Variant report
| Variant | rs6023477 |
|---|---|
| Chromosome Location | chr20:53286101-53286102 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:6)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:6 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr19:38993199..38994007-chr20:53285667..53286532,2 | MCF-7 | breast: | |
| 2 | chr20:53284416..53286265-chr3:64518639..64520757,22 | MCF-7 | breast: | |
| 3 | chr20:53285820..53286522-chr3:64519471..64520002,2 | MCF-7 | breast: | |
| 4 | chr20:53265522..53267786-chr20:53285191..53286958,2 | MCF-7 | breast: | |
| 5 | chr20:52840058..52843007-chr20:53284448..53286480,2 | MCF-7 | breast: | |
| 6 | chr15:52857884..52859774-chr20:53285881..53288351,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000163638 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs1012643 | 0.81[AMR][1000 genomes] |
| rs1474763 | 0.92[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs1997834 | 0.82[AMR][1000 genomes] |
| rs2870340 | 0.86[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs2904389 | 0.86[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs6014112 | 0.85[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs6023474 | 0.86[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs6023475 | 0.86[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs6064102 | 0.86[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs6068935 | 0.84[AMR][1000 genomes] |
| rs6127251 | 0.84[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 | 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 |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:53285600-53290000 | Weak transcription | iPS-18 Cell Line | embryonic stem cell |
