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Table 2 Summary of top associations from stage I dataset

From: A robust and efficient statistical method for genetic association studies using case and control samples from multiple cohorts

Locus

SNP name

Dist(kb) *

P value

BPP (%)

M 1

M 2

M 3

M 1

M 2

M 3

1p13.2-13.3

rs17654531

-

1.9 × 10-9

3.2 × 10-6

1.2 × 10-5

37

22

14

rs10857899

328

2.7 × 10-8

3.1 × 10-6

3.1 × 10-6

57

25

27

2p23.3

rs7564397

-

9.7 × 10-8

0.013

0.033

55

0

0

2q21.2

rs1474406

-

4.3 × 10-8

2.3 × 10-3

0.001

57

1

3

2q36.1

rs1447108

-

5.5 × 10-8

2.5 × 10-4

4.4 × 10-4

59

4

3

3p24.3

rs1605527

-

2.0 × 10-8

1.0 × 10-4

9.4 × 10-5

53

9

10

4p15.2

rs6820719

-

1.6 × 10-9

0.23

0.30

74

0

0

rs7676830

23

8.6 × 10-10

0.12

0.15

77

0

0

rs12649499

11

4.8 × 10-10

0.20

0.26

77

0

0

4q21

rs11931074

-

3.9 × 10-8

5.1 × 10-8

4.8 × 10-8

56

54

54

rs356220

2

7.7 × 10-11

3.4 × 10-8

7.0 × 10-8

81

56

52

rs3857059

34

5.3 × 10-8

4.0 × 10-8

3.6 × 10-8

56

55

56

rs2736990

3

6.3 × 10-12

2.9 × 10-9

5.7 × 10-9

88

71

67

6q27

rs2072638

-

1.1 × 10-11

0.014

0.012

86

0

0

7p14-p13

rs859522

-

1.8 × 10-8

9.7 × 10-6

3.4 × 10-5

62

21

14

7q21

rs3779331

-

6.6 × 10-8

0.028

0.01

56

0

0

7q21.11

rs10246477

-

9.3 × 10-8

2.3 × 10-5

5.3 × 10-5

56

13

10

8p23.2

rs7013027

-

5.8 × 10-8

4.3 × 10-6

1.9 × 10-6

56

23

29

rs4875773

63

1.6 × 10-8

0.02

0.044

63

0

0

8p22

rs7828611

-

8.4 × 10-8

1.2 × 10-4

6.2 × 10-4

55

6

3

rs2736050

1

9.9 × 10-10

1.0 × 10-5

2.0 × 10-4

74

18

5

rs2009817

3

2.0 × 10-9

1.3 × 10-5

2.1 × 10-4

72

16

5

8q24.23-24.3

rs4556079

-

4.8 × 10-8

5.0 × 10-6

4.8 × 10-6

60

20

22

rs11781101

14

7.3 × 10-8

5.4 × 10-6

5.3 × 10-6

56

21

22

rs7004938

12

3.1 × 10-8

3.0 × 10-6

3.0 × 10-6

59

24

25

rs11783351

1

7.7 × 10-8

5.0 × 10-6

5.5 × 10-6

53

21

21

9q21.31

rs2378554

-

6.6 × 10-8

2.0 × 10-6

2.9 × 10-5

54

29

13

10p11.21

rs2492448

-

3.8 × 10-8

1.6 × 10-6

3.8 × 10-6

61

29

24

rs11591754

12

4.8 × 10-10

2.5 × 10-7

1.7 × 10-6

80

43

30

rs7923172

102

7.0 × 10-8

1.1 × 10-5

1.4 × 10-5

54

17

16

rs4934704

23

7.3 × 10-8

1.2 × 10-5

1.5 × 10-5

54

17

16

rs10827492

97

9.7 × 10-8

1.3 × 10-5

1.7 × 10-5

52

16

16

10q24.3

rs17115100

-

2.7 × 10-8

6.9 × 10-6

2.5 × 10-5

37

19

13

11p15.2

rs11605276

-

3.4 × 10-11

0.079

0.19

86

0

0

rs10500796

45

1.9 × 10-8

0.18

0.30

61

0

0

11q13

rs1726764

-

6.6 × 10-8

0.088

0.20

53

0

0

12p13

rs10849446

-

6.7 × 10-9

1.1 × 10-4

3.7 × 10-5

68

6

12

16p13.3

rs11648673

-

5.5 × 10-8

1.3 × 10-5

4.8 × 10-7

56

15

38

17q21

rs169201

-

1.0 × 10-7

6.5 × 10-6

1.2 × 10-7

57

19

49

rs199533

39

4.1 × 10-8

2.8 × 10-6

5.0 × 10-8

60

24

55

17q24.3

rs558076

-

6.6 × 10-8

1.0 × 10-4

2.5 × 10-5

57

7

14

rs817097

42

5.0 × 10-8

8.1 × 10-6

6.2 × 10-6

56

18

18

20p12.1

rs6041636

-

9.9 × 10-9

0.16

0.24

66

0

0

21q22.3

rs2070535

-

5.0 × 10-8

0.060

0.096

54

0

0

  1. Significance and bootstrap posterior probabilities (BPP) for the 44 significant SNPs detected by Method 1 (M 1) from stage I dataset. Shadowed are the regions at which the genetic association was tested by Method 2 (M2) and Method 3 (M 3) at the same significance level. *Distance (kb) from previous significant SNP in the same chromosome region.