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Table 1 Clarity SNP association results, full sample

From: Independent replication analysis of genetic loci with previous evidence of association with juvenile idiopathic arthritis

     

Best test p§

Allelic

Evidence for replication?

Gene

SNP

Minor allele

Case MAF

Control MAF

P

OR (95% CI)

ADAD1-IL2-IL21

rs17388568[6]

A

0.25

0.24

0.29 R

0.55

1.07 (0.85, 1.36)

N

 

rs13143866[6]

A

0.28

0.26

0.28 D

0.31

1.12 (0.90, 1.40)

N

 

rs6822844[4, 5]

T

0.13

0.12

0.42 R

0.46

1.12 (0.83, 1.49)

N

AFF3

rs1160542[5]

G

0.49

0.46

0.16 R

0.25

1.12 (0.92, 1.36)

P

ANGPT1

rs1010824[6]

T

0.17

0.16

0.71 D

0.82

1.03 (0.79, 1.34)

N

ATXN2

rs653178[7]

G

0.55

0.46

0.00023 A

0.00023

1.44 (1.19, 1.76)

Y

BACH2

rs11755527[7]

G

0.44

0.46

0.34 D

0.41

0.92 (0.76, 1.12)

N

C12orf30

rs17696736[6, 8]

G

0.50

0.41

0.00044 T

0.0005

1.42 (1.16, 1.72)

Y

C3orf1

rs4688011[9]

A

0.24

0.19

0.016 D

0.02

1.32 (1.04, 1.68)

Y

CD14

rs2569190[11]

A

0.48

0.50

0.24 R

0.43

0.92 (0.76, 1.12)

N

CD226

rs763361[5]

T

0.52

0.48

0.059 A

0.059

1.21 (0.99, 1.47)

P

CLEC16A

rs6498169[12]

G

0.37

0.35

0.30 A

0.3

1.11 (0.91, 1.36)

N

COG6

rs7993214[6]

T

0.30

0.29

0.41 T

0.41

1.09 (0.88, 1.36)

N

CTLA4

rs3087243[5]

A

0.46

0.46

0.80 R

0.97

0.997 (0.82, 1.21)

N

DCN1*

rs939898[22]

G

0.21

0.18

0.057 D

0.11

1.22 (0.95, 1.56)

N

ERAP1†

rs30187[13]

T

0.39

0.37

0.36 D

0.46

1.08 (0.88, 1.32)

N

FHIT*

rs9311745[22]

C

0.07

0.08

0.86 A

0.86

0.97 (0.66, 1.41)

N

HUNK*

rs2833547[22]

T

0.25

0.26

0.46 D

0.66

0.95 (0.76, 1.19)

N

IL15

rs13139573[9]

T

0.47

0.43

0.0016 G

0.13

1.16 (0.96, 1.41)

?

IL23R

rs11209026[13]

A

0.07

0.05

0.22 T

0.23

1.29 (0.85, 1.94)

N

 

rs11465804[6]

G

0.06

0.05

0.44 T

0.45

1.18 (0.77, 1.80

N

IL2RA

rs12251307[6]

T

0.11

0.12

0.34 A

0.34

0.86 (0.63, 1.17)

N

 

rs706778[2]

A

0.45

0.43

0.26 T

0.26

1.12 (0.92, 1.36)

N

 

rs2104286[6, 14]

G

0.21

0.22

0.21 R

0.63

0.94 (0.74, 1.20)

N

IL7R

rs6897932[5]

T

0.25

0.23

0.17 D

0.19

1.16 (0.93, 1.46)

N

JMJD1C-REEP3

rs6479891[9]

T

0.17

0.18

0.44 D

0.64

0.94 (0.73, 1.21)

N

 

rs12411988[9]

C

0.16

0.17

0.47 R

0.74

0.96 (0.73, 1.24)

N

KIF5A

rs1678542[15]

C

0.36

0.39

0.22 A

0.22

0.88 (0.72, 1.08)

N

LPP

rs1464510[7]

T

0.46

0.46

0.81 R

0.93

1.01 (0.83, 1.23)

N

MBL2

rs1800451[16]

A

0.03

0.02

0.059 T

0.061

1.88 (0.96, 3.67)

P

MEFV

rs224204[17]

T

0.49

0.47

0.36 D

0.38

1.09 (0.90, 1.33)

N

NLRP30

rs3806265[17]

C

0.34

0.35

0.46 D

0.54

0.94 (0.76. 1.15)

N

NOD2

rs1861759[17]

C

0.39

0.37

0.26 D

0.64

1.05 (0.86, 1.28)

N

NRBF2-EGR2

rs10995450[9]

T

0.24

0.24

0.96 R

0.98

0.998 (0.79, 1.25)

N

PRKCQ

rs4750316[15]

C

0.17

0.18

0.33 R

0.42

0.90 (0.70, 1.17)

N

PSTPIP10

rs4078354[17]

T

0.33

0.36

0.13 A

 

0.85 (0.69, 1.05)

P

PTPN2

rs1893217[6]

C

0.20

0.18

0.50 A

0.5

1.09 (0.85, 1.40)

N

 

rs7234029[2, 6]

G

0.19

0.18

0.43 D

0.49

1.09 (0.85, 1.40)

N

 

rs2542151[6]

G

0.20

0.18

0.49 D

0.53

1.08 (0.85, 1.39)

N

PTPN22

rs2476601[6, 18]

A

0.10

0.07

0.006 A

0.006

1.62 (1.15, 2.30)

Y

RANTES (CCL5)

rs2107538[19]

T

0.21

0.18

0.039 D

0.097

1.23 (0.96, 1.58)

P∞

 

rs2280788[19]

G

0.02

0.02

0.30 T

0.31

1.45 (0.71, 2.96)

N

SLITRK5*

rs1074044[22]

C

0.44

0.44

0.81 D

0.9

1.01 (0.83, 1.23)

N

STAT4

rs8179673[15]

C

0.29

0.24

0.012 D

0.024

1.29 (1.03, 1.61)

Y

 

rs3821236[6]

A

0.25

0.21

0.013 D

0.038

1.28 (1.01, 1.61)

Y

 

rs7574865[6, 8, 15]

T

0.29

0.24

0.0091 D

0.025

1.29 (1.03, 1.61)

Y

TNFAIP3

rs6920220[8, 15]

A

0.22

0.20

0.29 A

0.29

1.14 (0.90, 1.44)

N

 

rs13207033[15]

A

0.26

0.29

0.26 D

0.29

0.89 (0.71, 1.11)

N

TRAF1-C5

rs2900180[15]

T

0.37

0.32

0.014 R

0.046

1.23 (1.00, 1.51)

Y

 

rs3761847[21]

A

0.42

0.40

0.32 A

0.32

1.11 (0.90, 1.36)

N

VTCN1

rs12046117[22]

T

0.17

0.15

0.33 A

0.33

1.14 (0.87, 1.49)

N

  1. * No gene attribution in original publication, closest gene by UCSC Genome Browser listed.
  2. † Associated specifically with enthesitis related JIA in original report.
  3. 0 Associated specifically with psoriatic JIA in original report.
  4. § Model providing most significant P value: A = allelic, G = genotypic, T = Cochrane Armitage Trend Test (additive), D = dominant, R = recessive.
  5. ‡ Evidence for replication Y = Yes, P = Partial, N = No. See text for definitions. ? = potential for A/T allele reversal with respect to the prior report.
  6. ∞ Finding listed as P (partially replicated) since for this SNP, prior evidence was for a non-significant trend towards association in a direction consistent with our own.