Variant report
| Variant | rs1402964 |
|---|---|
| Chromosome Location | chr3:179802694-179802695 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs10513767 | 0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11922602 | 0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs11926584 | 0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs1522117 | 0.83[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs28815318 | 0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4522765 | 0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55817353 | 0.89[EUR][1000 genomes] |
| rs57110106 | 0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs57938272 | 0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6774709 | 0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6796997 | 0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6806358 | 0.90[AMR][1000 genomes];0.95[EUR][1000 genomes] |
| rs73061327 | 0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73883501 | 0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7618809 | 0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7646858 | 0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9290692 | 1.00[ASN][1000 genomes] |
| rs9809361 | 0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9818637 | 0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9868564 | 0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes] |
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 | nsv534210 | chr3:179666123-179899347 | Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 2 | nsv1000756 | chr3:179672703-179827373 | Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 3 | nsv1012880 | chr3:179772283-179835563 | Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1402964 | LYPD5 | trans | brain | seeQTL |
| rs1402964 | TTC14 | cis | multi-tissue | Pritchard |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:179792400-179809800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
