Variant report
| Variant | rs6768356 |
|---|---|
| Chromosome Location | chr3:42494635-42494636 |
| allele | G/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] |
|---|---|
| rs12631333 | 0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs12633727 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1354992 | 0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1354993 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs1508207 | 0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1508208 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1508210 | 0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs17306848 | 1.00[CEU][hapmap];0.88[JPT][hapmap] |
| rs442075 | 0.95[CEU][hapmap] |
| rs56301624 | 0.85[EUR][1000 genomes] |
| rs57117562 | 0.86[EUR][1000 genomes] |
| rs59200964 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs59779882 | 0.86[EUR][1000 genomes] |
| rs600792 | 0.95[CEU][hapmap] |
| rs601204 | 0.95[CEU][hapmap] |
| rs73067984 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs7619038 | 0.85[EUR][1000 genomes] |
| rs9818643 | 0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs9828788 | 0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs9876105 | 0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv529987 | chr3:41921995-42591771 | Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 32 gene(s) | inside rSNPs | diseases |
| 2 | nsv1005533 | chr3:41953873-42596375 | Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 31 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6768356 | ZNF197 | cis | parietal | SCAN |
| rs6768356 | CCR9 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:42493400-42496800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
