Variant report
| Variant | rs6023090 |
|---|---|
| Chromosome Location | chr20:52905173-52905174 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:7)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:7 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52887148..52889148-chr20:52903005..52905781,2 | MCF-7 | breast: | |
| 2 | chr20:52903809..52908618-chr20:52965034..52968390,4 | MCF-7 | breast: | |
| 3 | chr20:52864152..52866358-chr20:52903811..52906264,2 | MCF-7 | breast: | |
| 4 | chr20:52883328..52886194-chr20:52903780..52906080,2 | MCF-7 | breast: | |
| 5 | chr20:52769773..52772486-chr20:52904523..52906497,2 | MCF-7 | breast: | |
| 6 | chr20:52837175..52839951-chr20:52903324..52905854,2 | MCF-7 | breast: | |
| 7 | chr19:35738580..35741475-chr20:52904507..52907195,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000105699 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs1293129 | 0.82[EUR][1000 genomes] |
| rs1293131 | 0.82[EUR][1000 genomes] |
| rs4535116 | 0.88[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs6013962 | 0.95[EUR][1000 genomes] |
| rs6023094 | 0.93[EUR][1000 genomes] |
| rs6023100 | 0.85[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs6097892 | 0.96[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs6097894 | 0.88[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs6127164 | 0.96[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs73914345 | 0.83[AMR][1000 genomes];0.82[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 | nsv962638 | chr20:52883415-52917517 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS | Chromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
