Variant report
| Variant | rs265560 |
|---|---|
| Chromosome Location | chr12:58487055-58487056 |
| allele | C/T |
| 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:10)
| rs_ID | r2[population] |
|---|---|
| rs1027800 | 0.93[AFR][1000 genomes] |
| rs10877069 | 0.88[ASN][1000 genomes] |
| rs1395511 | 0.93[AFR][1000 genomes] |
| rs1567130 | 0.93[AFR][1000 genomes] |
| rs1995655 | 0.89[ASN][1000 genomes] |
| rs2036451 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2260688 | 0.91[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs2733451 | 1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs7975711 | 0.83[AMR][1000 genomes];0.87[ASN][1000 genomes] |
| rs7976016 | 0.86[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv899124 | chr12:58391839-58883507 | Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | esv3502230 | chr12:58458209-58490226 | Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | esv3502241 | chr12:58458223-58490223 | Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 4 | esv2830232 | chr12:58470456-58498926 | Enhancers Weak transcription Flanking Active TSS Active TSS | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:13)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs265560 | XRCC6BP1 | cis | Heart Left Ventricle | GTEx |
| rs265560 | XRCC6BP1 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs265560 | XRCC6BP1 | cis | Artery Tibial | GTEx |
| rs265560 | XRCC6BP1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs265560 | XRCC6BP1 | cis | Esophagus Mucosa | GTEx |
| rs265560 | XRCC6BP1 | cis | lung | GTEx |
| rs265560 | XRCC6BP1 | cis | Nerve Tibial | GTEx |
| rs265560 | XRCC6BP1 | cis | Adipose Subcutaneous | GTEx |
| rs265560 | XRCC6BP1 | cis | Thyroid | GTEx |
| rs265560 | XRCC6BP1 | cis | Esophagus Muscularis | GTEx |
| rs265560 | XRCC6BP1 | cis | Whole Blood | GTEx |
| rs265560 | XRCC6BP1 | cis | Artery Aorta | GTEx |
| rs265560 | XRCC6BP1 | cis | Muscle Skeletal | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:58485600-58487400 | Weak transcription | Pancreas | Pancrea |
| 2 | chr12:58486800-58487600 | Weak transcription | Skeletal Muscle Female | skeletal muscle |
