Variant report
| Variant | rs12230563 |
|---|---|
| Chromosome Location | chr12:105359368-105359369 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:3)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:3 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000136052 | Chromatin interaction |
| ENSG00000151131 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs10861300 | 0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes] |
| rs11112268 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs11112269 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4130161 | 1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs4964309 | 0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes] |
| rs4964318 | 0.82[JPT][hapmap] |
| rs6539173 | 1.00[ASN][1000 genomes] |
| rs6539174 | 0.91[ASN][1000 genomes] |
| rs6539178 | 1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes] |
| rs6539179 | 0.88[ASN][1000 genomes] |
| rs6539180 | 0.88[ASN][1000 genomes] |
| rs7307234 | 1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes] |
| rs73383489 | 0.85[AFR][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 | nsv899495 | chr12:104990469-105527011 | Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 36 gene(s) | inside rSNPs | diseases |
| 2 | nsv899498 | chr12:105173598-105461620 | Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive region | 22 gene(s) | inside rSNPs | diseases |
| 3 | nsv832505 | chr12:105315352-105497765 | Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 20 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12230563 | C12orf75 | cis | cerebellum | SCAN |
| rs12230563 | ASCL1 | cis | parietal | SCAN |
| rs12230563 | SLC5A8 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:105356600-105359400 | Enhancers | Cortex derived primary cultured neurospheres | brain |
| 2 | chr12:105358800-105360000 | Enhancers | GM12878-XiMat | blood |
