Variant report
| Variant | rs4670719 |
|---|---|
| Chromosome Location | chr2:37669487-37669488 |
| allele | G/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] |
|---|---|
| rs10181043 | 0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs12476654 | 0.86[AMR][1000 genomes] |
| rs12712533 | 0.93[EUR][1000 genomes] |
| rs12987182 | 0.90[ASN][1000 genomes] |
| rs13014680 | 0.86[ASN][1000 genomes] |
| rs13019075 | 0.85[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs13035644 | 0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes] |
| rs2216116 | 0.85[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs2373002 | 0.84[CHB][hapmap];0.85[JPT][hapmap] |
| rs2373106 | 0.91[ASN][1000 genomes] |
| rs2373107 | 0.91[ASN][1000 genomes] |
| rs34105303 | 0.86[ASN][1000 genomes] |
| rs34652606 | 0.86[ASN][1000 genomes] |
| rs34658454 | 0.86[ASN][1000 genomes] |
| rs4490163 | 0.83[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs4670713 | 0.99[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs62133308 | 0.89[ASN][1000 genomes] |
| rs6544076 | 0.85[AMR][1000 genomes] |
| rs71437580 | 0.87[ASN][1000 genomes] |
| rs7568035 | 0.92[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv833814 | chr2:37643132-37840247 | Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 2 | nsv456374 | chr2:37669487-37868214 | Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv470453 | chr2:37669487-37868214 | Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 4 | nsv581473 | chr2:37669487-37868214 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4670719 | ATL2 | cis | cerebellum | SCAN |
| rs4670719 | FEZ2 | cis | lymphoblastoid | seeQTL |
| rs4670719 | GEMIN6 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:37668200-37669800 | ZNF genes & repeats | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
| 2 | chr2:37669200-37675200 | Weak transcription | IMR90 fetal lung fibroblasts Cell Line | lung |
