Variant report
| Variant | rs4811499 |
|---|---|
| Chromosome Location | chr20:52897596-52897597 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr20:52823411..52826205-chr20:52895497..52899712,3 | MCF-7 | breast: | |
| 2 | chr20:52897327..52899009-chr20:52901309..52903934,2 | K562 | blood: | |
| 3 | chr10:7914281..7916763-chr20:52896829..52898926,2 | MCF-7 | breast: | |
| 4 | chr20:52835609..52839947-chr20:52897046..52901468,5 | 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:12)
| rs_ID | r2[population] |
|---|---|
| rs10485793 | 1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs1382011 | 0.91[GIH][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes] |
| rs1477722 | 0.89[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs1477723 | 0.83[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs1477731 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs28555372 | 0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4811500 | 1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs6097867 | 0.93[CEU][hapmap] |
| rs6123369 | 0.90[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs6127152 | 0.81[JPT][hapmap] |
| rs62216588 | 0.90[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs62216601 | 0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 |
| 4 | nsv962638 | chr20:52883415-52917517 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS | Chromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4811499 | KCNG1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr20:52895400-52899200 | Weak transcription | Fetal Brain Male | brain |
