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Table 4 Obesity case-control association study of the 14 PTPN1 SNPs and haplotypes.

From: Analysis of common PTPN1gene variants in type 2 diabetes, obesity and associated phenotypes in the French population

    

OBM vs C2

SO vs C2

 

MAF in the OBM group (n = 616)

MAF in the SO group (n = 688)

MAF in the C2 group (n = 736)

Allelic p-values

OR [95% CI]

Allelic p-values

OR [95% CI]

-7077 G/C

38.4

38.0

37.4

0.60

1.04 [0.89–1.22]

0.83

1.02 [0.87–1.19]

rs6020563 T/G

48.4

50.2

47.3

0.56

1.05 [0.89–1.23]

0.14

1.12 [0.96–1.31]

rs2426157 A/G

28.9

27.8

29.0

0.96

1.00 [0.84–1.18]

0.39

1.07 [0. 91–1.27]

rs3787335 T/G

8.5

9.6

8.1

0.67

1.06 [0.81–1.40]

0.13

1.22 [0.94–1.58]

rs6126033 C/T

7.0

8.7

6.8

0.81

1.04 [0.77–1.41]

0.05

1.32 [1.0–1.75]

rs941798 A/G

44.6

45.2

45.1

0.76

1.02 [0.88–1.19]

0.97

1.00 [0.86–1.16]

rs1570179 C/T

35.4

35.9

35.4

0.99

1.00 [0.85–1.17]

0.82

1.02 [0.87–1.19]

rs2426159 A/G

48.9

49.4

47.2

0.36

1.07 [0.92–1.25]

0.22

1.10 [0.95–1.27]

rs3787345 C/T

40.4

42.0

39.8

0.76

1.02 [0.88–1.20]

0.23

1.10 [0.94–1.28]

rs6020608 C/T

28.7

27.8

29.1

0.85

1.02 [0.86–1.20]

0.41

1.07 [0. 91–1.12]

rs754118 C/T

35.5

37.4

35.6

0.93

1.00 [0.86–1.18]

0.35

1.08 [0.92–1.27]

rs2282146 C/T

6.2

7.0

6.7

0.65

1.08 [0.77–1.53]

0.69

1.06 [0.79–1.43]

rs718050 G/A

36.7

38.7

36.3

0.84

1.02 [0.87–1.19]

0.20

1.11 [0.95–1.29]

rs914458 C/G

26.7

27.5

30.4

0.04

1.20 [1.01–1.43]

0.07

1.17 [0.99–1.39]

Haplotype

Frequencies in OBM

Frequencies in SO

Frequencies in C2

Individual p-values

Overall p-value

Individual p-values

Overall p-value

GGCC

32.3

34.4

31.5

0.53

 

0.17

 

CACC

24.3

20.5

21.8

0.25

 

0.71

 

GGCG

12.0

11.3

13.3

0.22

 

0.19

 

GACC

12.2

11.1

11.0

0.38

0.32

0.91

0.78

CACG

5.8

8.7

8.5

0.04

 

0.58

 

GACG

6.2

6.3

6.5

0.58

 

0.70

 

CATC

4.7

6.0

5.0

0.78

 

0.55

 
  1. Genotype and allele frequencies were estimated for each group. All genotypes were in Hardy-Weinberg equilibrium in the populations tested, except for SNP rs914458 C/G in the group of subjects with severe obesity. The p-values for chi-square tests, odds-ratios (ORs) and 95% confidence intervals (CI95) are given. The individual and overall p-values of the haplotypes are indicated. We estimated the empirical p-value of the CACG haplotype in the group of moderate obese subjects (p = 0.30) using 1000 permutations.
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BMC Medical Genetics

ISSN: 1471-2350

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