Variant report
| Variant | rs2025128 |
|---|---|
| Chromosome Location | chr20:53459662-53459663 |
| allele | A/T |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:53419453..53421420-chr20:53458481..53461385,2 | MCF-7 | breast: | |
| 2 | chr20:53455825..53458211-chr20:53458861..53461984,3 | MCF-7 | breast: | |
| 3 | chr20:53458659..53460997-chr21:40686277..40688957,2 | MCF-7 | breast: | |
| 4 | chr20:53456314..53458987-chr20:53459309..53462293,2 | MCF-7 | breast: | |
| 5 | chr20:53458657..53461544-chr20:53468848..53472413,4 | MCF-7 | breast: | |
| 6 | chr20:53458903..53460576-chr20:53530268..53532313,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000255568 | Chromatin interaction |
| ENSG00000238141 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs1512065 | 0.90[EUR][1000 genomes] |
| rs2025129 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs2048504 | 0.88[EUR][1000 genomes] |
| rs2063519 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2063521 | 0.88[AFR][1000 genomes] |
| rs4811538 | 0.89[EUR][1000 genomes] |
| rs6014185 | 0.88[EUR][1000 genomes] |
| rs6023624 | 0.86[EUR][1000 genomes] |
| rs6023625 | 0.86[EUR][1000 genomes] |
| rs6023640 | 0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs6023645 | 0.88[EUR][1000 genomes] |
| rs6023649 | 0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs6064117 | 0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs6098273 | 0.92[ASN][1000 genomes] |
| rs6098274 | 0.92[ASN][1000 genomes] |
| rs6127294 | 0.92[ASN][1000 genomes] |
| rs912507 | 0.87[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:53459600-53460200 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |
