Variant report
| Variant | rs3891849 |
|---|---|
| Chromosome Location | chr10:90155863-90155864 |
| allele | C/T |
| 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] |
|---|---|
| rs10509546 | 0.91[CEU][hapmap] |
| rs10887831 | 0.89[ASW][hapmap] |
| rs11202766 | 0.81[ASW][hapmap] |
| rs1325900 | 0.89[ASW][hapmap] |
| rs1325906 | 0.81[ASW][hapmap] |
| rs1418481 | 0.91[CEU][hapmap] |
| rs1418482 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17111999 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17112121 | 1.00[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs17343157 | 0.91[CEU][hapmap] |
| rs1891431 | 0.80[ASW][hapmap];0.81[MEX][hapmap] |
| rs4933478 | 0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs4933483 | 0.81[ASW][hapmap] |
| rs4934396 | 1.00[CEU][hapmap] |
| rs4934402 | 1.00[CEU][hapmap];0.87[EUR][1000 genomes] |
| rs4934408 | 0.91[CEU][hapmap] |
| rs4934413 | 0.91[CEU][hapmap] |
| rs7076491 | 0.89[ASW][hapmap] |
| rs72820020 | 0.87[EUR][1000 genomes] |
| rs72820031 | 0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][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 | nsv895879 | chr10:90015725-90219298 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer | Chromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 2 | nsv482385 | chr10:90066140-90259751 | Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats | Chromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv948664 | chr10:90076715-90517150 | Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 4 | nsv1054984 | chr10:90122512-90278038 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription | Chromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 5 | nsv1050587 | chr10:90146582-90272627 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats | Chromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 6 | nsv540739 | chr10:90146582-90272627 | Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats | Chromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3891849 | PTEN | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr10:90155200-90156000 | ZNF genes & repeats | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
