Variant report
| Variant | rs12486879 |
|---|---|
| Chromosome Location | chr3:159805043-159805044 |
| 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 | chr3:159804455..159806862-chr3:159807790..159810359,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs10936188 | 0.84[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs12106808 | 0.91[EUR][1000 genomes] |
| rs12107002 | 0.84[EUR][1000 genomes] |
| rs12107028 | 0.91[EUR][1000 genomes] |
| rs12107046 | 0.93[AFR][1000 genomes];0.94[EUR][1000 genomes] |
| rs12107357 | 0.84[EUR][1000 genomes] |
| rs12107558 | 0.87[AFR][1000 genomes];0.94[EUR][1000 genomes] |
| rs12107783 | 0.93[AFR][1000 genomes];0.94[EUR][1000 genomes] |
| rs12489962 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs12492873 | 0.84[EUR][1000 genomes] |
| rs12496326 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs16831052 | 0.84[EUR][1000 genomes] |
| rs16831059 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs16831062 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs17217088 | 0.96[ASN][1000 genomes] |
| rs17217095 | 0.96[ASN][1000 genomes] |
| rs1818023 | 0.81[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs60235173 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs60906496 | 0.85[EUR][1000 genomes] |
| rs6789027 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs7620652 | 0.84[AFR][1000 genomes];0.81[EUR][1000 genomes] |
| rs7620832 | 0.84[AFR][1000 genomes];0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv829769 | chr3:159606913-159805282 | Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 12 gene(s) | inside rSNPs | diseases |
| 2 | nsv532666 | chr3:159777847-160703202 | Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 271 gene(s) | inside rSNPs | diseases |
| 3 | esv13734 | chr3:159794041-159814966 | Weak transcription Enhancers | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 4 | nsv819439 | chr3:159800647-159815768 | Weak transcription Enhancers | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 5 | esv3438561 | chr3:159800887-159807595 | Weak transcription Enhancers | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 6 | esv3345690 | chr3:159802154-159808833 | Enhancers Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 7 | esv3341529 | chr3:159802235-159806612 | Enhancers Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:159801000-159814600 | Weak transcription | Gastric | stomach |
| 2 | chr3:159802800-159808000 | Weak transcription | Esophagus | oesophagus |
