293.2

93

10001

73

rs5765113

43.7736

0

1.9 × 10-3

20

35.8

7.9 × 10-8

0.057

2462

1125

1438.2

200

10001

19

rs6007503

43.989

0

0.069

80

396.5

9.0 × 10-3

0.78

2539

1211

1766.3

130

10001

3

rs12159871

47.74

0

0.39

1077

1902

1.4 × 10-3

1

8620

4397

3781

1802

10001

141

rs4528878

47.8062

0

0.38

1013

1851.9

0.01

1

5139

3175

2708.2

432

10001

53

rs17013240

48.9997

0

0.56

2735

2671.8

0.016

1

6241

3666

3134.9

529

10001

63

rs5994481

30.8996

0.06

0.016

25

123

5.0 × 10-6

0.52

3586

2136

2155.4

15

10001

13

rs136414

30.9051

0.33

4.5 × 10-6

6

8.4

1.6 × 10-13

1.8 × 10-4

3809

2301

2013.1

87

10001

49

rs136416

30.9052

0.32

5.1 × 10-6

7

8.8

1.7 × 10-14

2.0 × 10-4

5726

3452

2751.9

1

10001

77

rs136417

30.9053

0.32

5.2 × 10-6

8

9.5

2.3 × 10-14

2.0 × 10-4

8015

4246

3470.7

3

10001

139

rs136422

30.9064

0.32

6.4 × 10-6

9

10.5

5.3 × 10-14

2.6 × 10-4

6769

3882

3050.7

3

10001

106

rs136457

30.9147

0.22

1.7 × 10-5

11

11.9

5.1 × 10-13

1.4 × 10-3

8810

4429

3750.6

7

10001

159

rs136458

30.9147

0.22

1.7 × 10-5

12

12.4

5.1 × 10-13

1.4 × 10-3

8871

4437

3789

155

10001

158

rs136460

30.9148

0.22

1.6 × 10-5

10

11.2

3.7 × 10-13

1.4 × 10-3

8222

4310

3530.7

8

10001

144

rs136477

30.9184

0.22

2.0 × 10-5

14

13.3

2.1 × 10-12

1.4 × 10-3

4543

2791

2557.2

165

10001

37

rs136485

30.9221

0.22

1.8 × 10-5

13

11.7

7.0 × 10-13

1.4 × 10-3

5008

3092

2649

3

10001

54

  1. aLD, linkage disequilibrium between the major causal SNP and other SNPs (measured by r2)
  2. bE(p), averaged p-value over 200 replications
  3. crank E(p), rank of the averaged p-value over 200 replications
  4. dE rank(p), averaged rank of p-values (similarly for entry number)
  5. eMax.e, 10001 if the SNP was not in any of the first 10000 models
  6. fOut, count of replicates for which the SNP was excluded in the LASSO solution path (up to 10,000 models)
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BMC Proceedings

ISSN: 1753-6561

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