Variant report
| Variant | rs549968 |
|---|---|
| Chromosome Location | chr3:23028598-23028599 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:4)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:4 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | MAFK | chr3:23028480-23028832 | HepG2 | liver: | n/a | chr3:23028646-23028663 |
| 2 | MAFF | chr3:23028509-23028812 | HepG2 | liver: | n/a | n/a |
| 3 | MAFK | chr3:23028491-23028771 | IMR90 | lung: | n/a | chr3:23028646-23028663 |
| 4 | MAFK | chr3:23028516-23028837 | HepG2 | liver: | n/a | chr3:23028646-23028663 |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| SALL4P5 | TF binding region |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs506284 | 0.89[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs520582 | 0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs528649 | 0.87[EUR][1000 genomes] |
| rs529219 | 0.92[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs535689 | 0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs537660 | 0.89[EUR][1000 genomes] |
| rs55652823 | 0.81[EUR][1000 genomes] |
| rs601598 | 0.85[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs621200 | 0.89[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs633464 | 0.84[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs711725 | 0.88[EUR][1000 genomes] |
| rs822768 | 0.88[EUR][1000 genomes] |
| rs822775 | 0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs822776 | 0.81[AFR][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 | nsv1014828 | chr3:22554271-23033498 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs549968 | RARB | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:23024800-23029800 | Weak transcription | Fetal Heart | heart |
