Variant report
| Variant | rs7306124 |
|---|---|
| Chromosome Location | chr12:58303349-58303350 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:5 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:58301453..58303781-chr12:58303962..58305605,2 | K562 | blood: | |
| 2 | chr12:58301268..58304747-chr12:58305010..58307816,3 | MCF-7 | breast: | |
| 3 | chr12:58237044..58239762-chr12:58301232..58304430,3 | MCF-7 | breast: | |
| 4 | chr12:58301756..58303544-chr12:58307967..58310549,2 | K562 | blood: | |
| 5 | chr12:58290453..58292772-chr12:58301540..58304170,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000175215 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs11172375 | 0.83[EUR][1000 genomes] |
| rs11172378 | 0.84[EUR][1000 genomes] |
| rs1962047 | 0.83[EUR][1000 genomes] |
| rs3751330 | 0.81[ASN][1000 genomes] |
| rs3751331 | 0.83[EUR][1000 genomes] |
| rs4128707 | 0.81[ASN][1000 genomes] |
| rs4237845 | 0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs4553410 | 0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs4628718 | 0.87[EUR][1000 genomes] |
| rs4630335 | 0.87[EUR][1000 genomes] |
| rs61935769 | 0.83[EUR][1000 genomes] |
| rs6581157 | 0.83[EUR][1000 genomes] |
| rs6650217 | 0.80[AMR][1000 genomes];0.81[ASN][1000 genomes] |
| rs6650218 | 0.81[ASN][1000 genomes] |
| rs6650219 | 0.81[ASN][1000 genomes] |
| rs7954591 | 0.80[AMR][1000 genomes];0.82[ASN][1000 genomes] |
| rs7954957 | 0.82[AMR][1000 genomes];0.82[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 |
|---|---|---|---|---|
| rs7306124 | XRCC6BP1 | cis | Artery Tibial | GTEx |
| rs7306124 | XRCC6BP1 | cis | Stomach | GTEx |
| rs7306124 | XRCC6BP1 | cis | Esophagus Mucosa | GTEx |
| rs7306124 | XRCC6BP1 | cis | Muscle Skeletal | GTEx |
| rs7306124 | XRCC6BP1 | cis | Whole Blood | GTEx |
| rs7306124 | XRCC6BP1 | cis | Thyroid | GTEx |
| rs7306124 | XRCC6BP1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs7306124 | XRCC6BP1 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs7306124 | XRCC6BP1 | cis | Esophagus Muscularis | GTEx |
| rs7306124 | XRCC6BP1 | cis | Heart Left Ventricle | GTEx |
| rs7306124 | XRCC6BP1 | cis | lung | GTEx |
| rs7306124 | XRCC6BP1 | cis | Adipose Subcutaneous | GTEx |
| rs7306124 | XRCC6BP1 | cis | Nerve Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:58302800-58303400 | Bivalent Enhancer | H9 Derived Neuron Cultured Cells | ES cell derived |
| 2 | chr12:58303000-58303400 | Enhancers | Fetal Thymus | thymus |
