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Table 2 Association results of nine significant SNPs from the combined meta-analysis of all three stages

From: A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians

SNP

Chr.

Gene

 

Risk allele

Stage 1 Indo. P*

OR

(95% CI)

Stage 2 Indo. P*

OR

(95% CI)

Indo. allele freq.

Stage 3 Russ. P*

OR

(95% CI)

Russ allele freq.

Indo. & Russ. P

OR

(95% CI)

rs2273061

20

JAG1

 

G

0.004

1.80

1.18

2.72

0.01

1.24

1.05

1.46

0.28

0.008

1.14

1.03

1.25

0.43

0.0004

1.16

1.07

1.26

rs4461087

16

DYNLR

 

A

0.009

1.62

1.10

2.37

0.03

1.18

1.01

1.38

0.38

0.01

1.18

1.04

1.34

0.16

0.001

1.18

1.07

1.30

rs10515787

5

EBF1

 

A

0.006

0.57

0.38

0.88

0.02

0.81

0.68

0.96

0.26

0.02

0.73

0.56

0.96

0.03

0.001

0.79

0.68

0.91

rs10497744

2

TMEFF2

Both SNPs in LD r2 = 0.99 D' = 1.00

A

0.002

0.55

0.38

0.82

0.02

0.83

0.71

0.97

0.35

0.02

0.89

0.80

0.98

0.30

0.001

0.87

0.80

0.95

rs1020941

2

TMEFF2

 

C

0.004

0.57

0.38

0.83

0.03

0.84

0.72

0.98

0.35

0.03

0.89

0.81

0.99

0.30

0.002

0.88

0.81

0.95

rs188872

16

CCL17

 

A

0.004

0.51

0.33

0.78

0.02

0.82

0.70

0.97

0.30

0.04

0.89

0.80

0.99

0.25

0.002

0.87

0.80

0.95

rs10245298

7

HAUS6

 

A

0.03

2.37

1.09

5.16

0.03

1.40

1.04

1.89

0.07

0.04

1.18

1.01

1.39

0.09

0.005

1.23

1.06

1.41

rs6985962

8

PENK

 

C

0.02

2.01

1.12

3.61

0.04

1.26

1.01

1.59

0.13

0.047

1.14

1.00

1.29

0.15

0.006

1.17

1.05

1.31

rs1418267

9

TXNDC4

 

A

0.0004

3.19

1.71

5.99

0.04

1.28

1.01

1.62

0.12

0.04

1.11

1.01

1.22

0.40

0.007

1.13

1.03

1.23

  1. Chr.- chromosome, LD- linkage disequilibrium, r2 - R square, D' - D prime, Indo.- Indonesia, P- P-value, OR- odds ratio, 95%
  2. CI- 95% confidence interval, freq.- frequency, Russ.- Russia
  3. • See Additional file 2, Supplementary Table S2 for genotype counts