Variant report
| Variant | rs6682504 |
|---|---|
| Chromosome Location | chr1:239248743-239248744 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:20)
| rs_ID | r2[population] |
|---|---|
| rs10925808 | 1.00[ASN][1000 genomes] |
| rs10925814 | 1.00[ASN][1000 genomes] |
| rs1156168 | 1.00[ASN][1000 genomes] |
| rs12084592 | 1.00[ASN][1000 genomes] |
| rs12092103 | 1.00[ASN][1000 genomes] |
| rs1509692 | 1.00[ASN][1000 genomes] |
| rs2136520 | 0.98[ASN][1000 genomes] |
| rs2175167 | 0.82[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs2175168 | 0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2202901 | 1.00[ASN][1000 genomes] |
| rs2202902 | 1.00[ASN][1000 genomes] |
| rs2202903 | 1.00[ASN][1000 genomes] |
| rs61834577 | 0.89[ASN][1000 genomes] |
| rs61834579 | 1.00[ASN][1000 genomes] |
| rs61834580 | 1.00[ASN][1000 genomes] |
| rs6677311 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7416262 | 1.00[ASN][1000 genomes] |
| rs7525377 | 0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs7545552 | 0.95[ASN][1000 genomes] |
| rs989217 | 1.00[ASN][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 | nsv873348 | chr1:239023492-239356155 | Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
| 2 | nsv998542 | chr1:239102274-239424608 | Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 3 | nsv1002301 | chr1:239182255-239774393 | Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| 4 | nsv1000227 | chr1:239247968-239421826 | Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 5 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6682504 | ERO1LB | cis | cerebellum | SCAN |
| rs6682504 | CHRM3 | cis | parietal | SCAN |
| rs6682504 | TOMM20 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:239245000-239248800 | ZNF genes & repeats | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
