Variant report
| Variant | rs11931812 |
|---|---|
| Chromosome Location | chr4:59844473-59844474 |
| 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 | chr4:59844325-59844485 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000251339 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs10014993 | 0.83[ASN][1000 genomes] |
| rs10434209 | 0.99[ASN][1000 genomes] |
| rs11944208 | 0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs1495726 | 0.99[ASN][1000 genomes] |
| rs17493148 | 0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs28792511 | 0.83[ASN][1000 genomes] |
| rs28896231 | 0.83[ASN][1000 genomes] |
| rs4490528 | 0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4860149 | 0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs62298283 | 0.99[ASN][1000 genomes] |
| rs62301193 | 0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs67500083 | 0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs6822690 | 0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap] |
| rs756216 | 0.89[ASN][1000 genomes] |
| rs7687063 | 0.99[ASN][1000 genomes] |
| rs7687986 | 0.82[CEU][hapmap] |
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 | nsv879031 | chr4:59434110-59915131 | Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 2 | esv3446251 | chr4:59622409-59949840 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 3 | nsv1011113 | chr4:59647956-60263029 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 4 | esv2752957 | chr4:59655302-59923634 | Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 5 | nsv1000048 | chr4:59709475-59889707 | ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS | TF binding regionChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11931812 | CLOCK | cis | parietal | SCAN |
| rs11931812 | TMEM165 | cis | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
