Variant report
| Variant | rs11907588 |
|---|---|
| Chromosome Location | chr20:53290369-53290370 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:53290085..53292614-chr20:53295758..53297521,2 | MCF-7 | breast: | |
| 2 | chr20:52823364..52826013-chr20:53290303..53292148,2 | MCF-7 | breast: | |
| 3 | chr20:53290237..53291789-chr3:64522620..64525418,2 | MCF-7 | breast: | |
| 4 | chr2:47214206..47214770-chr20:53290236..53290902,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000101132 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs11906377 | 0.80[AFR][1000 genomes] |
| rs11907565 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs2426523 | 1.00[AMR][1000 genomes] |
| rs2426527 | 1.00[AMR][1000 genomes] |
| rs2426528 | 1.00[AMR][1000 genomes] |
| rs2426532 | 1.00[AMR][1000 genomes] |
| rs2426533 | 1.00[AMR][1000 genomes] |
| rs2426534 | 1.00[AMR][1000 genomes] |
| rs55924953 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs57213108 | 0.97[AFR][1000 genomes] |
| rs61035069 | 0.97[AFR][1000 genomes] |
| rs7268298 | 1.00[AMR][1000 genomes] |
| rs73913652 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs73913655 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs8116736 | 0.97[AFR][1000 genomes] |
| rs8123380 | 0.97[AFR][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 | nsv1067497 | chr20:53146241-53751820 | Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 66 gene(s) | inside rSNPs | diseases |
| 2 | nsv1064144 | chr20:53175264-53750137 | Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 66 gene(s) | inside rSNPs | diseases |
| 3 | nsv544302 | chr20:53175264-53750137 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 66 gene(s) | inside rSNPs | diseases |
| 4 | nsv1060552 | chr20:53234716-53655115 | Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 54 gene(s) | inside rSNPs | diseases |
| 5 | nsv586283 | chr20:53288595-53311415 | Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS | Chromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
| 6 | esv17576 | chr20:53289505-53294132 | Weak transcription Enhancers | Chromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:53290000-53290400 | Enhancers | iPS-18 Cell Line | embryonic stem cell |
| 2 | chr20:53290200-53290600 | Enhancers | hESC Derived CD56+ Ectoderm Cultured Cells | ES cell derived |
