Variant report
| Variant | rs2159935 |
|---|---|
| Chromosome Location | chr4:55521017-55521018 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:12)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:12 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | USF2 | chr4:55520980-55521249 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 2 | USF1 | chr4:55520942-55521219 | H1-hESC | embryonic stem cell: | n/a | chr4:55521094-55521105 |
| 3 | USF1 | chr4:55521003-55521183 | HepG2 | liver: | n/a | chr4:55521094-55521105 |
| 4 | USF1 | chr4:55520926-55521287 | K562 | blood: | n/a | chr4:55521094-55521105 |
| 5 | USF1 | chr4:55520999-55521331 | ECC-1 | luminal epithelium: | n/a | chr4:55521094-55521105 |
| 6 | USF1 | chr4:55520928-55521362 | K562 | blood: | n/a | chr4:55521094-55521105 |
| 7 | USF1 | chr4:55520930-55521268 | H1-hESC | embryonic stem cell: | n/a | chr4:55521094-55521105 |
| 8 | MAX | chr4:55520986-55521298 | H1-hESC | embryonic stem cell: | n/a | n/a |
| 9 | USF1 | chr4:55520965-55521190 | SK-N-SH_RA | brain: | n/a | chr4:55521094-55521105 |
| 10 | USF1 | chr4:55520895-55521355 | HCT-116 | colon: | n/a | chr4:55521094-55521105 |
| 11 | USF1 | chr4:55520924-55521224 | SK-N-SH_RA | brain: | n/a | chr4:55521094-55521105 |
| 12 | USF1 | chr4:55520821-55521345 | HCT-116 | colon: | n/a | chr4:55521094-55521105 |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr4:55519656..55521557-chr4:55522615..55525022,3 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| KIT | TF binding region |
| ENSG00000157404 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs12503461 | 0.80[CEU][hapmap] |
| rs13106834 | 0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs2237029 | 1.00[JPT][hapmap] |
| rs2237030 | 0.83[AMR][1000 genomes];0.81[ASN][1000 genomes] |
| rs2237038 | 1.00[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs2855778 | 0.82[ASN][1000 genomes] |
| rs35960771 | 0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs3819386 | 0.82[ASN][1000 genomes] |
| rs3819391 | 0.82[ASN][1000 genomes] |
| rs3819393 | 0.82[ASN][1000 genomes] |
| rs6554195 | 0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs6554198 | 1.00[JPT][hapmap] |
| rs6554199 | 1.00[JPT][hapmap] |
| rs6554200 | 0.82[ASN][1000 genomes] |
| rs723585 | 0.85[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs7656088 | 0.84[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs7684939 | 0.88[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs981959 | 1.00[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs999020 | 1.00[JPT][hapmap];0.82[ASN][1000 genomes] |
| rs999021 | 0.95[JPT][hapmap];0.82[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1008793 | chr4:55060925-55535807 | Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv537098 | chr4:55060925-55535807 | Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv999400 | chr4:55143598-55776995 | Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 9 gene(s) | inside rSNPs | diseases |
| 4 | nsv997430 | chr4:55253397-55529288 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 5 | esv3367952 | chr4:55437113-55724644 | Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 6 gene(s) | inside rSNPs | diseases |
| 6 | nsv1010702 | chr4:55440944-55528450 | Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
