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Table 1 Independent genetic variants reaching genome-wide level of significance in the subset-based meta-analysis and showing pleiotropic effects across diseases

From: Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Region

Position (bp)

SNP

Gene

A1

P2sided

Best subset

1p36.32

2,534,978

rs6664969

MMEL1

A

2.86E−10

CeD RA

1p36.13

17,655,407

rs1748041

PADI4

C

3.63E−08

RA SSc

1p13.2

114,377,568

rs2476601

PTPN22

A

6.36E−119

RA T1D

1p13.2

114,388,804

rs1217403

PTPN22

C

4.66E−11

RA* T1D*

1q24.3

172,674,776

rs10912267

FASLG

A

3.90E−09

CeD T1D

2q11.2

100,764,004

rs13415465

AFF3

G

3.72E−12

CeD RA T1D

2q31.3

182,057,640

rs12619531

ITGA4

G

1.18E−18

CeD SSc

2q32.3

191,538,562

rs10931468

NAB1

A

1.56E−08

RA SSc

2q32.3

191,902,184

rs6749371

STAT4

T

3.84E−08

CeD SSc*

2q32.3

191,964,633

rs7574865

STAT4

T

3.16E−09

CeD* RA SSc T1D*

2q33.2

204,612,058

rs7426056

CD28

A

6.68E−12

CeD RA

2q33.2

204,738,919

rs3087243

CTLA4

A

5.08E−16

RA T1D

3p14.3

58,183,636

rs35677470

DNASE1L3

A

1.04E−11

RA SSc

3q25.33

159,647,674

rs17753641

IL12A

G

1.64E−29

CeD SSc*

4p15.2

26,088,128

rs16878091

RBPJ

A

2.53E−12

RA T1D

5q33.1

150,438,988

rs1422673

TNIP1

T

1.87E−09

CeD RA SSc

6q15

90,976,768

rs72928038

BACH2

A

9.34E−12

CeD RA T1D

6q23.3

138,003,822

rs11757201

TNFAIP3

C

1.27E−11

CeD RA T1D

6q23.3

138,243,739

rs58721818

TNFAIP3

T

5.26E−10

RA SSc

6q25.3

159,470,417

rs212407

TAGAP

G

6.74E−14

CeD RA T1D

7p14.1

37,382,465

rs60600003

ELMO1

G

4.25E−13

CeD SSc

7p12.1

51,015,193

rs7780389

COBL

T

2.25E−08

RA T1D

7q32.1

128,572,766

rs4731532

IRF5

A

1.25E−10

RA SSc

9p13.3

34,710,260

rs2812378

CCL21

G

1.04E−09

CeD RA

10p15.1

6,101,713

rs3118470

IL2RA

C

5.92E−09

RA T1D

10p15.1

6,116,254

rs72776098

IL2RA

A

7.10E−10

SSc T1D

10p15.1

6,390,450

rs947474

PRKCQ

G

1.28E−08

CeD RA T1D

10p14

8,102,272

rs3802604

GATA3

G

4.67E−08

RA T1D

10q22.3

81,045,280

rs1250568

ZMIZ1

C

3.87E−15

CeD SSc T1D

11q23.3

118,726,843

rs10892299

DDX6

T

2.25E−13

CeD SSc T1D

12q13.2

56,470,625

rs11171739

IKZF4

C

1.87E−20

RA T1D

15q14

38,828,140

rs8043085

RASGRP1

T

1.53E−08

RA T1D

15q25.1

79,234,957

rs34593439

CTSH

A

1.47E−14

CeD T1D

17q12

38,033,277

rs1054609

ORMDL3

C

3.70E−08

RA SSc T1D

18p11.21

12,777,573

rs2542148

PTPN2

C

5.11E−16

CeD T1D

19p13.2

10,427,721

rs74956615

TYK2

A

1.62E−17

RA SSc T1D

21q22.3

43,855,067

rs1893592

UBASH3A

C

4.86E−12

CeD T1D

22q11.1

21,936,152

rs66534072

YDJC

G

2.05E−08

CeD SSc

  1. The selected lead SNP in each region is shown, together with the best subset obtained from the subset-based meta-analysis. Position (bp), base pair position in hg19; SNP, single nucleotide polymorphism; Gene, annotated gene as described in methods; A1, alternative allele used in the logistic regression; P2sided, p value from the two-sided subset-based meta-analysis; Best subset, phenotypes contributing to the association signal. Diseases included in the best subset and for which identified associations have not been previously reported are shown in bold; novel signals within known risk loci are indicated by “*”