Variant report
| Variant | rs4809962 |
|---|---|
| Chromosome Location | chr20:52931148-52931149 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:8)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:8 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52836744..52838613-chr20:52929896..52931739,2 | MCF-7 | breast: | |
| 2 | chr20:52925826..52928871-chr20:52929162..52931995,4 | MCF-7 | breast: | |
| 3 | chr20:52823610..52826517-chr20:52930381..52934247,3 | MCF-7 | breast: | |
| 4 | chr20:52922776..52924284-chr20:52931074..52933006,2 | MCF-7 | breast: | |
| 5 | chr20:52898596..52901613-chr20:52930745..52932671,3 | MCF-7 | breast: | |
| 6 | chr20:52823879..52827026-chr20:52929276..52932008,3 | MCF-7 | breast: | |
| 7 | chr17:59492385..59494445-chr20:52930380..52933375,2 | MCF-7 | breast: | |
| 8 | chr20:52746471..52748529-chr20:52930718..52933120,2 | 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:1)
| rs_ID | r2[population] |
|---|---|
| rs1891647 | 0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][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 | 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 |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4809962 | C20orf107 | cis | cerebellum | SCAN |
| rs4809962 | C20orf106 | cis | cerebellum | SCAN |
| rs4809962 | AURKA | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
