Variant report
| Variant | rs1477731 |
|---|---|
| Chromosome Location | chr20:52925303-52925304 |
| allele | C/T |
| 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 | chr20:52923632..52926364-chr20:52926650..52929482,4 | MCF-7 | breast: | |
| 2 | chr20:52924066..52926760-chr20:56284105..56286787,2 | MCF-7 | breast: | |
| 3 | chr20:52911450..52915662-chr20:52921093..52925920,4 | MCF-7 | breast: | |
| 4 | chr20:52863453..52865968-chr20:52924698..52926232,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000124225 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs10485793 | 0.86[EUR][1000 genomes] |
| rs1382011 | 0.84[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1841863 | 0.90[ASN][1000 genomes] |
| rs1891647 | 0.80[ASN][1000 genomes] |
| rs28555372 | 0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs4811499 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs4811500 | 0.82[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6123369 | 0.81[EUR][1000 genomes] |
| rs6127167 | 0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs62216588 | 0.81[EUR][1000 genomes] |
| rs62216601 | 0.85[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 | 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 |
Chromatin state (count:0 , 50 per page) page:
| No data |
