Variant report
| Variant | rs62292260 |
|---|---|
| Chromosome Location | chr3:179858534-179858535 |
| 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:28)
| rs_ID | r2[population] |
|---|---|
| rs11709960 | 0.83[ASN][1000 genomes] |
| rs12492526 | 0.85[EUR][1000 genomes] |
| rs12631680 | 0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12631948 | 0.83[ASN][1000 genomes] |
| rs12637429 | 0.83[ASN][1000 genomes] |
| rs1404743 | 0.92[EUR][1000 genomes] |
| rs1404744 | 0.93[ASN][1000 genomes] |
| rs1525277 | 0.81[ASN][1000 genomes] |
| rs1568860 | 0.87[EUR][1000 genomes] |
| rs16831126 | 0.82[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs1830044 | 0.97[ASN][1000 genomes] |
| rs28703130 | 0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs2879654 | 0.83[EUR][1000 genomes] |
| rs4854959 | 0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs58582741 | 0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs59555202 | 0.99[ASN][1000 genomes] |
| rs60057308 | 0.86[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs60202080 | 0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs62290558 | 0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs67979781 | 0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs6803764 | 0.90[ASN][1000 genomes] |
| rs7635210 | 0.96[ASN][1000 genomes] |
| rs7637854 | 0.84[ASN][1000 genomes] |
| rs7649655 | 0.81[ASN][1000 genomes] |
| rs9821124 | 0.81[ASN][1000 genomes] |
| rs9851723 | 0.91[ASN][1000 genomes] |
| rs9857420 | 0.98[ASN][1000 genomes] |
| rs9871928 | 0.96[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 | nsv1012271 | chr3:179806875-180234871 | Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 3 | nsv878040 | chr3:179823887-180128288 | Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:179848600-179859600 | Weak transcription | HMEC | breast |
| 2 | chr3:179853800-179859800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
