Variant report
| Variant | rs4633808 |
|---|---|
| Chromosome Location | chr18:40158156-40158157 |
| allele | C/T |
| 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-RIT2-5 | chr18:40157399-40158567 | ucscGeneNc_uc002lax_2 |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:27)
| rs_ID | r2[population] |
|---|---|
| rs10775472 | 0.86[ASN][1000 genomes] |
| rs12954826 | 0.84[ASN][1000 genomes] |
| rs1431836 | 0.84[ASN][1000 genomes] |
| rs3924664 | 0.91[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs4243262 | 0.87[EUR][1000 genomes] |
| rs4243264 | 0.84[EUR][1000 genomes] |
| rs4300738 | 0.84[ASN][1000 genomes] |
| rs4303629 | 0.85[ASN][1000 genomes] |
| rs4474776 | 0.82[ASN][1000 genomes] |
| rs4514768 | 0.93[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs4629063 | 0.93[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs57032575 | 0.84[ASN][1000 genomes] |
| rs7228101 | 0.85[EUR][1000 genomes] |
| rs7229728 | 0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs7230640 | 0.85[EUR][1000 genomes] |
| rs7231626 | 0.87[EUR][1000 genomes] |
| rs7232069 | 0.84[EUR][1000 genomes] |
| rs7238529 | 0.85[EUR][1000 genomes] |
| rs7239787 | 0.85[ASN][1000 genomes] |
| rs7506104 | 0.83[ASN][1000 genomes] |
| rs8086796 | 0.84[ASN][1000 genomes] |
| rs9951191 | 0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs9956876 | 0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs9959682 | 0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs9964460 | 0.87[EUR][1000 genomes] |
| rs9964813 | 0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9967058 | 0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3447158 | chr18:40045478-40320720 | Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| 2 | esv2754458 | chr18:40070202-40164902 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS | Chromatin interactive regionlncRNA | n/a | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4633808 | SYT4 | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr18:40156000-40158400 | Weak transcription | Muscle Satellite Cultured Cells | -- |
| 2 | chr18:40156600-40158400 | Weak transcription | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
