Variant report
| Variant | rs1471729 |
|---|---|
| Chromosome Location | chr4:80180855-80180856 |
| allele | C/T |
| 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:32)
| rs_ID | r2[population] |
|---|---|
| rs10015645 | 1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs10518214 | 1.00[ASN][1000 genomes] |
| rs12501238 | 1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs13113216 | 1.00[ASN][1000 genomes] |
| rs17003679 | 1.00[ASN][1000 genomes] |
| rs28455975 | 1.00[ASN][1000 genomes] |
| rs28460261 | 1.00[ASN][1000 genomes] |
| rs28546466 | 1.00[ASN][1000 genomes] |
| rs28651876 | 1.00[ASN][1000 genomes] |
| rs28656884 | 1.00[ASN][1000 genomes] |
| rs28688839 | 1.00[ASN][1000 genomes] |
| rs28704600 | 1.00[ASN][1000 genomes] |
| rs28727508 | 1.00[ASN][1000 genomes] |
| rs34078327 | 1.00[ASN][1000 genomes] |
| rs34655076 | 1.00[ASN][1000 genomes] |
| rs4246716 | 1.00[ASN][1000 genomes] |
| rs4246717 | 1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs4413431 | 1.00[ASN][1000 genomes] |
| rs4975165 | 1.00[JPT][hapmap] |
| rs59072456 | 1.00[ASN][1000 genomes] |
| rs6816121 | 1.00[JPT][hapmap];1.00[ASN][1000 genomes] |
| rs6821709 | 1.00[ASN][1000 genomes] |
| rs6853888 | 1.00[ASN][1000 genomes] |
| rs6858130 | 1.00[ASN][1000 genomes] |
| rs72662701 | 1.00[ASN][1000 genomes] |
| rs72664018 | 1.00[ASN][1000 genomes] |
| rs73828224 | 1.00[ASN][1000 genomes] |
| rs73828232 | 1.00[ASN][1000 genomes] |
| rs7681755 | 0.90[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9790513 | 1.00[ASN][1000 genomes] |
| rs982992 | 1.00[ASN][1000 genomes] |
| rs9991698 | 1.00[JPT][hapmap];1.00[ASN][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 | nsv1000907 | chr4:79838948-80224764 | Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv879505 | chr4:79887043-80293046 | Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1471729 | BMP2K | cis | parietal | SCAN |
| rs1471729 | RASGEF1B | cis | parietal | SCAN |
| rs1471729 | CDKL2 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:80165400-80194000 | Weak transcription | Aorta | Aorta |
| 2 | chr4:80180400-80181800 | Enhancers | Breast Myoepithelial Primary Cells | Breast |
