Variant report
| Variant | rs10783857 |
|---|---|
| Chromosome Location | chr12:58313144-58313145 |
| allele | A/G |
| 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 | chr12:58313105..58315372-chr12:58334865..58337363,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000166896 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs10431506 | 0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes] |
| rs10747788 | 0.88[AMR][1000 genomes];0.80[ASN][1000 genomes] |
| rs10877039 | 0.84[AMR][1000 genomes];0.80[ASN][1000 genomes] |
| rs10877040 | 0.87[AMR][1000 genomes] |
| rs10877041 | 0.85[AMR][1000 genomes] |
| rs11172388 | 0.86[AMR][1000 genomes] |
| rs11172389 | 0.86[AMR][1000 genomes] |
| rs2372309 | 0.85[AMR][1000 genomes] |
| rs3751325 | 0.85[AMR][1000 genomes] |
| rs4590915 | 0.87[AMR][1000 genomes] |
| rs4760344 | 0.87[AMR][1000 genomes];0.80[ASN][1000 genomes] |
| rs7358584 | 0.84[AMR][1000 genomes] |
| rs9971803 | 0.88[AMR][1000 genomes];0.80[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 | nsv559046 | chr12:58162085-58478598 | Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 261 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:13)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10783857 | XRCC6BP1 | cis | Thyroid | GTEx |
| rs10783857 | XRCC6BP1 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs10783857 | XRCC6BP1 | cis | Whole Blood | GTEx |
| rs10783857 | XRCC6BP1 | cis | Muscle Skeletal | GTEx |
| rs10783857 | XRCC6BP1 | cis | Esophagus Muscularis | GTEx |
| rs10783857 | XRCC6BP1 | cis | Nerve Tibial | GTEx |
| rs10783857 | XRCC6BP1 | cis | Adipose Subcutaneous | GTEx |
| rs10783857 | XRCC6BP1 | cis | lung | GTEx |
| rs10783857 | XRCC6BP1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs10783857 | XRCC6BP1 | cis | Artery Aorta | GTEx |
| rs10783857 | XRCC6BP1 | cis | Artery Tibial | GTEx |
| rs10783857 | XRCC6BP1 | cis | Esophagus Mucosa | GTEx |
| rs10783857 | XRCC6BP1 | cis | Heart Left Ventricle | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:58311200-58313800 | Enhancers | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
| 2 | chr12:58312200-58325800 | Weak transcription | Thymus | Thymus |
