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Table 1 The 8 splice site SNPs prioritised for further analysis after following the bioinformatic pipeline set out

From: The splice site variant rs11078928 may be associated with a genotype-dependent alteration in expression of GSDMB transcripts

Proxy (i.e. splice site SNP)

GWAS variants in LD with splice site SNPs

P value

Phenotype (risk allele)

PID

r 2

Host gene of splice site SNP

Alleles for splice site SNP

Consequence to transcript

Prediction/location

rs11078928

rs2872507

5 × 10-11

Ulcerative colitis (A)

21297633

1

GSDMB

A > G

Essential Splice Site

Destroys AG of acceptor splice site intron 5: Predicted skip of exon 6 (Alamut)

 

rs2872507

5 × 10-9

Crohn’s disease (A)

18587394

1

    
 

rs9303277

2 × 10-9

Primary biliary cirrhosis (T)

20639880

0.905

    
 

rs2290400

6 × 10-13

Type 1 diabetes (?)

19430480

0.905

    
 

rs7216389

9 × 10-11

(Asthma (T))

17611496

0.905

    

rs2014886

rs703842

5 × 10-11

multiple sclerosis (A)

19525955

0.964

TSFM

C > T

Essential Splice Site

Introduces cryptic donor splice site intron 2: Likely to result in alternative exon inclusion

rs1260326

rs780094

7 × 10-15

C-reactive protein (A)

18439548

0.933

GCKR

T > C

Splice Site

1 bp from GT of splice donor exon 15, alters splice site score

 

rs780093

5 × 10-11

Crohn’s disease (T)

21102463

0.901

    

rs10263341

rs886774

3 × 10-8

Ulcerative colitis (G)

19915572

0.803

DLD

T > C

Splice Site

May interrupt polpyrimidine tract intron 6

rs1322077

rs2301436

1 × 10-12

Crohn’s disease (T)

18587394

0.904

FGFR1OP

T > C

Splice Site

May interrupt polpyrimidine tract intron 5

rs2020854

rs2066808

1 × 10-9

Psoriasis (A)

19169254

1

STAT2

A > G

Splice Site

May introduce cryptic donor site intron 14

rs55719896

rs8049439

2 × 10-9

Inflammatory bowel disease, early onset (G)

19915574

0.965

ATXN2L

G > A

Splice Site

Destroys AG of cryptic acceptor splice site intron 20

 

rs4788084

3 × 10-13

Type 1 diabetes (G)

19430480

0.824

    

rs3764021

rs3764021

5 × 10-8

Type 1 diabetes (G)

17554300

1

CLEC2D

C > T

Splice Site

May introduce cryptic donor splice site exon 2

  1. The table shows the 8 SNPs that lie within splice sites of the genes listed. The index GWAS autoimmune/ inflammatory SNPs that are in LD (r2 < 0.8) with the splice site SNPs are shown, as well as the splice site prediction/location. PID PubMed Accession, LD linkage disequilibrium.