Variant report
| Variant | rs17654962 |
|---|---|
| Chromosome Location | chr12:62428385-62428386 |
| 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] |
|---|---|
| rs10506433 | 1.00[CEU][hapmap] |
| rs10506435 | 1.00[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes] |
| rs11836835 | 1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs11837618 | 1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs12313846 | 0.86[CEU][hapmap] |
| rs17125704 | 1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs17125724 | 1.00[CEU][hapmap] |
| rs17654475 | 0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs17654643 | 1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs17654661 | 1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs17654807 | 1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs17656359 | 0.86[CEU][hapmap] |
| rs17656662 | 0.86[CEU][hapmap] |
| rs17706308 | 1.00[CEU][hapmap] |
| rs17713184 | 0.86[CEU][hapmap] |
| rs3892748 | 1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs56111414 | 0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs73122033 | 0.87[EUR][1000 genomes] |
| rs73122055 | 0.96[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs9669548 | 1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[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 | nsv1039741 | chr12:62046850-62491052 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 2 | nsv832435 | chr12:62407000-62601835 | Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17654962 | TSPAN31 | cis | parietal | SCAN |
| rs17654962 | MIP | cis | parietal | SCAN |
| rs17654962 | KIF5A | cis | parietal | SCAN |
| rs17654962 | BAZ2A | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:62422600-62429000 | Weak transcription | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
