Variant report
| Variant | rs17319860 |
|---|---|
| Chromosome Location | chr4:160647109-160647110 |
| 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:6)
| rs_ID | r2[population] |
|---|---|
| rs10015117 | 0.86[EUR][1000 genomes] |
| rs12108371 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17320556 | 0.84[AMR][1000 genomes] |
| rs2348620 | 1.00[ASN][1000 genomes] |
| rs28493940 | 1.00[ASN][1000 genomes] |
| rs61217796 | 1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1015469 | chr4:160389277-160841619 | Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 2 | nsv537316 | chr4:160389277-160841619 | Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 3 | nsv595813 | chr4:160574450-160665365 | Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer | Chromatin interactive regionlncRNA | n/a | inside rSNPs | diseases |
| 4 | nsv968019 | chr4:160646974-160653132 | Weak transcription Enhancers | n/a | n/a | inside rSNPs | diseases |
mRNA abundance (count:7)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17319860 | LAPTM5 | trans | brain | seeQTL |
| rs17319860 | TSPO | trans | brain | seeQTL |
| rs17319860 | CYBA | trans | brain | seeQTL |
| rs17319860 | LY86 | trans | brain | seeQTL |
| rs17319860 | VAMP8 | trans | brain | seeQTL |
| rs17319860 | C3 | trans | brain | seeQTL |
| rs17319860 | PDPN | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:160644800-160648000 | Weak transcription | Pancreas | Pancrea |
