Variant report
| Variant | rs60515738 |
|---|---|
| Chromosome Location | chr2:142899416-142899417 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | EP300 | chr2:142899395-142900677 | SK-N-SH | brain: | n/a | chr2:142900002-142900016 |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:142886506..142889089-chr2:142896828..142901902,6 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000244125 | TF binding region |
| ENSG00000168702 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs11886791 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs11903026 | 0.83[AMR][1000 genomes] |
| rs58439740 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs60109017 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs72998331 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs72998341 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs72998344 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs72998354 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs7564081 | 0.83[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 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 | nsv997274 | chr2:142760393-143599193 | Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 2 | nsv875254 | chr2:142833327-142931146 | Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 3 | nsv1006247 | chr2:142851056-143289465 | Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 4 | nsv875255 | chr2:142894573-142963976 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 5 | nsv875256 | chr2:142894573-142994328 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 6 | nsv875257 | chr2:142894573-143041082 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:142889200-142900800 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
