SNP Report
Basic Info
| Name | rs1800629 dbSNP Ensembl | ||
|---|---|---|---|
| Location | 6:31575254 - 31575254(+) | ||
| Variant Seq | A | ||
| Ancestral Allele | G | ||
| Ref Seq | G | ||
| Minor Allele Frequence | 0.0902556 | ||
| Annotation | downstream_gene_variant; upstream_gene_variant | ||
| Variant Effect | downstream_gene_variant(ENST00000471842, ENST00000489638, ENST00000418386, ENST00000454783); upstream_gene_variant(ENST00000449264) | ||
| SIFT Annotation | tolerated | ||
| SIFT Variant Effect | tolerated(ENST00000454783, ENST00000418386) | ||
| PolyPhen Annotation | benign | ||
| PolyPhen Variant Effect | benign(ENST00000454783, ENST00000418386) | ||
| rSNP? | Yes Link in rVarBase | ||
| Related Regulatory Elements | TF binding region;Chromatin interactive region | ||
| Chromatin State | Enhancers;Weak transcription;Flanking Active TSS;Bivalent/Poised TSS;Active TSS;Bivalent Enhancer | ||
| No. of Marker's Association Results | 1 (Positive: 1; Negative: 0; Trend: 0) | ||
| Source | Literature | ||
SNP related association results
| Reference | Phenotype | Statistical Values | Author Comments | Marker's Category |
|---|---|---|---|---|
| Bruenig, D.,2017(a) | CAPS score | ANOVA: F(2,280)=3.314, P-value=0.038. Post-hoc comparation: ...... ANOVA: F(2,280)=3.314, P-value=0.038. Post-hoc comparation: AA/AG vs GG: P-value=0.045. More... | The GG genotype showing significantly higher CAPS scores tha...... The GG genotype showing significantly higher CAPS scores than the pooled AA/AG genotype. More... | Significant |
SNP related genes (count: 4)
| Approved Symbol | Approved Name | Location | No. of Association Results (Positive/Negative/Trend)  |
|---|---|---|---|
| CLIC1 | chloride intracellular channel 1 | 6p21.3 | rSNP target |
| LTA | lymphotoxin alpha | 6p21.3 | Mapped by Literature SNP |
| SNORA38 | small nucleolar RNA, H/ACA box 38 | 6p21.33 | rSNP target |
| TNF | tumor necrosis factor | 6p21.3 | 1(1/0/0) |
SNPs in LD with rs1800629 (count: 4)
Literature-origin SNPs (count: 0)
LD-proxies (count: 4)
SNP related eQTL (count: 1)