Variant report
| Variant | rs163953 |
|---|---|
| Chromosome Location | chr5:92289537-92289538 |
| 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:7)
| rs_ID | r2[population] |
|---|---|
| rs1387514 | 0.83[AMR][1000 genomes] |
| rs17283654 | 0.83[AMR][1000 genomes] |
| rs17284205 | 0.83[AMR][1000 genomes] |
| rs186982 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs345922 | 1.00[AMR][1000 genomes] |
| rs345926 | 1.00[ASN][1000 genomes] |
| rs345930 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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 | nsv1015770 | chr5:91911877-92498264 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
| 2 | nsv1022712 | chr5:92191693-92415111 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 3 | nsv1028930 | chr5:92194772-92415111 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:8)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs163953 | EGR2 | trans | brain | seeQTL |
| rs163953 | EGR4 | trans | brain | seeQTL |
| rs163953 | CCL3 | trans | brain | seeQTL |
| rs163953 | FOSB | trans | brain | seeQTL |
| rs163953 | PTGS2 | trans | brain | seeQTL |
| rs163953 | ZNF331 | trans | brain | seeQTL |
| rs163953 | CCL4 | trans | brain | seeQTL |
| rs163953 | FOS | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:92288600-92289800 | ZNF genes & repeats | H1 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
