Variant report
| Variant | rs414845 |
|---|---|
| Chromosome Location | chr21:40254465-40254466 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr21:40253690..40256394-chr21:40265438..40267658,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000272015 | Chromatin interaction |
| ENSG00000227721 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs17230954 | 0.82[JPT][hapmap] |
| rs17230961 | 0.82[JPT][hapmap] |
| rs2298560 | 0.82[JPT][hapmap] |
| rs2410062 | 0.82[JPT][hapmap] |
| rs2836715 | 0.82[JPT][hapmap] |
| rs2836717 | 0.82[JPT][hapmap] |
| rs2836724 | 0.82[JPT][hapmap] |
| rs2836743 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs28420538 | 0.82[JPT][hapmap] |
| rs59086904 | 0.86[EUR][1000 genomes] |
| rs7279299 | 0.82[JPT][hapmap] |
| rs9979509 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1062425 | chr21:40172471-40380976 | Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 47 gene(s) | inside rSNPs | diseases |
| 2 | nsv544442 | chr21:40172471-40380976 | Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 47 gene(s) | inside rSNPs | diseases |
| 3 | nsv587477 | chr21:40228920-40512004 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' | TF binding regionChromatin interactive regionlncRNA | 35 gene(s) | inside rSNPs | diseases |
| 4 | nsv587478 | chr21:40243459-40275033 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats | TF binding regionChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs414845 | NCRNA00257 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr21:40247800-40259400 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
