Variant report
| Variant | rs1033057 |
|---|---|
| Chromosome Location | chr3:161789788-161789789 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs1154807 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs12107164 | 0.84[ASN][1000 genomes] |
| rs1397246 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs1510344 | 0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs1983208 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs41497744 | 0.90[ASN][1000 genomes] |
| rs4856745 | 0.90[ASN][1000 genomes] |
| rs4856747 | 0.90[ASN][1000 genomes] |
| rs56340997 | 0.90[ASN][1000 genomes] |
| rs6809637 | 0.87[ASN][1000 genomes] |
| rs73018723 | 0.90[ASN][1000 genomes] |
| rs73018726 | 0.90[ASN][1000 genomes] |
| rs73024748 | 0.87[ASN][1000 genomes] |
| rs7620145 | 0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs7639999 | 0.87[ASN][1000 genomes] |
| rs962873 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs9826218 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs9850826 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9884026 | 0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs993595 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv533237 | chr3:161019834-161804660 | Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 91 gene(s) | inside rSNPs | diseases |
| 2 | nsv460918 | chr3:161754109-161791399 | Enhancers Weak transcription Active TSS ZNF genes & repeats | n/a | n/a | inside rSNPs | diseases |
| 3 | nsv592143 | chr3:161754109-161791399 | Enhancers Weak transcription Active TSS ZNF genes & repeats | n/a | n/a | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1033057 | SMC4 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:161789400-161793400 | Enhancers | H9 Derived Neuron Cultured Cells | ES cell derived |
