Variant report
| Variant | rs6123368 |
|---|---|
| Chromosome Location | chr20:52862820-52862821 |
| 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 | chr20:52854512..52856527-chr20:52861978..52864576,3 | MCF-7 | breast: | |
| 2 | chr20:52862270..52864864-chr20:52907686..52911430,3 | MCF-7 | breast: | |
| 3 | chr20:52846307..52849581-chr20:52862205..52864323,3 | MCF-7 | breast: | |
| 4 | chr20:52824622..52827357-chr20:52861656..52863680,2 | MCF-7 | breast: | |
| 5 | chr20:52861957..52864454-chr20:52866467..52868333,2 | MCF-7 | breast: | |
| 6 | chr20:52862806..52864902-chr6:27860738..27862382,2 | MCF-7 | breast: | |
| 7 | chr20:52848398..52850983-chr20:52861832..52863422,2 | MCF-7 | breast: | |
| 8 | chr20:52861825..52864272-chr20:52956863..52959337,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000196331 | Chromatin interaction |
| ENSG00000101132 | Chromatin interaction |
| ENSG00000233224 | Chromatin interaction |
| ENSG00000197153 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs2585417 | 0.85[ASN][1000 genomes] |
| rs2585418 | 0.85[ASN][1000 genomes] |
| rs292113 | 0.81[ASN][1000 genomes] |
| rs292118 | 0.92[ASN][1000 genomes] |
| rs292119 | 0.92[ASN][1000 genomes] |
| rs3479 | 0.87[ASN][1000 genomes] |
| rs368933 | 0.99[ASN][1000 genomes] |
| rs391235 | 0.84[ASN][1000 genomes] |
| rs422257 | 0.84[ASN][1000 genomes] |
| rs441506 | 0.91[ASN][1000 genomes] |
| rs6013938 | 0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs6091837 | 0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][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 | 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 |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
