Variant report
| Variant | rs4535116 |
|---|---|
| Chromosome Location | chr20:52914057-52914058 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52908114..52910241-chr20:52912363..52914987,2 | MCF-7 | breast: | |
| 2 | chr20:52912716..52914955-chr20:53070123..53071877,2 | MCF-7 | breast: | |
| 3 | chr20:52824392..52826194-chr20:52913141..52916044,3 | MCF-7 | breast: | |
| 4 | chr20:52911450..52915662-chr20:52921093..52925920,4 | MCF-7 | breast: | |
| 5 | chr20:52912718..52914464-chr20:52993225..52995964,3 | 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:18)
| rs_ID | r2[population] |
|---|---|
| rs1293129 | 1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs1293131 | 1.00[ASN][1000 genomes] |
| rs1477727 | 0.82[ASN][1000 genomes] |
| rs28654312 | 1.00[ASN][1000 genomes] |
| rs6013952 | 1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs6013961 | 0.88[ASN][1000 genomes] |
| rs6013962 | 0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs6023090 | 0.88[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs6023094 | 0.87[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6023100 | 0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6023101 | 0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes] |
| rs6023103 | 0.88[ASN][1000 genomes] |
| rs6097877 | 0.82[ASN][1000 genomes] |
| rs6097892 | 0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6097894 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6123370 | 0.82[ASN][1000 genomes] |
| rs6127164 | 0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73914345 | 1.00[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 | nsv962638 | chr20:52883415-52917517 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS | Chromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:52910000-52915200 | Weak transcription | Foreskin Melanocyte Primary Cells skin01 | Skin |
| 2 | chr20:52911400-52915000 | Weak transcription | Foreskin Melanocyte Primary Cells skin03 | Skin |
