Variant report
| Variant | rs12667972 |
|---|---|
| Chromosome Location | chr7:25553702-25553703 |
| 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] |
|---|---|
| rs10230604 | 0.89[ASN][1000 genomes] |
| rs10242326 | 0.90[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs10486459 | 0.89[ASN][1000 genomes] |
| rs12668322 | 0.95[ASN][1000 genomes] |
| rs12668343 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs12672646 | 0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs12673720 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs1393675 | 0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs17151744 | 0.92[ASN][1000 genomes] |
| rs17151747 | 0.93[ASN][1000 genomes] |
| rs17151750 | 0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs17151753 | 0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs17151766 | 0.93[ASN][1000 genomes] |
| rs17151770 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs61238582 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs731007 | 0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes] |
| rs731008 | 0.80[ASN][1000 genomes] |
| rs73275511 | 0.94[ASN][1000 genomes] |
| rs73275554 | 0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs7796244 | 0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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 | nsv606426 | chr7:25254125-25621579 | Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv1016813 | chr7:25405859-26150509 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 108 gene(s) | inside rSNPs | diseases |
| 3 | nsv538803 | chr7:25405859-26150509 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 108 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12667972 | HOXA3 | cis | cerebellum | SCAN |
| rs12667972 | CDCA7L | cis | parietal | SCAN |
| rs12667972 | CDCA7L | cis | cerebellum | SCAN |
| rs12667972 | HOXA9 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:25551400-25559000 | Weak transcription | Primary T cells from cord blood | blood |
| 2 | chr7:25552400-25557400 | Weak transcription | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
