Variant report
| Variant | rs2004278 |
|---|---|
| Chromosome Location | chr15:75264363-75264364 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr15:75262612..75265587-chr15:75267566..75269417,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000261813 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs12050494 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs12050759 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs12592377 | 0.82[ASN][1000 genomes] |
| rs12594897 | 0.82[ASN][1000 genomes] |
| rs1867153 | 0.81[ASN][1000 genomes] |
| rs57684159 | 0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs59270710 | 0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs60228621 | 0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs60740187 | 0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs6495132 | 0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs67271490 | 0.81[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv569993 | chr15:75242155-75483752 | Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 72 gene(s) | inside rSNPs | diseases |
| 2 | nsv1612 | chr15:75247725-75281284 | Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 46 gene(s) | inside rSNPs | diseases |
| 3 | nsv977735 | chr15:75257534-75268830 | Enhancers Bivalent Enhancer Weak transcription | Chromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2004278 | SCAMP5 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr15:75257600-75270800 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
