Variant report
| Variant | rs10499882 |
|---|---|
| Chromosome Location | chr7:84504645-84504646 |
| 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:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr7:84504421-84504905 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| HMGN2P11 | TF binding region |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs11761247 | 0.82[CHB][hapmap];0.81[JPT][hapmap] |
| rs11984418 | 0.81[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs12538302 | 0.87[ASN][1000 genomes] |
| rs12673176 | 1.00[YRI][hapmap] |
| rs1919285 | 0.82[ASN][1000 genomes] |
| rs1919287 | 0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes] |
| rs2141416 | 0.82[ASN][1000 genomes] |
| rs2195648 | 0.85[ASN][1000 genomes] |
| rs2286184 | 1.00[GIH][hapmap];0.95[JPT][hapmap] |
| rs34107456 | 0.86[AFR][1000 genomes];0.86[AMR][1000 genomes] |
| rs34516090 | 0.85[ASN][1000 genomes] |
| rs35715078 | 0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs35895941 | 0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs3886737 | 0.84[ASN][1000 genomes] |
| rs62474494 | 0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs6972054 | 0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs7458400 | 0.91[AMR][1000 genomes];0.85[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv529344 | chr7:83714286-84592857 | Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
| 2 | nsv949446 | chr7:84003501-84763823 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 20 gene(s) | inside rSNPs | diseases |
| 3 | esv34238 | chr7:84279023-84591966 | Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
| 4 | nsv831050 | chr7:84355996-84527261 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10499882 | CROT | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr7:84504400-84504800 | ZNF genes & repeats | K562 | blood |
