Variant report
| Variant | rs4553790 |
|---|---|
| Chromosome Location | chr2:11984089-11984090 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:8)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:8 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | CEBPB | chr2:11983759-11984102 | K562 | blood: | n/a | chr2:11983926-11983937 |
| 2 | CEBPB | chr2:11983766-11984111 | IMR90 | lung: | n/a | chr2:11983926-11983937 |
| 3 | FOXA2 | chr2:11983776-11984099 | HepG2 | liver: | n/a | n/a |
| 4 | CEBPB | chr2:11983749-11984129 | HepG2 | liver: | n/a | chr2:11983926-11983937 |
| 5 | FOXA1 | chr2:11983755-11984093 | HepG2 | liver: | n/a | n/a |
| 6 | CEBPB | chr2:11983757-11984115 | A549 | lung: | n/a | chr2:11983926-11983937 |
| 7 | CEBPB | chr2:11983766-11984110 | HepG2 | liver: | n/a | chr2:11983926-11983937 |
| 8 | CEBPB | chr2:11983825-11984090 | Hela-S3 | cervix: | n/a | chr2:11983926-11983937 |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000224184 | TF binding region |
rSNPs within LD-proxies of this variant (count:5)
| rs_ID | r2[population] |
|---|---|
| rs1012566 | 0.95[ASN][1000 genomes] |
| rs1370548 | 0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs2118403 | 0.83[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs3749071 | 0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs4668741 | 0.83[EUR][1000 genomes];0.86[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1010506 | chr2:11430965-12057286 | Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 88 gene(s) | inside rSNPs | diseases |
| 2 | nsv535585 | chr2:11430965-12057286 | Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 88 gene(s) | inside rSNPs | diseases |
| 3 | nsv1003899 | chr2:11789374-12248081 | Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 26 gene(s) | inside rSNPs | diseases |
| 4 | nsv833403 | chr2:11944552-12125634 | Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 10 gene(s) | inside rSNPs | diseases |
| 5 | nsv508710 | chr2:11982971-12028555 | Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:11978800-11987800 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
