Variant report
| Variant | rs10747758 |
|---|---|
| Chromosome Location | chr12:56001327-56001328 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
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| Variant related genes | Relation type |
|---|---|
| OR6U2P | TF binding region |
rSNPs within LD-proxies of this variant (count:24)
| rs_ID | r2[population] |
|---|---|
| rs10783760 | 0.80[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs10876814 | 0.80[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs10876818 | 0.80[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs10876844 | 0.81[CEU][hapmap] |
| rs11171573 | 0.80[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs11171574 | 0.89[EUR][1000 genomes] |
| rs11171579 | 0.80[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs11171588 | 0.88[EUR][1000 genomes] |
| rs11171589 | 0.90[EUR][1000 genomes] |
| rs11171590 | 0.87[EUR][1000 genomes] |
| rs11171591 | 0.87[EUR][1000 genomes] |
| rs11171592 | 0.90[EUR][1000 genomes] |
| rs1896035 | 0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs1896037 | 0.90[EUR][1000 genomes] |
| rs2555036 | 0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs4759162 | 0.80[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs4759163 | 0.90[EUR][1000 genomes] |
| rs4759173 | 0.82[AMR][1000 genomes];0.98[EUR][1000 genomes] |
| rs7134292 | 0.91[EUR][1000 genomes] |
| rs7137741 | 0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs7138577 | 0.80[AMR][1000 genomes];0.91[EUR][1000 genomes] |
| rs7299541 | 0.81[AMR][1000 genomes] |
| rs7299562 | 0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs7305194 | 0.91[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv559001 | chr12:55507465-56057708 | Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 45 gene(s) | inside rSNPs | diseases |
| 2 | nsv948625 | chr12:55838718-56118833 | Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 43 gene(s) | inside rSNPs | diseases |
| 3 | nsv983247 | chr12:56000681-56011266 | Enhancers ZNF genes & repeats | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 4 | esv3509550 | chr12:56001135-56005383 | Enhancers | TF binding region | 1 gene(s) | inside rSNPs | diseases |
| 5 | esv1815294 | chr12:56001327-56004059 | Enhancers | TF binding region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10747758 | OR9K2 | cis | cerebellum | SCAN |
| rs10747758 | DNAJC14 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:56001000-56001600 | Enhancers | Liver | Liver |
| 2 | chr12:56001000-56001800 | Enhancers | HepG2 | liver |
| 3 | chr12:56001200-56003000 | Enhancers | Breast Myoepithelial Primary Cells | Breast |
