Variant report
| Variant | rs7572690 |
|---|---|
| Chromosome Location | chr2:30605798-30605799 |
| allele | A/G |
| 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 | chr2:30453659..30455818-chr2:30603684..30605946,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000213626 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:25)
| rs_ID | r2[population] |
|---|---|
| rs10514770 | 0.85[EUR][1000 genomes] |
| rs11127273 | 0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1252616 | 0.85[EUR][1000 genomes] |
| rs1252617 | 0.81[EUR][1000 genomes] |
| rs1252618 | 0.84[EUR][1000 genomes] |
| rs12993465 | 0.85[EUR][1000 genomes] |
| rs13000021 | 0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs13012193 | 0.85[EUR][1000 genomes] |
| rs13033921 | 0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2030744 | 0.85[EUR][1000 genomes] |
| rs35909231 | 0.84[EUR][1000 genomes] |
| rs4519571 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs6548012 | 0.94[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs6548013 | 0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7583194 | 0.87[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs7583844 | 0.93[EUR][1000 genomes] |
| rs7593766 | 0.85[EUR][1000 genomes] |
| rs829588 | 0.97[EUR][1000 genomes] |
| rs829590 | 0.85[EUR][1000 genomes] |
| rs829610 | 0.85[CEU][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes] |
| rs829611 | 0.85[CEU][hapmap];0.81[EUR][1000 genomes] |
| rs829612 | 0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes] |
| rs829613 | 0.85[CEU][hapmap];0.82[EUR][1000 genomes] |
| rs829614 | 0.89[CEU][hapmap];0.82[EUR][1000 genomes] |
| rs9917125 | 0.85[EUR][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 | nsv533886 | chr2:30130019-31068764 | ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 32 gene(s) | inside rSNPs | diseases |
| 2 | nsv833648 | chr2:30505882-30696275 | Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
| 3 | nsv873769 | chr2:30585638-30625264 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats | Chromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7572690 | CHCHD3 | trans | cerebellum | SCAN |
| rs7572690 | PREB | cis | parietal | SCAN |
| rs7572690 | DAB2IP | trans | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:30585600-30605800 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
