Variant report
| Variant | rs1547161 |
|---|---|
| Chromosome Location | chr13:30552901-30552902 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs10492461 | 1.00[EUR][1000 genomes] |
| rs11839078 | 0.96[EUR][1000 genomes] |
| rs11839379 | 0.96[EUR][1000 genomes] |
| rs11840419 | 0.89[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs11840423 | 0.96[EUR][1000 genomes] |
| rs11841787 | 0.96[EUR][1000 genomes] |
| rs11842198 | 0.96[EUR][1000 genomes] |
| rs11842819 | 0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs17074166 | 1.00[EUR][1000 genomes] |
| rs17074176 | 1.00[EUR][1000 genomes] |
| rs1807336 | 0.96[EUR][1000 genomes] |
| rs4578499 | 0.83[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs496557 | 1.00[EUR][1000 genomes] |
| rs524939 | 0.80[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs525768 | 1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs552465 | 0.80[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs638278 | 0.80[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs729285 | 1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs73159369 | 0.89[EUR][1000 genomes] |
| rs73159387 | 0.86[EUR][1000 genomes] |
| rs73450391 | 1.00[EUR][1000 genomes] |
| rs745251 | 1.00[EUR][1000 genomes] |
| rs745252 | 1.00[EUR][1000 genomes] |
| rs9508611 | 0.86[EUR][1000 genomes] |
| rs9508613 | 0.86[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3520592 | chr13:30243601-30648554 | Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| 2 | esv3520593 | chr13:30243601-30648554 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1547161 | SCGN | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr13:30552600-30553000 | Weak transcription | Foreskin Melanocyte Primary Cells skin03 | Skin |
