Variant report
| Variant | rs1477739 |
|---|---|
| Chromosome Location | chr20:52916042-52916043 |
| allele | A/C |
| 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:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52824392..52826194-chr20:52913141..52916044,3 | MCF-7 | breast: | |
| 2 | chr20:52915087..52916709-chr20:52940823..52942611,2 | MCF-7 | breast: | |
| 3 | chr20:52887540..52889848-chr20:52915513..52918256,2 | MCF-7 | breast: | |
| 4 | chr20:52901774..52903726-chr20:52915299..52918140,2 | 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:20)
| rs_ID | r2[population] |
|---|---|
| rs16999399 | 1.00[EUR][1000 genomes] |
| rs2219732 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs2616329 | 1.00[EUR][1000 genomes] |
| rs2616331 | 1.00[EUR][1000 genomes] |
| rs2616334 | 1.00[EUR][1000 genomes] |
| rs2616337 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs2797969 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs55972874 | 1.00[EUR][1000 genomes] |
| rs57927391 | 1.00[EUR][1000 genomes] |
| rs6014025 | 1.00[EUR][1000 genomes] |
| rs60215168 | 1.00[EUR][1000 genomes] |
| rs6022993 | 1.00[EUR][1000 genomes] |
| rs6022994 | 1.00[EUR][1000 genomes] |
| rs6023260 | 1.00[EUR][1000 genomes] |
| rs6023271 | 1.00[EUR][1000 genomes] |
| rs6091884 | 1.00[EUR][1000 genomes] |
| rs6097991 | 1.00[EUR][1000 genomes] |
| rs6097995 | 1.00[EUR][1000 genomes] |
| rs61495423 | 1.00[EUR][1000 genomes] |
| rs793039 | 1.00[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 | nsv586224 | chr20:52474850-53279490 | Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 338 gene(s) | inside rSNPs | diseases |
| 2 | nsv834010 | chr20:52759824-52932939 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 119 gene(s) | inside rSNPs | diseases |
| 3 | nsv834011 | chr20:52858341-53086042 | Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS | Chromatin interactive regionlncRNA | 55 gene(s) | inside rSNPs | diseases |
| 4 | nsv962638 | chr20:52883415-52917517 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS | Chromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:52915000-52916200 | Enhancers | Foreskin Melanocyte Primary Cells skin03 | Skin |
