Variant report
| Variant | rs17499829 |
|---|---|
| Chromosome Location | chr4:82297896-82297897 |
| allele | A/C/G/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 | chr4:82296919..82298708-chr4:82299908..82301828,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:26)
| rs_ID | r2[population] |
|---|---|
| rs11723619 | 0.85[ASN][1000 genomes] |
| rs11732408 | 0.86[EUR][1000 genomes] |
| rs1452374 | 0.86[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs1473160 | 0.87[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs17005118 | 0.97[ASN][1000 genomes] |
| rs17427571 | 0.91[CEU][hapmap];0.85[EUR][1000 genomes] |
| rs17499732 | 0.87[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs17499843 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17500149 | 0.86[AMR][1000 genomes];0.84[ASN][1000 genomes] |
| rs2034629 | 0.82[EUR][1000 genomes] |
| rs2058368 | 0.86[EUR][1000 genomes] |
| rs2839753 | 0.96[ASN][1000 genomes] |
| rs34347934 | 0.86[EUR][1000 genomes] |
| rs41501452 | 0.86[EUR][1000 genomes] |
| rs41515854 | 0.86[EUR][1000 genomes] |
| rs62302352 | 0.84[EUR][1000 genomes] |
| rs62303570 | 0.87[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs6812825 | 0.86[EUR][1000 genomes] |
| rs6824784 | 0.86[EUR][1000 genomes] |
| rs725826 | 0.81[ASN][1000 genomes] |
| rs7656390 | 0.85[ASN][1000 genomes] |
| rs7658313 | 0.87[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs7669368 | 0.86[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs7685840 | 0.85[ASN][1000 genomes] |
| rs7696324 | 0.86[EUR][1000 genomes] |
| rs7698361 | 0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][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 | nsv999729 | chr4:81802554-82627820 | Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 7 gene(s) | inside rSNPs | diseases |
| 2 | nsv537156 | chr4:81802554-82627820 | Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 7 gene(s) | inside rSNPs | diseases |
| 3 | nsv829985 | chr4:82199328-82353656 | Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17499829 | PRKG2 | cis | parietal | SCAN |
| rs17499829 | PAQR3 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:82297200-82303000 | Enhancers | Fetal Intestine Small | intestine |
| 2 | chr4:82297800-82298000 | Enhancers | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
| 3 | chr4:82297800-82302800 | Enhancers | Fetal Intestine Large | intestine |
