Variant report
| Variant | rs2168999 |
|---|---|
| Chromosome Location | chr17:15237488-15237489 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:3)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:3 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | SIN3AK20 | chr17:15237465-15238300 | MCF-7 | breast: | n/a | n/a |
| 2 | MAX | chr17:15237474-15238075 | A549 | lung: | n/a | chr17:15237751-15237760 chr17:15237746-15237765 |
| 3 | SIN3AK20 | chr17:15237451-15238251 | MCF-7 | breast: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr17:15177773..15180242-chr17:15236243..15238817,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| TEKT3 | TF binding region |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs1014027 | 0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs11078289 | 0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs1380182 | 0.94[ASN][1000 genomes] |
| rs1380184 | 0.93[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs16951407 | 0.82[ASN][1000 genomes] |
| rs1903112 | 0.86[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs2286516 | 0.91[ASN][1000 genomes] |
| rs7209263 | 0.90[ASN][1000 genomes] |
| rs7213020 | 0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7213079 | 0.88[ASN][1000 genomes] |
| rs7223727 | 0.82[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7224677 | 0.88[ASN][1000 genomes] |
| rs725341 | 0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs8072399 | 0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs9902480 | 0.86[AMR][1000 genomes];0.83[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 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 | nsv1066329 | chr17:14983674-15294071 | Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 22 gene(s) | inside rSNPs | diseases |
| 2 | nsv543212 | chr17:14983674-15294071 | Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 22 gene(s) | inside rSNPs | diseases |
| 3 | nsv492304 | chr17:15043353-15611753 | Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 58 gene(s) | inside rSNPs | diseases |
| 4 | nsv916652 | chr17:15093600-15856310 | Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 73 gene(s) | inside rSNPs | diseases |
| 5 | nsv427990 | chr17:15154329-15434020 | Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 31 gene(s) | inside rSNPs | diseases |
| 6 | nsv907703 | chr17:15199907-15370701 | Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 10 gene(s) | inside rSNPs | diseases |
| 7 | nsv949172 | chr17:15206970-15416808 | Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 14 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr17:15237000-15238000 | Weak transcription | iPS-20b Cell Line | embryonic stem cell |
