Variant report
| Variant | rs2731071 |
|---|---|
| Chromosome Location | chr12:48917007-48917008 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:48917007..48919445-chr12:48952290..48954111,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000198678 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:32)
| rs_ID | r2[population] |
|---|---|
| rs10783256 | 1.00[CEU][hapmap];0.81[EUR][1000 genomes] |
| rs10875804 | 1.00[CEU][hapmap] |
| rs11168547 | 0.82[CEU][hapmap] |
| rs11168576 | 1.00[CEU][hapmap] |
| rs11168629 | 1.00[CEU][hapmap] |
| rs11168630 | 1.00[CEU][hapmap] |
| rs11168631 | 1.00[CEU][hapmap] |
| rs11168634 | 1.00[CEU][hapmap] |
| rs11168635 | 1.00[CEU][hapmap] |
| rs11168636 | 1.00[CEU][hapmap] |
| rs11168638 | 1.00[CEU][hapmap];0.84[TSI][hapmap] |
| rs11168639 | 1.00[CEU][hapmap];0.84[TSI][hapmap] |
| rs11168640 | 0.85[CEU][hapmap] |
| rs12230448 | 1.00[CEU][hapmap];0.84[TSI][hapmap] |
| rs12230471 | 1.00[CEU][hapmap] |
| rs17237094 | 1.00[CEU][hapmap] |
| rs17237198 | 1.00[CEU][hapmap];0.84[TSI][hapmap] |
| rs17834022 | 1.00[CEU][hapmap] |
| rs2251773 | 0.81[EUR][1000 genomes] |
| rs2468942 | 1.00[CEU][hapmap] |
| rs2705123 | 1.00[CEU][hapmap];0.84[EUR][1000 genomes] |
| rs2705126 | 1.00[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes] |
| rs2705133 | 1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes] |
| rs2705158 | 0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2705159 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2705161 | 1.00[CEU][hapmap];1.00[YRI][hapmap] |
| rs2731069 | 0.85[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs2731073 | 1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes] |
| rs2731101 | 1.00[CEU][hapmap];0.96[EUR][1000 genomes] |
| rs57022528 | 0.83[ASN][1000 genomes] |
| rs61227501 | 0.83[ASN][1000 genomes] |
| rs6580674 | 0.81[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 | nsv427911 | chr12:48670336-48979396 | Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 35 gene(s) | inside rSNPs | diseases |
| 2 | esv1803653 | chr12:48905575-48923774 | Weak transcription Active TSS ZNF genes & repeats Enhancers | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2731071 | AMIGO2 | cis | parietal | SCAN |
| rs2731071 | C12orf54 | cis | cerebellum | SCAN |
| rs2731071 | ANP32D | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
