Skip to main content

Table 2 PTPN22 analysis with LR and the Mantel statistic (adjusted p-values)

From: Comparison of the power of haplotype-based versus single- and multilocus association methods for gene × environment (gene × sex) interactions and application to gene × smoking and gene × sex interactions in rheumatoid arthritis

       

Model 4f

Model 5g

Mantelh

Marker

MAFa

D'b

r 2b

Model 1c

Model 2d

Model 3e

Main

Int.

Main

Int.

I

II

III

rs3789604

0.20

1.00

0.04

0.97

0.96

0.96

0.95

0.95

0.97

0.94

0.40

0.03 i

<0.001

rs3811021

0.20

0.95

0.04

0.97

0.96

0.97

0.95

0.95

0.97

0.95

0.40

0.03

<0.001

rs1217413

0.21

0.99

0.46

0.05

0.026

0.15

0.94

0.62

0.37

0.86

0.35

0.02

<0.001

ss38346942

0.01

0.60

0.00

0.95

0.96

0.97

1.00

1.00

0.97

0.97

0.35

0.02

<0.001

rs1217388

0.25

0.99

0.40

0.21

0.10

0.41

0.68

0.39

0.60

0.90

0.35

0.02

<0.001

ss38346943

0.03

0.05

0.00

0.81

0.88

0.97

0.95

0.96

0.28

0.49

0.40

0.02

<0.001

rs1310182

0.45

0.99

0.17

0.40

0.21

0.78

0.43

0.20

0.49

0.81

0.40

0.03

<0.001

ss38346944

0.02

0.19

0.00

0.97

0.96

0.91

0.94

0.94

1.00

1.00

0.40

0.03

<0.001

R620W

0.10

1.00

1.00

0.004

0.001

0.02

0.18

0.01

0.28

0.86

0.40

0.02

<0.001

rs12730735

0.30

0.94

0.05

0.81

0.74

0.78

0.95

0.94

0.97

0.94

0.40

0.03

<0.001

rs11102685

0.08

0.99

0.02

0.97

0.96

0.94

1.00

1.00

0.86

0.78

0.32

0.03

<0.001

rs12760457

0.29

0.97

0.06

0.90

0.88

0.87

0.93

0.81

0.97

0.92

0.38

0.03

<0.001

rs2488458

0.25

0.99

0.40

0.15

0.08

0.31

0.85

0.56

0.65

0.94

0.23

0.03

<0.001

rs1217414

0.26

1.00

0.05

0.69

0.47

0.97

0.74

0.54

0.09

0.21

0.23

0.03

<0.001

  1. aMinor allele frequency among controls
  2. bLD values calculated using the control population. All LR models consider one SNP at a time and include main effects of sex and smoking.
  3. cModel 1, main effect
  4. dModel 2, interaction term with sex
  5. eModel 3, interaction term with smoking
  6. fModel 4, main and interaction with sex
  7. gModel 5, main and interaction with smoking
  8. hMantel statistics: I, main effect (M0); II, joint effect (M1) with sex; III, joint effect (M1) with smoking
  9. ip-Values ≤ 0.05 are given in bold.