Variant report
| Variant | rs609103 |
|---|---|
| Chromosome Location | chr6:49779046-49779047 |
| allele | A/C |
| 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:21)
| rs_ID | r2[population] |
|---|---|
| rs12191200 | 1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap] |
| rs12194388 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs12194551 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs12195902 | 1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs12196185 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs12196205 | 1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap] |
| rs12198437 | 0.86[CEU][hapmap] |
| rs12204651 | 1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap] |
| rs12207762 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs1572882 | 1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap] |
| rs493206 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs55824128 | 0.90[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs587310 | 0.96[AMR][1000 genomes] |
| rs593009 | 1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs609927 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs684749 | 1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs686522 | 1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs700002 | 0.93[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs7738293 | 1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap] |
| rs780443 | 1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs9473667 | 1.00[CEU][hapmap];0.99[EUR][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 | nsv933942 | chr6:49480550-50004231 | Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 25 gene(s) | inside rSNPs | diseases |
| 2 | nsv933833 | chr6:49515134-49961765 | Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 23 gene(s) | inside rSNPs | diseases |
| 3 | nsv969302 | chr6:49767553-49782099 | Weak transcription Enhancers ZNF genes & repeats Strong transcription | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 4 | esv3434423 | chr6:49771042-49788886 | Weak transcription Enhancers ZNF genes & repeats Strong transcription | TF binding regionChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs609103 | GCM1 | cis | cerebellum | SCAN |
| rs609103 | GPR115 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:49774200-49782600 | Weak transcription | Fetal Intestine Large | intestine |
