Variant report
| Variant | rs12906171 |
|---|---|
| Chromosome Location | chr15:79029640-79029641 |
| 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:20)
| rs_ID | r2[population] |
|---|---|
| rs12901331 | 0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1383635 | 0.80[ASN][1000 genomes] |
| rs1904920 | 0.80[ASN][1000 genomes] |
| rs2005263 | 0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs2017295 | 0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes] |
| rs34067845 | 0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs34099810 | 0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs34422348 | 0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs34550457 | 0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs34552906 | 0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs34653907 | 0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs35602248 | 0.93[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs35701817 | 0.84[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs35704045 | 0.81[ASN][1000 genomes] |
| rs35741852 | 0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs58526289 | 0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs62010555 | 0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs62010556 | 0.81[ASN][1000 genomes] |
| rs67775542 | 0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs7169223 | 0.83[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 | nsv917303 | chr15:78491050-79205255 | Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 122 gene(s) | inside rSNPs | diseases |
| 2 | nsv974606 | chr15:78996783-79048337 | Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | nsv904431 | chr15:79006442-79155088 | Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 4 | nsv977797 | chr15:79029383-79031049 | Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS | n/a | n/a | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12906171 | CHRNA3 | cis | Muscle Skeletal | GTEx |
| rs12906171 | RP11-650L12.2 | cis | Muscle Skeletal | GTEx |
| rs12906171 | CHRNA5 | cis | Muscle Skeletal | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr15:79028000-79030400 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
| 2 | chr15:79029600-79029800 | Enhancers | Spleen | Spleen |
