Variant report
| Variant | rs9854256 |
|---|---|
| Chromosome Location | chr3:157340576-157340577 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr3:157338004..157341097-chr3:157342767..157346033,3 | K562 | blood: | |
| 2 | chr3:157338817..157342476-chr3:157350629..157354187,3 | K562 | blood: | |
| 3 | chr3:157338817..157341754-chr3:157350629..157353502,2 | K562 | blood: | |
| 4 | chr3:157333608..157336028-chr3:157339790..157343103,3 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs1027083 | 0.87[EUR][1000 genomes] |
| rs11719499 | 1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs11915485 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs11921638 | 0.80[EUR][1000 genomes] |
| rs11924940 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4680387 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4680391 | 0.87[EUR][1000 genomes] |
| rs62278746 | 0.94[EUR][1000 genomes] |
| rs67734933 | 0.94[EUR][1000 genomes] |
| rs951633 | 0.95[EUR][1000 genomes] |
| rs962110 | 0.96[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs9837055 | 0.93[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs9838813 | 0.81[EUR][1000 genomes] |
| rs9850567 | 0.94[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs9854132 | 0.81[EUR][1000 genomes] |
| rs9863208 | 0.85[EUR][1000 genomes] |
| rs9867899 | 0.91[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs9876529 | 0.81[EUR][1000 genomes] |
| rs9876844 | 0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv829767 | chr3:157306411-157490444 | Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 2 | nsv4081 | chr3:157318466-157347655 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 3 | esv2427927 | chr3:157338497-157343574 | Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 4 | esv2762351 | chr3:157338661-157341682 | Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 5 | nsv441845 | chr3:157339388-157341682 | Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
| 6 | esv3369725 | chr3:157339408-157343323 | Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9854256 | VEPH1 | cis | parietal | SCAN |
| rs9854256 | CCNL1 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:157338200-157342400 | Weak transcription | Foreskin Fibroblast Primary Cells skin01 | Skin |
