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 |