Variant report
| Variant | rs2368295 |
|---|---|
| Chromosome Location | chr2:183353338-183353339 |
| allele | C/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 | chr2:183344989..183346517-chr2:183352874..183355064,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:28)
| rs_ID | r2[population] |
|---|---|
| rs1347732 | 1.00[JPT][hapmap] |
| rs1595445 | 1.00[JPT][hapmap] |
| rs1595448 | 1.00[JPT][hapmap] |
| rs1595449 | 1.00[JPT][hapmap] |
| rs1595450 | 1.00[JPT][hapmap] |
| rs16823158 | 1.00[JPT][hapmap] |
| rs16823179 | 1.00[JPT][hapmap] |
| rs16823201 | 1.00[JPT][hapmap] |
| rs16823203 | 1.00[JPT][hapmap] |
| rs16823207 | 1.00[JPT][hapmap] |
| rs16823222 | 1.00[JPT][hapmap] |
| rs16823227 | 1.00[JPT][hapmap] |
| rs16823234 | 1.00[JPT][hapmap] |
| rs16823236 | 1.00[JPT][hapmap] |
| rs16823243 | 1.00[JPT][hapmap] |
| rs2368294 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2448980 | 1.00[JPT][hapmap] |
| rs2577649 | 1.00[JPT][hapmap] |
| rs2577660 | 1.00[JPT][hapmap] |
| rs2623409 | 1.00[JPT][hapmap] |
| rs2623410 | 1.00[JPT][hapmap] |
| rs2623430 | 1.00[JPT][hapmap] |
| rs2623432 | 1.00[JPT][hapmap] |
| rs2623436 | 1.00[JPT][hapmap] |
| rs6747766 | 1.00[JPT][hapmap] |
| rs833120 | 1.00[JPT][hapmap] |
| rs833122 | 1.00[JPT][hapmap] |
| rs833123 | 1.00[JPT][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:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2368295 | PDE1A | cis | parietal | SCAN |
| rs2368295 | CGA | trans | parietal | SCAN |
| rs2368295 | PDE1A | cis | Brain Pons | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:183343200-183353800 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
| 2 | chr2:183347800-183355800 | Weak transcription | H9 Derived Neuron Cultured Cells | ES cell derived |
