Variant report
| Variant | rs6023260 |
|---|---|
| Chromosome Location | chr20:53079301-53079302 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:10)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:10 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:53078251..53081040-chr20:53122129..53124438,2 | MCF-7 | breast: | |
| 2 | chr20:53077777..53080190-chr20:53081758..53084535,2 | K562 | blood: | |
| 3 | chr20:52823643..52826054-chr20:53076802..53080484,4 | MCF-7 | breast: | |
| 4 | chr20:53062423..53064765-chr20:53078870..53080771,2 | MCF-7 | breast: | |
| 5 | chr20:53066739..53069116-chr20:53078549..53080137,4 | MCF-7 | breast: | |
| 6 | chr20:52894243..52896440-chr20:53078562..53080828,2 | MCF-7 | breast: | |
| 7 | chr20:53065913..53067901-chr20:53077459..53079852,2 | MCF-7 | breast: | |
| 8 | chr20:53076124..53079561-chr20:53086768..53089276,3 | MCF-7 | breast: | |
| 9 | chr17:57182328..57184217-chr20:53077721..53079540,2 | MCF-7 | breast: | |
| 10 | chr17:57161393..57162806-chr20:53079285..53079935,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000108395 | Chromatin interaction |
| ENSG00000224738 | Chromatin interaction |
| ENSG00000101132 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:23)
| rs_ID | r2[population] |
|---|---|
| rs1477739 | 1.00[EUR][1000 genomes] |
| rs16999399 | 1.00[EUR][1000 genomes] |
| rs16999732 | 1.00[EUR][1000 genomes] |
| rs2219732 | 1.00[EUR][1000 genomes] |
| rs2426520 | 1.00[EUR][1000 genomes] |
| rs2426521 | 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[EUR][1000 genomes] |
| rs2797969 | 1.00[EUR][1000 genomes] |
| rs56977264 | 1.00[EUR][1000 genomes] |
| rs57927391 | 1.00[EUR][1000 genomes] |
| rs6014025 | 0.88[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs60215168 | 1.00[EUR][1000 genomes] |
| rs6023271 | 1.00[EUR][1000 genomes] |
| rs6091884 | 0.83[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs6091909 | 1.00[EUR][1000 genomes] |
| rs6097991 | 1.00[EUR][1000 genomes] |
| rs6097995 | 0.82[ASW][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs61495423 | 1.00[EUR][1000 genomes] |
| rs62214388 | 1.00[EUR][1000 genomes] |
| rs793039 | 1.00[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 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 | 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 |
| 3 | nsv834012 | chr20:52921007-53097177 | Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 43 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:53075000-53084000 | Weak transcription | Skeletal Muscle Female | skeletal muscle |
