Variant report
| Variant | rs17144523 |
|---|---|
| Chromosome Location | chr5:118085674-118085675 |
| 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:23)
| rs_ID | r2[population] |
|---|---|
| rs1110512 | 0.97[AFR][1000 genomes];0.94[ASN][1000 genomes] |
| rs12110125 | 0.88[ASN][1000 genomes] |
| rs12110310 | 0.87[ASN][1000 genomes] |
| rs13152964 | 1.00[EUR][1000 genomes] |
| rs13171299 | 0.91[EUR][1000 genomes] |
| rs1559072 | 0.90[ASN][1000 genomes] |
| rs17144517 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17144520 | 1.00[AFR][1000 genomes];1.00[EUR][1000 genomes] |
| rs17144526 | 1.00[AFR][1000 genomes];1.00[EUR][1000 genomes] |
| rs17144550 | 1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[ASN][1000 genomes] |
| rs17144551 | 0.97[AFR][1000 genomes] |
| rs17144552 | 1.00[YRI][hapmap] |
| rs17144554 | 1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[ASN][1000 genomes] |
| rs17144584 | 0.94[ASN][1000 genomes] |
| rs1835048 | 0.84[ASN][1000 genomes] |
| rs34694285 | 0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs58999502 | 0.97[AFR][1000 genomes] |
| rs721065 | 0.84[ASN][1000 genomes] |
| rs73249197 | 0.92[AFR][1000 genomes] |
| rs73789377 | 0.97[AFR][1000 genomes];0.90[ASN][1000 genomes] |
| rs7719304 | 0.94[ASN][1000 genomes] |
| rs888710 | 0.97[AFR][1000 genomes];0.94[ASN][1000 genomes] |
| rs888711 | 0.97[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 | nsv1032241 | chr5:117900051-118157400 | Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
| 2 | nsv882767 | chr5:117931730-118385691 | Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 21 gene(s) | inside rSNPs | diseases |
| 3 | nsv1034487 | chr5:118047803-118085925 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS | Chromatin interactive regionlncRNA | n/a | inside rSNPs | n/a |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17144523 | CCDC112 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:118084600-118085800 | Enhancers | Cortex derived primary cultured neurospheres | brain |
| 2 | chr5:118085400-118088200 | Weak transcription | Fetal Lung | lung |
