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Table 1 SNPs with opposite risk profiles in different autoimmune diseases

From: Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

SNP

Gene

Chra

A1b

Annotation

Diseasesc

Ref

     

RA-AS-

 

rs11752919

ZSCAN23

6

C

in small intron

 

[3]

     

T1D/ATD-MS

 
    

Asp527Asn (in CDSN); less than 2.6

RA-AS-

 

rs3130981

CDSN/PSORS1C1

6

A

  

[3]

    

kb from rs1265048

T1D/ATD-MS

 
    

intergenic; 1.2kb upstream of

RA-AS-

 

rs1265048

 

6

C

  

[3]

    

PSORS1C1

T1D/ATD-MS

 
     

RA-AS-

 

rs151719

HLA-DMB

6

G

in small intron

 

[3]

     

T1D/ATD-MS

 
     

ATD-MS/RA-

 

rs10484565

TAP2

6

T

in 3' UTR

 

[3]

     

AS-T1D

 
     

RA-AS-

 

0rs1264303

VARS2

6

G

in 5'UTR

 

[3]

     

T1D/ATD-MS

 
     

RA-AS-

 

rs2076530

BTNL2

6

G

splice site altering/protein truncation

 

[3]

     

T1D/ATD-MS

 
    

intergenic; 0.7 kb downstream

RA-AS-MS/T1D-

 

rs3129953

 

6

T

  

[3]

    

BTNL2

ATD

 
     

RA-AS-

 

rs757262

TRIM40

6

T

Thr183Met

 

[3]

     

T1D/ATD-MS

 
    

intronic; close to alternatively spliced

RA-AS-T1D-

 

rs2517646

TRIM10

6

G

  

[3]

    

exon

ATD/MS

 
     

RA-AS-

 

rs2071286

NOTCH4

6

A

intronic

 

[3]

     

T1D/ATD-MS

 
     

CD/T1D-RA-

 

rs2476601

PTPN22

1

T

Arg620TRP

 

[6, 6064]

     

SLE-GD

 
    

about 1kb downstream the

  

rs3024505

IL10

1

A

 

T1D/CD-UC

[4]

    

transcription end site

  
    

about 1kb downstream the

  

rs917997

IL18RAP

2

T

 

T1D/CD

[4]

    

transcription end site

  

rs9388489

 

6

G

intergenic

CD/T1D

[4]

rs4788084

 

16

T

intergenic

T1D/CD

[4]

     

T1D-ATD-

 

rs1063635

MICA

6

A

Gln274Arg

 

[3]

     

MS/AS

 

rs1634717

 

6

A

intergenic

RA/T1D-ATD-

[3]

     

MS

 
     

RA-AS-MS/T1D-

 

rs204991

GPSM3

6

C

intronic

 

[3]

     

ATD

 

rs2242655

C6orf47

6

C

Lys92Asn

ATD-MS/RA-

[3]

     

AS-T1D

 
     

ATD-MS/RA-

 

rs2299851

MSH5

6

T

Intronic

 

[3]

     

AS-T1D

 
     

AS/RA-T1D-

 

rs2248462

 

6

A

intergenic

 

[3]

     

ATD-MS

 
    

intronic; close to alternatively spliced

RA-AS-

 

rs2844463

BAT3

6

T

  

[3]

    

exon

ATD/T1D-MS

 
     

RA-AS-MS/T1D-

 

rs3135363

 

6

C

intergenic

 

[3]

     

ATD

 
     

RA-AS-MS/T1D-

 

rs4428528

 

6

C

intergenic

 

[3]

     

ATD

 
     

MS/RA-AS-T1D-

 

rs887464

 

6

A

intergenic (upstream PSORS1C3)

 

[3]

     

ATD

 
     

ATD-MS/RA-

 

rs9267954

 

6

T

intergenic

 

[3]

     

AS-T1D

 

rs2201841

IL23R

1

G

intronic

UC/psoriasis

[65, 66]

rs744166

STAT3

17

G

intronic

CD/MS

[67, 68]

  1. a chromosome
  2. b minor allele in CEU
  3. c diseases are shown in order depending on the predisposing/protective effect of the minor allele.