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Table 2 Allele-based associations with RA (case-control comparison, odds ratios (ORs) estimated for minor allele)

From: Meta-genetic association of rheumatoid arthritis and PTPN22using PedGenie 2.1

 

PedGenie 2.1

 
 

NARAC Study 1a

NARAC Study 2b

Meta-analysis

Previously publishedc,d

PTPN22

MAFe

OR

95% CI

p f

MAFe

OR

95% CI

p f

OR

95% CI

p g

OR

95% CI

p h

Rs3789604

0.182

1.11

0.88–1.41

0.36

0.175

1.15

0.95–1.39

0.17

1.13

0.98–1.32

0.10

1.15

0.97–1.35

0.11

Rs3811021

0.182

1.11

0.88–1.40

0.38

0.176

1.14

0.95–1.37

0.17

1.13

0.97–1.31

0.11

1.15

0.97–1.36

0.10

rs1217413

0.210

1.38

1.13–1.70

0.003

0.230

1.28

1.07–1.53

0.002

1.32

1.16–1.51

<0.001

1.37

1.18–1.60

<0.001

ss38346942

0.015

1.21

0.61–2.37

0.59

0.012

1.22

0.65–2.27

0.56

1.21

0.75–1.97

0.42

1.03

0.59–1.79

1.00

rs1217388

0.246

1.29

1.04–1.59

0.017

0.260

1.20

1.01–1.42

0.028

1.23

1.07–1.42

0.003

1.28

1.11–1.49

0.001

ss38346943

0.031

0.32

0.16–0.67

0.001

0.023

0.84

0.47–1.48

0.55

0.60

0.39–0.92

0.020

0.63

0.40–1.01

0.05

rs1310182

0.430

1.28

1.06–1.56

0.008

0.435

1.28

1.09–1.49

0.001

1.28

1.13–1.45

<0.001

1.35

1.18–1.54

<0.001

ss38346944

0.029

1.14

0.65–1.99

0.63

0.019

1.37

0.84–2.22

0.24

1.26

0.85–1.85

0.24

1.29

0.87–1.93

0.21

rs2476601

0.087

1.79

1.39–2.30

<0.001

0.085

2.19

1.75–2.74

<0.001

2.03

1.70–2.42

<0.001

1.93

1.58–2.37

<0.001

(R620W)

           

2.184

1.76–2.70

<0.001

rs12730735

0.292

0.83

0.68–1.01

0.07

0.295

0.89

0.76–1.04

0.14

0.86

0.76–0.98

0.025

0.81

0.70–0.94

0.006

rs11102685

0.076

1.21

0.87–1.77

0.26

0.078

1.20

0.93–1.55

0.19

1.20

0.98–1.49

0.09

1.27

1.01–1.60

0.040

rs12760457

0.291

0.83

0.68–1.02

0.09

0.296

0.88

0.74–1.05

0.14

0.86

0.76–0.98

0.022

0.82

0.71–0.96

0.010

rs2488458

0.246

1.29

1.05–1.58

0.014

0.260

1.20

1.01–1.41

0.037

1.23

1.08–1.41

0.003

1.27

1.10–1.48

0.002

rs1217414

0.282

0.88

0.70–1.10

0.20

0.270

0.84

0.72–0.99

0.06

0.86

0.76–0.97

0.018

0.84

0.72–0.98

0.020

  1. aProblem 2, 446 family cases and 103 family controls in 202 NARAC pedigrees, 664 independent NYC controls; excludes Plenge et al. [6] samples.
  2. bProblem 2, samples in Plenge et al. [6] candidate gene file, 839 family cases in 463 pedigrees and 854 independent NYC controls.
  3. cCarlton et al. [5] sample set 2 (661 randomly selected independent cases from NARAC pedigrees and 1322 independent NYC controls).
  4. dPlenge et al. [6] second collection; 840 family cases (NARAC) and 867 independent NYC controls: R620W SNP only.
  5. eMinor allele frequency in controls.
  6. fEmpirical confidence intervals and chi-square p-values, 1000 simulations; p < 0.05 in bold.
  7. gEmpirical confidence intervals and CMH chi-square general association test, 1000 simulations; p < 0.05 in bold.
  8. hFisher's exact chi-square test; p < 0.05 in bold.