Variant report
| Variant | rs6708398 |
|---|---|
| Chromosome Location | chr2:86631075-86631076 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:86630182..86633982-chr2:86666784..86669925,4 | MCF-7 | breast: | |
| 2 | chr2:86630213..86633133-chr2:86645838..86647616,2 | MCF-7 | breast: | |
| 3 | chr2:86630490..86633465-chr2:86635525..86637778,2 | MCF-7 | breast: | |
| 4 | chr2:86629640..86632102-chr2:86632580..86634181,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000115548 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs1033288 | 1.00[ASN][1000 genomes] |
| rs1033289 | 1.00[ASN][1000 genomes] |
| rs11678201 | 0.85[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs11687162 | 0.87[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs11903855 | 0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12714182 | 0.83[AMR][1000 genomes];0.82[EUR][1000 genomes] |
| rs1964087 | 0.89[ASN][1000 genomes] |
| rs1964088 | 0.96[ASN][1000 genomes] |
| rs2113608 | 0.89[ASN][1000 genomes] |
| rs2113609 | 0.89[ASN][1000 genomes] |
| rs2367238 | 0.99[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs3952742 | 0.83[ASN][1000 genomes] |
| rs4832281 | 0.89[ASN][1000 genomes] |
| rs4832283 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6547680 | 0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6710124 | 0.89[ASN][1000 genomes] |
| rs6713586 | 0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs6720331 | 1.00[ASN][1000 genomes] |
| rs6736462 | 0.85[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs6756146 | 0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs7573005 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs908789 | 1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 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 |
| 2 | nsv532724 | chr2:86622295-87086407 | Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 45 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6708398 | VPS24 | Cis_1M | lymphoblastoid | RTeQTL |
Chromatin state (count:0 , 50 per page) page:
| No data |
