Variant report
| Variant | rs3952742 |
|---|---|
| Chromosome Location | chr2:86605679-86605680 |
| allele | C/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 | chr2:86604394..86606277-chr2:86665879..86668412,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000115548 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs10208989 | 0.85[EUR][1000 genomes] |
| rs1033288 | 0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs1033289 | 0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs11903855 | 0.83[ASN][1000 genomes] |
| rs12714183 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs13420491 | 0.83[EUR][1000 genomes] |
| rs1964087 | 0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs1964088 | 0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs1964089 | 0.80[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs2113608 | 0.90[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs2113609 | 0.90[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs4832281 | 0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs4832283 | 0.83[ASN][1000 genomes] |
| rs6547677 | 0.80[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6547680 | 0.83[ASN][1000 genomes] |
| rs6708398 | 0.83[ASN][1000 genomes] |
| rs6710124 | 0.90[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs6716701 | 0.80[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs6720331 | 0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs7573005 | 0.83[ASN][1000 genomes] |
| rs908789 | 0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3412938 | chr2:86370969-86867936 | Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 77 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3952742 | VPS24 | Cis_1M | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
