Variant report
| Variant | rs6804828 |
|---|---|
| Chromosome Location | chr3:48393556-48393557 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:2 , 50 per page) page:
1
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000172113 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:30)
| rs_ID | r2[population] |
|---|---|
| rs11130165 | 0.96[EUR][1000 genomes] |
| rs11130166 | 0.98[EUR][1000 genomes] |
| rs11706939 | 0.96[EUR][1000 genomes] |
| rs12185901 | 0.96[EUR][1000 genomes] |
| rs12486935 | 1.00[CEU][hapmap];0.98[EUR][1000 genomes] |
| rs12486944 | 1.00[CEU][hapmap];0.98[EUR][1000 genomes] |
| rs12498074 | 0.93[EUR][1000 genomes] |
| rs13069884 | 0.95[EUR][1000 genomes] |
| rs13082217 | 0.96[EUR][1000 genomes] |
| rs13082269 | 0.98[EUR][1000 genomes] |
| rs13087050 | 1.00[CEU][hapmap];0.98[EUR][1000 genomes] |
| rs13094496 | 0.98[EUR][1000 genomes] |
| rs1471217 | 0.96[EUR][1000 genomes] |
| rs17593974 | 0.98[EUR][1000 genomes] |
| rs2017858 | 0.95[EUR][1000 genomes] |
| rs2017859 | 0.95[EUR][1000 genomes] |
| rs34008503 | 0.92[EUR][1000 genomes] |
| rs35460860 | 0.97[EUR][1000 genomes] |
| rs62263035 | 0.98[EUR][1000 genomes] |
| rs62263037 | 0.95[EUR][1000 genomes] |
| rs62263038 | 0.97[EUR][1000 genomes] |
| rs6779517 | 0.96[EUR][1000 genomes] |
| rs6791930 | 0.84[YRI][hapmap] |
| rs6794644 | 0.87[YRI][hapmap] |
| rs6800492 | 0.87[YRI][hapmap] |
| rs71323399 | 0.95[EUR][1000 genomes] |
| rs7640221 | 0.80[EUR][1000 genomes] |
| rs936426 | 0.81[CEU][hapmap] |
| rs9818937 | 0.87[YRI][hapmap] |
| rs9833309 | 0.87[YRI][hapmap] |
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 | nsv834683 | chr3:48301504-48493261 | Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 73 gene(s) | inside rSNPs | diseases |
| 2 | nsv834684 | chr3:48385699-48589323 | Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 66 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:21)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6804828 | NME6 | cis | Adipose Subcutaneous | GTEx |
| rs6804828 | NME6 | cis | Artery Aorta | GTEx |
| rs6804828 | CDC25A | cis | Thyroid | GTEx |
| rs6804828 | MRPS18AP1 | cis | Artery Tibial | GTEx |
| rs6804828 | NME6 | cis | Nerve Tibial | GTEx |
| rs6804828 | MRPS18AP1 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs6804828 | MRPS18AP1 | cis | lung | GTEx |
| rs6804828 | MRPS18AP1 | cis | Thyroid | GTEx |
| rs6804828 | ZNF589 | cis | Esophagus Mucosa | GTEx |
| rs6804828 | CDC25A | cis | Muscle Skeletal | GTEx |
| rs6804828 | MRPS18AP1 | cis | Artery Aorta | GTEx |
| rs6804828 | MRPS18AP1 | cis | Muscle Skeletal | GTEx |
| rs6804828 | CDC25A | cis | Adipose Subcutaneous | GTEx |
| rs6804828 | MRPS18AP1 | cis | Esophagus Muscularis | GTEx |
| rs6804828 | ZNF589 | cis | Artery Aorta | GTEx |
| rs6804828 | NME6 | Cis_1M | lymphoblastoid | RTeQTL |
| rs6804828 | MRPS18AP1 | cis | Esophagus Mucosa | GTEx |
| rs6804828 | ZNF589 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs6804828 | ZNF589 | cis | Thyroid | GTEx |
| rs6804828 | NME6 | cis | Esophagus Muscularis | GTEx |
| rs6804828 | ZNF589 | cis | Brain Pons | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:48389400-48393600 | Weak transcription | Foreskin Keratinocyte Primary Cells skin03 | Skin |
| 2 | chr3:48389600-48393600 | Weak transcription | NHEK | skin |
| 3 | chr3:48391400-48393800 | Weak transcription | Foreskin Melanocyte Primary Cells skin03 | Skin |
| 4 | chr3:48393200-48394800 | Enhancers | Breast Myoepithelial Primary Cells | Breast |
| 5 | chr3:48393400-48393800 | Weak transcription | Foreskin Melanocyte Primary Cells skin01 | Skin |
