Variant report
| Variant | rs4666589 |
|---|---|
| Chromosome Location | chr2:183424775-183424776 |
| 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:27)
| rs_ID | r2[population] |
|---|---|
| rs10167605 | 1.00[CHB][hapmap] |
| rs10931017 | 0.91[CEU][hapmap];1.00[CHB][hapmap] |
| rs10931020 | 1.00[CEU][hapmap] |
| rs10931022 | 0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[TSI][hapmap] |
| rs11892516 | 1.00[CHB][hapmap] |
| rs12473783 | 0.84[EUR][1000 genomes] |
| rs12621579 | 0.84[CEU][hapmap];1.00[CHB][hapmap] |
| rs1430156 | 0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1594306 | 0.84[CEU][hapmap];1.00[CHB][hapmap] |
| rs16823616 | 1.00[CHB][hapmap] |
| rs2082135 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[TSI][hapmap] |
| rs2368281 | 0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2368282 | 0.80[EUR][1000 genomes] |
| rs2368300 | 0.91[CEU][hapmap];1.00[CHB][hapmap] |
| rs2368301 | 0.91[CEU][hapmap];1.00[CHB][hapmap] |
| rs2368302 | 0.91[CEU][hapmap];1.00[CHB][hapmap] |
| rs4666845 | 0.84[CEU][hapmap];1.00[CHB][hapmap] |
| rs6433976 | 1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[TSI][hapmap] |
| rs6747766 | 0.84[CEU][hapmap];1.00[CHB][hapmap] |
| rs6758080 | 0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6760317 | 0.90[CEU][hapmap];1.00[CHB][hapmap] |
| rs7570144 | 0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7581455 | 1.00[CHB][hapmap] |
| rs7597921 | 1.00[CHB][hapmap] |
| rs7598587 | 0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs934260 | 1.00[CEU][hapmap];1.00[CHB][hapmap] |
| rs934261 | 1.00[CEU][hapmap];1.00[CHB][hapmap] |
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 | nsv533782 | chr2:183059730-183500040 | Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 2 | nsv1009882 | chr2:183213152-184171519 | Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 35 gene(s) | inside rSNPs | diseases |
| 3 | esv2830429 | chr2:183300759-183545378 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4666589 | PDE1A | cis | Brain Pons | GTEx |
| rs4666589 | PDE1A | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:183423400-183424800 | Enhancers | Muscle Satellite Cultured Cells | -- |
| 2 | chr2:183424000-183424800 | Enhancers | Osteobl | bone |
