Variant report
| Variant | rs2555725 |
|---|---|
| Chromosome Location | chr8:125959864-125959865 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:3)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
1
| No data |
(count:2 , 50 per page) page:
1
(count:3 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-ZNF572-1 | chr8:125959785-125960034 | ENSG00000249816 |
| 2 | lnc-ZNF572-1 | chr8:125959785-125960034 | XLOC_006916 |
| 3 | lnc-ZNF572-1 | chr8:125959785-125960034 | XLOC_006916 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000255313 | TF binding region |
| ENSG00000147687 | Chromatin interaction |
| ENSG00000147684 | Chromatin interaction |
| ENSG00000249816 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs2555724 | 0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2590665 | 0.88[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2590667 | 0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2725878 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs28455785 | 0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs28558480 | 0.93[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs28870400 | 0.91[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3866472 | 0.85[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3909714 | 0.85[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs3909715 | 0.85[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4006739 | 0.93[AMR][1000 genomes];1.00[ASN][1000 genomes] |
| rs4099573 | 0.85[AMR][1000 genomes];1.00[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 |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2555725 | LINC00964 | cis | Skin Sun Exposed Lower leg | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:125959800-125960000 | Strong transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
