Variant report
| Variant | rs5007413 |
|---|---|
| Chromosome Location | chr8:63891887-63891888 |
| allele | A/C |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-RP11-32K4.2.1-6 | chr8:63890420-63897460 | NONHSAT126909 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:24)
| rs_ID | r2[population] |
|---|---|
| rs10090886 | 0.81[EUR][1000 genomes] |
| rs10100456 | 0.89[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs10808728 | 0.85[EUR][1000 genomes] |
| rs12115136 | 0.87[EUR][1000 genomes] |
| rs12335094 | 1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs12679222 | 0.89[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs1455574 | 0.81[EUR][1000 genomes] |
| rs2353388 | 0.83[EUR][1000 genomes] |
| rs4279586 | 1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs4352845 | 0.83[EUR][1000 genomes] |
| rs4377959 | 0.91[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs4397399 | 0.91[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs4400383 | 0.91[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs4413770 | 0.83[EUR][1000 genomes] |
| rs4446729 | 0.82[MEX][hapmap];0.89[MKK][hapmap];0.81[AFR][1000 genomes] |
| rs6998134 | 0.82[MEX][hapmap] |
| rs6999604 | 0.82[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs7000012 | 0.82[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs7003413 | 0.82[MEX][hapmap] |
| rs7010484 | 1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs7387326 | 0.89[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs7388305 | 1.00[CEU][hapmap] |
| rs7839216 | 0.83[AMR][1000 genomes];0.96[EUR][1000 genomes] |
| rs7839874 | 0.83[AMR][1000 genomes];0.96[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1018879 | chr8:63281724-63937632 | Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 2 | nsv1033527 | chr8:63673915-64073735 | Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
| 3 | nsv890964 | chr8:63848556-63898146 | Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS | Chromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs5007413 | CLVS1 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr8:63868600-63895800 | Weak transcription | Fetal Brain Female | brain |
| 2 | chr8:63878000-63892000 | Weak transcription | Brain Germinal Matrix | brain |
