Variant report
| Variant | rs55957910 |
|---|---|
| Chromosome Location | chr20:53078959-53078960 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:9)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:9 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:53078251..53081040-chr20:53122129..53124438,2 | MCF-7 | breast: | |
| 2 | chr20:53077777..53080190-chr20:53081758..53084535,2 | K562 | blood: | |
| 3 | chr20:52823643..52826054-chr20:53076802..53080484,4 | MCF-7 | breast: | |
| 4 | chr20:53062423..53064765-chr20:53078870..53080771,2 | MCF-7 | breast: | |
| 5 | chr20:53066739..53069116-chr20:53078549..53080137,4 | MCF-7 | breast: | |
| 6 | chr20:52894243..52896440-chr20:53078562..53080828,2 | MCF-7 | breast: | |
| 7 | chr20:53065913..53067901-chr20:53077459..53079852,2 | MCF-7 | breast: | |
| 8 | chr20:53076124..53079561-chr20:53086768..53089276,3 | MCF-7 | breast: | |
| 9 | chr17:57182328..57184217-chr20:53077721..53079540,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000101132 | Chromatin interaction |
| ENSG00000108395 | Chromatin interaction |
| ENSG00000224738 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs17317237 | 0.80[AMR][1000 genomes] |
| rs55665963 | 0.86[EUR][1000 genomes] |
| rs56302497 | 0.94[AFR][1000 genomes] |
| rs58143732 | 0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6014020 | 0.84[AMR][1000 genomes] |
| rs6023248 | 0.89[AMR][1000 genomes] |
| rs6023254 | 0.82[AMR][1000 genomes] |
| rs6023258 | 0.84[AMR][1000 genomes] |
| rs60780716 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6091886 | 0.85[EUR][1000 genomes] |
| rs6097988 | 0.84[AMR][1000 genomes] |
| rs6097998 | 0.85[EUR][1000 genomes] |
| rs6097999 | 0.85[EUR][1000 genomes] |
| rs68091706 | 0.95[AFR][1000 genomes] |
| rs7264143 | 0.84[AMR][1000 genomes] |
| rs7271481 | 0.85[EUR][1000 genomes] |
| rs7271579 | 0.85[EUR][1000 genomes] |
| rs73141254 | 0.94[AMR][1000 genomes] |
| rs73141258 | 0.94[AMR][1000 genomes];0.83[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:
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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 | 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 |
