Variant report
| Variant | rs3760019 |
|---|---|
| Chromosome Location | chr16:55688297-55688298 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:3)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:3 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | GATA2 | chr16:55687915-55688307 | SH-SY5Y | brain: | n/a | n/a |
| 2 | EP300 | chr16:55688161-55692249 | SK-N-SH | brain: | n/a | chr16:55689705-55689718 chr16:55690020-55690029 chr16:55689885-55689894 |
| 3 | MXI1 | chr16:55685637-55688813 | SK-N-SH | brain: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| SLC6A2 | TF binding region |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs11076111 | 0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs13333066 | 0.95[EUR][1000 genomes] |
| rs1362620 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1362621 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17307291 | 0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs2242446 | 0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs2397771 | 0.86[ASN][1000 genomes] |
| rs28386840 | 0.97[EUR][1000 genomes] |
| rs28501300 | 0.93[EUR][1000 genomes] |
| rs28665972 | 0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes] |
| rs28693487 | 0.92[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs3785147 | 0.92[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs747107 | 0.84[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 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 | nsv906673 | chr16:55631035-55798370 | Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 2 | nsv431501 | chr16:55639454-55789570 | Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv517827 | chr16:55656355-55698027 | Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 4 | esv2758426 | chr16:55669396-55983590 | Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
| 5 | esv2758649 | chr16:55669396-55983590 | Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3760019 | SLC6A2 | cis | Skin Sun Exposed Lower leg | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr16:55687800-55689400 | Bivalent Enhancer | HepG2 | liver |
