Variant report
| Variant | rs4683357 |
|---|---|
| Chromosome Location | chr3:43175207-43175208 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:43146026..43148649-chr3:43173688..43176557,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000144647 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs11718469 | 0.91[EUR][1000 genomes] |
| rs12639294 | 0.89[TSI][hapmap] |
| rs13061707 | 0.91[EUR][1000 genomes] |
| rs13087759 | 0.88[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs13098435 | 0.81[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs1878724 | 0.83[EUR][1000 genomes] |
| rs2372337 | 0.92[EUR][1000 genomes] |
| rs34118369 | 0.91[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs7648947 | 0.85[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][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 | nsv460522 | chr3:42967597-43175207 | Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 2 | nsv590149 | chr3:42967597-43175207 | Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 3 | nsv834672 | chr3:43132722-43306272 | Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4683357 | SLC6A20 | cis | parietal | SCAN |
| rs4683357 | TRAK1 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
