Variant report
| Variant | rs56894192 |
|---|---|
| Chromosome Location | chr20:52864253-52864254 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:10)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:10 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52823769..52826753-chr20:52862832..52866442,3 | MCF-7 | breast: | |
| 2 | chr20:52854512..52856527-chr20:52861978..52864576,3 | MCF-7 | breast: | |
| 3 | chr20:52863453..52865968-chr20:52924698..52926232,2 | MCF-7 | breast: | |
| 4 | chr20:52834806..52836428-chr20:52863803..52865518,2 | MCF-7 | breast: | |
| 5 | chr20:52862270..52864864-chr20:52907686..52911430,3 | MCF-7 | breast: | |
| 6 | chr20:52846307..52849581-chr20:52862205..52864323,3 | MCF-7 | breast: | |
| 7 | chr20:52861957..52864454-chr20:52866467..52868333,2 | MCF-7 | breast: | |
| 8 | chr20:52862806..52864902-chr6:27860738..27862382,2 | MCF-7 | breast: | |
| 9 | chr20:52864152..52866358-chr20:52903811..52906264,2 | MCF-7 | breast: | |
| 10 | chr20:52861825..52864272-chr20:52956863..52959337,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000101132 | Chromatin interaction |
| ENSG00000196331 | Chromatin interaction |
| ENSG00000197153 | Chromatin interaction |
| ENSG00000233224 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs1293129 | 0.88[EUR][1000 genomes] |
| rs1293131 | 0.88[EUR][1000 genomes] |
| rs1477727 | 0.85[ASN][1000 genomes] |
| rs17312067 | 0.98[EUR][1000 genomes] |
| rs58311082 | 0.89[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs59112455 | 0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs59763311 | 0.96[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs59783244 | 0.86[EUR][1000 genomes] |
| rs6097873 | 0.95[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs6097877 | 0.93[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs6123370 | 0.85[ASN][1000 genomes] |
| rs6127144 | 0.94[ASN][1000 genomes] |
| rs6127150 | 1.00[ASN][1000 genomes] |
| rs6127151 | 0.95[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs6512949 | 0.85[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs73914309 | 0.98[EUR][1000 genomes] |
| rs73914345 | 0.88[EUR][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 | 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 |
| No data |
Chromatin state (count:0 , 50 per page) page:
| No data |
