Variant report
| Variant | rs4505105 |
|---|---|
| Chromosome Location | chr12:58470456-58470457 |
| allele | A/C |
| 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 | chr12:58469881..58471988-chr12:58473422..58476197,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs1124448 | 1.00[EUR][1000 genomes] |
| rs17491039 | 1.00[EUR][1000 genomes] |
| rs17491749 | 1.00[EUR][1000 genomes] |
| rs17491966 | 1.00[EUR][1000 genomes] |
| rs17492213 | 1.00[EUR][1000 genomes] |
| rs17569631 | 1.00[EUR][1000 genomes] |
| rs17576604 | 1.00[EUR][1000 genomes] |
| rs17577748 | 0.97[EUR][1000 genomes] |
| rs17578745 | 0.97[EUR][1000 genomes] |
| rs1848130 | 1.00[EUR][1000 genomes] |
| rs1857942 | 1.00[EUR][1000 genomes] |
| rs2659663 | 1.00[EUR][1000 genomes] |
| rs2720174 | 1.00[EUR][1000 genomes] |
| rs2720175 | 1.00[EUR][1000 genomes] |
| rs2720177 | 1.00[EUR][1000 genomes] |
| rs4760176 | 0.94[EUR][1000 genomes] |
| rs73339741 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4505105 | XRCC6BP1 | cis | multi-tissue | Pritchard |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:58466200-58473600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr12:58469800-58472000 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |
