Variant report
| Variant | rs4389758 |
|---|---|
| Chromosome Location | chr6:23645720-23645721 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr6:23645624-23645821 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000219453 | TF binding region |
rSNPs within LD-proxies of this variant (count:6)
| rs_ID | r2[population] |
|---|---|
| rs2224484 | 0.83[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs7745468 | 0.91[ASN][1000 genomes] |
| rs7762475 | 0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs9358642 | 0.84[ASN][1000 genomes] |
| rs9379530 | 0.81[ASN][1000 genomes] |
| rs9393424 | 0.84[EUR][1000 genomes];0.86[ASN][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 | nsv1029930 | chr6:23481989-24289948 | Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv883478 | chr6:23615399-23659465 | Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | n/a |
| 3 | nsv462656 | chr6:23629281-23721032 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | n/a |
| 4 | nsv601125 | chr6:23629281-23721032 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | n/a |
| 5 | nsv1027773 | chr6:23644898-23776497 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4389758 | HIST1H1A | cis | parietal | SCAN |
| rs4389758 | BTN3A1 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
