Variant report
| Variant | rs1834716 |
|---|---|
| Chromosome Location | chr8:125959763-125959764 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
1
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:125551315..125552840-chr8:125959019..125961791,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000255313 | TF binding region |
| ENSG00000147687 | Chromatin interaction |
| ENSG00000147684 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs10099730 | 0.82[CHB][hapmap] |
| rs12677337 | 1.00[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes] |
| rs13281583 | 0.91[ASN][1000 genomes] |
| rs1427086 | 0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs1427087 | 0.82[CHB][hapmap];0.82[CHD][hapmap] |
| rs16900152 | 1.00[CEU][hapmap];0.94[EUR][1000 genomes] |
| rs2590669 | 0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2725879 | 0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2725881 | 0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes] |
| rs4634661 | 0.95[AMR][1000 genomes];0.94[ASN][1000 genomes] |
| rs56364633 | 0.88[EUR][1000 genomes] |
| rs7843302 | 0.88[EUR][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 | nsv891434 | chr8:125630655-126324432 | Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 80 gene(s) | inside rSNPs | diseases |
| 2 | nsv1030803 | chr8:125868684-125969635 | Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
| 3 | nsv1024405 | chr8:125868684-125971035 | Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
| 4 | nsv1020502 | chr8:125868684-125972572 | Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 36 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1834716 | NSMCE2 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:125958600-125959800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
