Variant report
| Variant | rs9369860 |
|---|---|
| Chromosome Location | chr6:49098856-49098857 |
| allele | C/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 | chr1:37939002..37941734-chr6:49098087..49100973,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000233621 | Chromatin interaction |
| ENSG00000163874 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:9)
| rs_ID | r2[population] |
|---|---|
| rs10948484 | 0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs2496356 | 0.83[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs2496368 | 0.94[ASN][1000 genomes] |
| rs2516121 | 0.83[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs2516123 | 0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs4510676 | 0.81[JPT][hapmap] |
| rs6938215 | 0.81[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs7776038 | 0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs9367347 | 0.82[EUR][1000 genomes];0.88[ASN][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 | nsv949690 | chr6:48595821-49289855 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 2 | nsv603049 | chr6:48931959-49169337 | Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv885880 | chr6:48975662-49102186 | Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 4 | esv2755862 | chr6:49081541-49298041 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9369860 | CENPQ | cis | Esophagus Muscularis | GTEx |
| rs9369860 | CENPQ | cis | Artery Tibial | GTEx |
| rs9369860 | MUT | cis | Nerve Tibial | GTEx |
| rs9369860 | CENPQ | cis | Adipose Subcutaneous | GTEx |
| rs9369860 | CENPQ | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:49090400-49103600 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
