Variant report
| Variant | rs9821488 |
|---|---|
| Chromosome Location | chr3:98087516-98087517 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:98086429..98088242-chr3:98311921..98314388,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000080819 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:30)
| rs_ID | r2[population] |
|---|---|
| rs11717178 | 0.81[ASN][1000 genomes] |
| rs1603602 | 0.81[ASN][1000 genomes] |
| rs1603603 | 0.81[ASN][1000 genomes] |
| rs34541751 | 0.81[ASN][1000 genomes] |
| rs34690476 | 0.81[ASN][1000 genomes] |
| rs34931219 | 0.81[ASN][1000 genomes] |
| rs35288084 | 0.81[ASN][1000 genomes] |
| rs35831406 | 0.81[ASN][1000 genomes] |
| rs58332056 | 0.93[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs62268863 | 0.81[ASN][1000 genomes] |
| rs62268864 | 0.81[ASN][1000 genomes] |
| rs6764487 | 0.81[ASN][1000 genomes] |
| rs6765125 | 0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs6772436 | 0.81[ASN][1000 genomes] |
| rs6775143 | 0.81[ASN][1000 genomes] |
| rs6809869 | 0.81[ASN][1000 genomes] |
| rs6810193 | 0.81[ASN][1000 genomes] |
| rs7609934 | 0.81[ASN][1000 genomes] |
| rs7610289 | 0.81[ASN][1000 genomes] |
| rs7610802 | 0.81[ASN][1000 genomes] |
| rs7621918 | 0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes] |
| rs7642283 | 0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7643309 | 0.81[ASN][1000 genomes] |
| rs9814187 | 0.81[ASN][1000 genomes] |
| rs9822335 | 0.81[ASN][1000 genomes] |
| rs9823733 | 0.81[ASN][1000 genomes] |
| rs9829822 | 0.81[ASN][1000 genomes] |
| rs9831068 | 0.81[ASN][1000 genomes] |
| rs9833818 | 0.81[ASN][1000 genomes] |
| rs9871143 | 0.85[CEU][hapmap];1.00[CHB][hapmap] |
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 | nsv1004820 | chr3:97852875-98169488 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 19 gene(s) | inside rSNPs | diseases |
| 2 | nsv1000834 | chr3:97859880-98095473 | Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 3 | nsv1009918 | chr3:97946030-98155450 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9821488 | ARL6 | cis | parietal | SCAN |
| rs9821488 | OR5K2 | cis | cerebellum | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
