Variant report
| Variant | rs6091849 |
|---|---|
| Chromosome Location | chr20:52924564-52924565 |
| 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 | chr20:52824550..52826498-chr20:52922860..52925164,2 | MCF-7 | breast: | |
| 2 | chr20:52923632..52926364-chr20:52926650..52929482,4 | MCF-7 | breast: | |
| 3 | chr20:52924066..52926760-chr20:56284105..56286787,2 | MCF-7 | breast: | |
| 4 | chr20:52911450..52915662-chr20:52921093..52925920,4 | MCF-7 | breast: | |
| 5 | chr20:52823568..52826063-chr20:52923324..52925181,2 | MCF-7 | breast: | |
| 6 | chr20:52897965..52899622-chr20:52923358..52924887,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000101132 | Chromatin interaction |
| ENSG00000124225 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs1293137 | 0.82[EUR][1000 genomes] |
| rs1293142 | 0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs1293143 | 0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs1293144 | 0.82[EUR][1000 genomes] |
| rs1343080 | 0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1382010 | 0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1418924 | 0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs1542522 | 0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2870320 | 0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs6013960 | 0.82[EUR][1000 genomes] |
| rs6023101 | 0.83[AFR][1000 genomes] |
| rs6097895 | 0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs6097896 | 0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
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| 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 |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:52924000-52924600 | Enhancers | H9 Cell Line | embryonic stem cell |
