Variant report
| Variant | rs6013946 |
|---|---|
| Chromosome Location | chr20:52891470-52891471 |
| allele | C/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 | chr20:52823927..52826251-chr20:52889879..52892276,2 | MCF-7 | breast: | |
| 2 | chr20:52891151..52893259-chr21:33433759..33435627,2 | MCF-7 | breast: | |
| 3 | chr20:52891210..52894147-chr20:52899496..52901678,2 | MCF-7 | breast: | |
| 4 | chr20:52832649..52834532-chr20:52889938..52891832,2 | MCF-7 | breast: | |
| 5 | chr20:52835239..52838782-chr20:52890174..52893182,4 | MCF-7 | breast: | |
| 6 | chr20:52891107..52893591-chr20:52960404..52961944,2 | 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] |
|---|---|
| rs13039589 | 0.81[EUR][1000 genomes] |
| rs13039601 | 0.81[EUR][1000 genomes] |
| rs13042527 | 0.84[EUR][1000 genomes] |
| rs13045683 | 0.84[EUR][1000 genomes] |
| rs1477725 | 0.88[EUR][1000 genomes] |
| rs1477736 | 0.82[EUR][1000 genomes] |
| rs2023531 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs28404865 | 0.90[EUR][1000 genomes] |
| rs28435070 | 0.84[EUR][1000 genomes] |
| rs28526259 | 0.81[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs28676447 | 0.83[EUR][1000 genomes] |
| rs28707344 | 0.84[EUR][1000 genomes] |
| rs28795767 | 0.94[EUR][1000 genomes] |
| rs292129 | 0.92[EUR][1000 genomes] |
| rs6023080 | 0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs6023083 | 0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 |
| 5 | nsv178887 | chr20:52885413-52894836 | Enhancers Weak transcription | Chromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:52890000-52893200 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
