Variant report
| Variant | rs11172457 |
|---|---|
| Chromosome Location | chr12:58466617-58466618 |
| 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 | chr12:58460641..58463046-chr12:58464806..58468044,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs10877066 | 0.83[EUR][1000 genomes] |
| rs10877067 | 0.83[EUR][1000 genomes] |
| rs10877068 | 0.87[ASN][1000 genomes] |
| rs11172446 | 0.80[EUR][1000 genomes] |
| rs11615925 | 0.82[EUR][1000 genomes] |
| rs12824706 | 0.83[EUR][1000 genomes] |
| rs1506884 | 0.90[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs1580976 | 0.83[EUR][1000 genomes] |
| rs2002580 | 0.83[EUR][1000 genomes] |
| rs34885501 | 0.83[EUR][1000 genomes] |
| rs4760364 | 0.83[EUR][1000 genomes] |
| rs4760365 | 0.83[EUR][1000 genomes] |
| rs4760366 | 0.83[EUR][1000 genomes] |
| rs66832796 | 0.90[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs7301724 | 0.86[EUR][1000 genomes] |
| rs7959717 | 0.83[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
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| 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 |
mRNA abundance (count:11)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11172457 | XRCC6BP1 | cis | lung | GTEx |
| rs11172457 | XRCC6BP1 | cis | Muscle Skeletal | GTEx |
| rs11172457 | XRCC6BP1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs11172457 | XRCC6BP1 | cis | Esophagus Mucosa | GTEx |
| rs11172457 | XRCC6BP1 | cis | Whole Blood | GTEx |
| rs11172457 | XRCC6BP1 | cis | Heart Left Ventricle | GTEx |
| rs11172457 | XRCC6BP1 | cis | Thyroid | GTEx |
| rs11172457 | XRCC6BP1 | cis | Esophagus Muscularis | GTEx |
| rs11172457 | XRCC6BP1 | cis | Nerve Tibial | GTEx |
| rs11172457 | XRCC6BP1 | cis | Adipose Subcutaneous | GTEx |
| rs11172457 | XRCC6BP1 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:58466200-58473600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
