Variant report
| Variant | rs1112962 |
|---|---|
| Chromosome Location | chr10:28089342-28089343 |
| allele | A/G |
| 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:29)
| rs_ID | r2[population] |
|---|---|
| rs10826347 | 0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs10826348 | 0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs10829311 | 0.93[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes] |
| rs11006695 | 0.93[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs11006701 | 0.85[EUR][1000 genomes] |
| rs11006706 | 0.94[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs11015961 | 0.93[CEU][hapmap] |
| rs11015964 | 0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes] |
| rs11015965 | 0.93[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs11015966 | 0.93[CEU][hapmap];0.84[EUR][1000 genomes] |
| rs12217587 | 0.86[CEU][hapmap];0.91[TSI][hapmap] |
| rs12217663 | 0.80[EUR][1000 genomes] |
| rs12258832 | 0.85[EUR][1000 genomes] |
| rs16928202 | 0.87[CEU][hapmap] |
| rs1907374 | 0.93[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs2246842 | 0.81[GIH][hapmap];0.94[MEX][hapmap] |
| rs2368249 | 0.81[EUR][1000 genomes] |
| rs2368250 | 0.81[EUR][1000 genomes] |
| rs2637291 | 0.90[JPT][hapmap] |
| rs2782343 | 0.85[JPT][hapmap];0.94[MEX][hapmap] |
| rs2815482 | 0.84[JPT][hapmap] |
| rs2815483 | 0.82[JPT][hapmap] |
| rs2815484 | 0.85[JPT][hapmap] |
| rs2815485 | 0.85[JPT][hapmap] |
| rs4417171 | 0.93[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes] |
| rs5024546 | 0.90[GIH][hapmap];0.83[TSI][hapmap] |
| rs72799605 | 0.85[EUR][1000 genomes] |
| rs72799619 | 1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs9651357 | 0.83[ASN][1000 genomes] |
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 | nsv831813 | chr10:28017606-28200651 | Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 2 | nsv917149 | chr10:28018919-28688694 | Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
| 3 | nsv971859 | chr10:28070066-28271252 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1112962 | KIAA1462 | cis | cerebellum | SCAN |
| rs1112962 | ALDH5A1 | trans | lymphoblastoid | seeQTL |
| rs1112962 | MYO3A | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr10:28081800-28096600 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
| 2 | chr10:28088200-28092800 | Weak transcription | Ovary | ovary |
| 3 | chr10:28089000-28089400 | Enhancers | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
