Variant report
| Variant | rs1015699 |
|---|---|
| Chromosome Location | chr4:48456631-48456632 |
| 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:
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| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:21)
| rs_ID | r2[population] |
|---|---|
| rs10805168 | 0.88[EUR][1000 genomes] |
| rs11731383 | 0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs12503644 | 0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs13150017 | 0.92[ASN][1000 genomes] |
| rs1352434 | 0.89[EUR][1000 genomes] |
| rs1488647 | 0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs1586540 | 0.88[EUR][1000 genomes] |
| rs16861305 | 0.91[ASN][1000 genomes] |
| rs1948167 | 0.88[EUR][1000 genomes] |
| rs2353314 | 0.89[EUR][1000 genomes] |
| rs2353315 | 1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs2353855 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs34975258 | 0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs35758434 | 0.88[EUR][1000 genomes] |
| rs4694895 | 0.86[EUR][1000 genomes] |
| rs4695377 | 0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs4695381 | 0.89[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs62309455 | 0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs62309458 | 0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs6834339 | 0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7438713 | 0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 | nsv470034 | chr4:48427773-48605628 | Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
| 2 | nsv594121 | chr4:48427773-48605628 | Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
| 3 | nsv1005268 | chr4:48444307-48484389 | Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 4 | nsv537086 | chr4:48444307-48484389 | Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1015699 | SLAIN2 | Cis_1M | lymphoblastoid | RTeQTL |
| rs1015699 | SLC10A4 | cis | lung | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:48452200-48457600 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
