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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.