Variant report
| Variant | rs4652420 |
|---|---|
| Chromosome Location | chr1:179562143-179562144 |
| 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 |
|---|---|
| ENSG00000227141 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs10157699 | 1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes] |
| rs10798708 | 1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap] |
| rs10913847 | 0.82[CHB][hapmap];0.83[JPT][hapmap] |
| rs12042786 | 0.84[EUR][1000 genomes] |
| rs1410594 | 1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap] |
| rs1590783 | 0.91[ASN][1000 genomes] |
| rs3930537 | 1.00[CHB][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap] |
| rs4443850 | 1.00[CHB][hapmap];0.86[JPT][hapmap] |
| rs4628468 | 1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes] |
| rs4652418 | 1.00[ASN][1000 genomes] |
| rs6700202 | 0.83[EUR][1000 genomes] |
| rs7534216 | 1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3424735 | chr1:179559954-179562502 | Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:6)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4652420 | TDRD5 | cis | Adipose Subcutaneous | GTEx |
| rs4652420 | TDRD5 | cis | cerebellum | SCAN |
| rs4652420 | TDRD5 | cis | Nerve Tibial | GTEx |
| rs4652420 | FAM163A | cis | parietal | SCAN |
| rs4652420 | NPHS2 | cis | cerebellum | SCAN |
| rs4652420 | TDRD5 | cis | parietal | SCAN |
Chromatin state (count:0 , 50 per page) page:
| No data |
