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Table 3 Top single-marker hits in genes from the four genetic pathways associated with SLE

From: Genome-wide association study meta-analysis identifies five new loci for systemic lupus erythematosus

Gene

Marker

Chr

bp

MA

OR

p (Spain)

p (EUR)

p (meta)

Pathway

BCL10

rs12084253

1

85,720,326

T

1.11

0.020

0.0015

0.00012

BCR

FCER1G

rs1136224

1

161,184,097

G

0.91

0.023

0.022

0.0024

VASC

FCGR2B

rs182968886

1

161,642,985

A

0.86

0.044

0.0018

0.00023

BCR

CD247

rs113305799

1

167,416,006

A

1.17

0.0035

0.044

0.0022

CTLA4

PROC

rs6740067

2

128,156,366

T

1.16

0.043

0.018

0.0026

VASC

CTLA4

rs733618

2

204,730,944

C

1.19

0.026

0.0018

0.00016

CTLA4

PPP3CA

rs13120190

4

102,056,663

G

0.93

0.025

0.047

0.0060

BCR

IL2

rs45522533

4

123,396,876

T

1.16

0.016

0.0058

0.00044

CTLA4

SLC7A11

rs74843273

4

139,150,464

T

0.81

0.025

0.0066

0.00065

VASC

ITK

rs60714766

5

156,602,589

T

1.07

0.015

0.043

0.0042

CTLA4

CARD11

rs6461796

7

3,071,195

C

0.94

0.027

0.033

0.0042

BCR

LYN

rs17812659

8

56,889,862

G

0.86

0.013

2.57E-05

1.17E-06

BCR,VASC

ANGPT1

rs79847080

8

108,293,443

G

0.84

0.032

0.0028

0.00031

VASC

VAV2

rs2810536

9

136,812,625

G

1.08

0.030

0.011

0.0013

BCR

KRAS

rs17388587

12

25,389,220

G

1.13

0.036

0.048

0.0075

BCR, VASC

PRKCB

rs11641223

16

24,020,316

T

1.11

0.041

0.0010

0.00012

BCR

CD19

16:28955702:D

16

28,955,702

I

1.06

0.0077

0.047

0.0034

BCR

SLC7A6

rs55856208

16

68,324,210

T

1.08

0.045

0.049

0.0086

VASC

PLCG2

rs11548656

16

81,916,912

G

1.3

0.014

0.00062

0.000035

BCR

ATP1B2

rs1794287

17

7,578,837

A

0.9

0.023

0.024

0.0026

VASC

ITGB3

rs75211989

17

45,366,261

G

1.11

0.00014

0.020

0.00020

VASC

GRB2

rs36023980

17

73,341,284

T

0.85

0.00039

1.51E-06

4.73E-09

CTLA4, IL4, BCR, VASC

NFATC1

rs111354805

18

77,238,078

T

1.21

0.027

6.58E-05

5.26E-06

BCR

MAP2K2

rs350913

19

4,096,779

T

0.94

0.029

0.030

0.0039

BCR

CD79A

rs16975619

19

42,392,441

C

1.52

0.020

0.0099

0.00089

BCR

SIRPG

rs11696739

20

1,600,925

A

0.92

0.044

0.0050

0.00069

VASC

RAC2

rs229566

22

37,602,131

A

1.06

0.041

0.03

0.0047

BCR

  1. Suggestive risk variants were identified as those markers showing with the most significant meta-analysis p value (p (meta)), and that are associated in the two genome-wide association study cohorts (p < 0.05) and show the same direction of effect (OR) MA minor allele, OR odds ratio according to minor allele in European ancestry cohort, I insertion allele, Pathway biological pathway/s where the gene has been annotated, BCR B cell receptor pathway, CTLA4 CTLA4 pathway, IL4 interleukin-4 pathway, VASC vascular cell wall pathway
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Arthritis Research & Therapy

ISSN: 1478-6362

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