Variant report
| Variant | rs1394597 |
|---|---|
| Chromosome Location | chr3:59483014-59483015 |
| allele | C/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:22)
| rs_ID | r2[population] |
|---|---|
| rs11708862 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs11716806 | 0.88[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs11720835 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs11916409 | 0.91[ASN][1000 genomes] |
| rs11924123 | 0.91[ASN][1000 genomes] |
| rs12629410 | 0.86[ASW][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes] |
| rs12634753 | 0.91[ASN][1000 genomes] |
| rs1394596 | 0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs1502620 | 0.91[ASN][1000 genomes] |
| rs28606076 | 0.91[ASN][1000 genomes] |
| rs4679582 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs4679583 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs55914841 | 0.91[ASN][1000 genomes] |
| rs56218373 | 0.91[ASN][1000 genomes] |
| rs56227728 | 0.81[ASN][1000 genomes] |
| rs62250695 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs7340589 | 0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes] |
| rs7340623 | 0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes] |
| rs7340628 | 0.91[ASN][1000 genomes] |
| rs9852282 | 0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9866013 | 0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs9883594 | 0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][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 | nsv1011181 | chr3:58665373-59542339 | Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
| 2 | nsv536574 | chr3:58665373-59542339 | Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 18 gene(s) | inside rSNPs | diseases |
| 3 | nsv534257 | chr3:58855959-59606464 | Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1394597 | FAM107A | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr3:59481800-59484000 | Enhancers | GM12878-XiMat | blood |
| 2 | chr3:59482000-59483800 | Weak transcription | Fetal Thymus | thymus |
