Variant report
| Variant | rs17671005 |
|---|---|
| Chromosome Location | chr14:55280701-55280702 |
| allele | A/C |
| 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 | chr14:55279684..55281675-chr14:55367538..55369312,2 | MCF-7 | breast: | |
| 2 | chr14:55275299..55276942-chr14:55278821..55281562,2 | MCF-7 | breast: | |
| 3 | chr14:55273057..55275787-chr14:55279144..55281055,2 | K562 | blood: | |
| 4 | chr14:55279326..55281967-chr14:55362988..55365196,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000131979 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs17128008 | 0.83[CEU][hapmap] |
| rs17253584 | 0.85[CEU][hapmap];0.86[AMR][1000 genomes] |
| rs17671485 | 0.85[CEU][hapmap];0.83[AMR][1000 genomes] |
| rs17738863 | 0.85[CEU][hapmap] |
| rs17738966 | 0.83[AMR][1000 genomes] |
| rs17739146 | 0.85[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes] |
| rs2004633 | 0.86[AMR][1000 genomes] |
| rs41298434 | 0.83[AMR][1000 genomes] |
| rs45454691 | 0.86[AMR][1000 genomes] |
| rs7141175 | 1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs7148831 | 0.83[AMR][1000 genomes] |
| rs73278772 | 0.86[AMR][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 | nsv530042 | chr14:55208170-55386966 | Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| 2 | nsv983826 | chr14:55273339-55282030 | Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS | Chromatin interactive region | 4 gene(s) | inside rSNPs | n/a |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17671005 | TBPL2 | cis | parietal | SCAN |
| rs17671005 | PYGL | cis | cerebellum | SCAN |
| rs17671005 | EXOC5 | cis | cerebellum | SCAN |
| rs17671005 | LANCL3 | trans | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr14:55273000-55281400 | Weak transcription | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
