Variant report
| Variant | rs679711 |
|---|---|
| Chromosome Location | chr3:109529550-109529551 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-TRAT1-6 | chr3:109529521-109529708 | ENSG00000242029 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs586783 | 0.81[ASN][1000 genomes] |
| rs591350 | 0.81[ASN][1000 genomes] |
| rs601561 | 0.82[ASN][1000 genomes] |
| rs603474 | 0.89[ASN][1000 genomes] |
| rs605795 | 0.85[CHB][hapmap];0.87[JPT][hapmap] |
| rs619279 | 0.85[CHB][hapmap];0.87[JPT][hapmap] |
| rs620464 | 0.90[ASN][1000 genomes] |
| rs640194 | 0.97[ASN][1000 genomes] |
| rs652762 | 0.85[CHB][hapmap];0.80[JPT][hapmap] |
| rs653349 | 0.85[ASN][1000 genomes] |
| rs656615 | 0.90[CHB][hapmap];0.81[JPT][hapmap] |
| rs662417 | 0.82[ASN][1000 genomes] |
| rs686694 | 0.85[CHB][hapmap];0.87[JPT][hapmap] |
| rs687239 | 0.85[CHB][hapmap];0.87[JPT][hapmap] |
| rs687619 | 0.85[CHB][hapmap];0.87[JPT][hapmap] |
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 | nsv1009075 | chr3:109462019-109800029 | Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 2 | nsv591270 | chr3:109462400-109793785 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv1011265 | chr3:109474218-109625143 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS | Chromatin interactive regionlncRNA | n/a | inside rSNPs | diseases |
Variant related diseases (count:1)
| Disease | PMID | Source |
|---|---|---|
| Sleep depth | 23728906 | GWAS catalog |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:109527800-109530600 | Weak transcription | Primary T killer naive cells fromperipheralblood | blood |
