Variant report
| Variant | rs9683094 |
|---|---|
| Chromosome Location | chr3:49185392-49185393 |
| allele | A/G |
| 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] |
|---|---|
| rs12487580 | 0.97[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs12493001 | 0.96[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs12636030 | 0.96[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs13064784 | 0.82[AMR][1000 genomes] |
| rs3212 | 0.86[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs36133651 | 0.84[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs4279134 | 0.86[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs4364202 | 0.87[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs4513485 | 0.90[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs4521268 | 0.86[AMR][1000 genomes];0.84[EUR][1000 genomes] |
| rs4955410 | 0.96[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs61583136 | 0.94[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs6770112 | 0.97[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs6779394 | 0.86[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs6784111 | 0.96[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs7615235 | 0.80[AMR][1000 genomes] |
| rs7626445 | 0.82[AMR][1000 genomes] |
| rs7632267 | 0.89[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs7645551 | 0.92[AMR][1000 genomes];0.89[EUR][1000 genomes] |
| rs9840050 | 0.80[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv876764 | chr3:49040462-49245645 | Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 279 gene(s) | inside rSNPs | diseases |
| 2 | nsv834686 | chr3:49106047-49270556 | Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 53 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:22)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs9683094 | AMT | cis | Artery Aorta | GTEx |
| rs9683094 | PH-4 | Cis_1M | lymphoblastoid | RTeQTL |
| rs9683094 | WDR6 | cis | Whole Blood | GTEx |
| rs9683094 | WDR6 | cis | Artery Tibial | GTEx |
| rs9683094 | AMT | cis | Thyroid | GTEx |
| rs9683094 | AMT | cis | Whole Blood | GTEx |
| rs9683094 | WDR6 | cis | Adipose Subcutaneous | GTEx |
| rs9683094 | WDR6 | cis | Muscle Skeletal | GTEx |
| rs9683094 | WDR6 | cis | lung | GTEx |
| rs9683094 | WDR6 | cis | Esophagus Mucosa | GTEx |
| rs9683094 | NCKIPSD | cis | Nerve Tibial | GTEx |
| rs9683094 | NCKIPSD | cis | Muscle Skeletal | GTEx |
| rs9683094 | NCKIPSD | cis | Whole Blood | GTEx |
| rs9683094 | WDR6 | cis | Esophagus Muscularis | GTEx |
| rs9683094 | WDR6 | cis | Nerve Tibial | GTEx |
| rs9683094 | AMT | cis | Muscle Skeletal | GTEx |
| rs9683094 | NICN1 | cis | Thyroid | GTEx |
| rs9683094 | WDR6 | cis | Heart Left Ventricle | GTEx |
| rs9683094 | USP19 | cis | brain | BrainEAC |
| rs9683094 | NICN1-AS1 | cis | Thyroid | GTEx |
| rs9683094 | WDR6 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs9683094 | CCDC36 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:49172200-49200400 | Weak transcription | Colon Smooth Muscle | Colon |
| 2 | chr3:49179800-49187400 | Weak transcription | Esophagus | oesophagus |
| 3 | chr3:49181200-49185800 | Weak transcription | Foreskin Melanocyte Primary Cells skin01 | Skin |
| 4 | chr3:49182200-49187400 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
