Variant report
| Variant | rs60780716 |
|---|---|
| Chromosome Location | chr20:53077519-53077520 |
| allele | C/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 | chr20:52823643..52826054-chr20:53076802..53080484,4 | MCF-7 | breast: | |
| 2 | chr20:53075726..53077590-chr20:53115227..53118225,2 | MCF-7 | breast: | |
| 3 | chr17:79700376..79701322-chr20:53077179..53077836,2 | MCF-7 | breast: | |
| 4 | chr20:52835335..52837595-chr20:53075898..53078098,2 | MCF-7 | breast: | |
| 5 | chr20:52884063..52885700-chr20:53076206..53077738,2 | MCF-7 | breast: | |
| 6 | chr20:53065913..53067901-chr20:53077459..53079852,2 | MCF-7 | breast: | |
| 7 | chr20:53076124..53079561-chr20:53086768..53089276,3 | 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:28)
| rs_ID | r2[population] |
|---|---|
| rs16999643 | 0.83[EUR][1000 genomes] |
| rs17317237 | 0.80[AMR][1000 genomes] |
| rs55665963 | 0.94[EUR][1000 genomes] |
| rs55957910 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs56302497 | 0.87[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs58143732 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs6014019 | 0.83[EUR][1000 genomes] |
| rs6014020 | 0.84[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6023248 | 0.89[AMR][1000 genomes] |
| rs6023251 | 0.83[EUR][1000 genomes] |
| rs6023253 | 0.83[EUR][1000 genomes] |
| rs6023254 | 0.82[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6023258 | 0.84[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6091886 | 0.93[EUR][1000 genomes] |
| rs6097987 | 0.83[EUR][1000 genomes] |
| rs6097988 | 0.84[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6097998 | 0.93[EUR][1000 genomes] |
| rs6097999 | 0.93[EUR][1000 genomes] |
| rs68091706 | 0.89[AFR][1000 genomes] |
| rs7264053 | 0.83[EUR][1000 genomes] |
| rs7264143 | 0.84[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs7271481 | 0.93[EUR][1000 genomes] |
| rs7271579 | 0.93[EUR][1000 genomes] |
| rs73141254 | 0.94[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs73141258 | 0.94[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs73145271 | 0.83[AMR][1000 genomes] |
| rs73145273 | 0.80[AMR][1000 genomes] |
| rs73145277 | 0.80[AMR][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 | 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 |
| 3 | 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 | chr20:53075000-53084000 | Weak transcription | Skeletal Muscle Female | skeletal muscle |
