Variant report
| Variant | rs2725879 |
|---|---|
| Chromosome Location | chr8:125964505-125964506 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:7)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:7 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr8:125935909..125938271-chr8:125963994..125966987,3 | MCF-7 | breast: | |
| 2 | chr8:125869656..125872568-chr8:125963654..125965352,2 | MCF-7 | breast: | |
| 3 | chr8:125937794..125939551-chr8:125962673..125965178,2 | K562 | blood: | |
| 4 | chr8:125955052..125957030-chr8:125964288..125966212,2 | MCF-7 | breast: | |
| 5 | chr8:125964340..125966709-chr8:125985422..125987318,2 | K562 | blood: | |
| 6 | chr8:125908171..125909770-chr8:125964003..125966026,2 | MCF-7 | breast: | |
| 7 | chr8:125826052..125832853-chr8:125963334..125969415,10 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000249816 | Chromatin interaction |
| ENSG00000255313 | Chromatin interaction |
| ENSG00000180938 | Chromatin interaction |
| ENSG00000255080 | Chromatin interaction |
| ENSG00000255491 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs13281583 | 0.93[ASN][1000 genomes] |
| rs1427086 | 0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs1427093 | 0.83[CHB][hapmap] |
| rs1834716 | 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] |
| rs2248055 | 0.82[CHB][hapmap];0.80[CHD][hapmap] |
| rs2555726 | 0.83[CHB][hapmap] |
| rs2590669 | 0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2590674 | 0.83[CHB][hapmap] |
| rs2725881 | 0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes] |
| rs4634661 | 0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
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| 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 |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:125960000-125969400 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
