Variant report
| Variant | rs28386840 |
|---|---|
| Chromosome Location | chr16:55686818-55686819 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:11)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:11 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr16:55686687-55686958 | SK-N-SH | brain: | n/a | n/a |
| 2 | GATA3 | chr16:55685971-55686873 | SK-N-SH | brain: | n/a | chr16:55686483-55686492 chr16:55685997-55686005 |
| 3 | EP300 | chr16:55685034-55688103 | SK-N-SH | brain: | n/a | n/a |
| 4 | MXI1 | chr16:55685637-55688813 | SK-N-SH | brain: | n/a | n/a |
| 5 | EP300 | chr16:55685988-55686877 | SK-N-SH_RA | brain: | n/a | n/a |
| 6 | GATA3 | chr16:55686007-55686963 | SH-SY5Y | brain: | n/a | chr16:55686483-55686492 |
| 7 | GATA2 | chr16:55685967-55686980 | SH-SY5Y | brain: | n/a | chr16:55686483-55686492 chr16:55685997-55686005 |
| 8 | TCF12 | chr16:55685816-55686936 | SK-N-SH | brain: | n/a | n/a |
| 9 | REST | chr16:55685969-55686869 | SK-N-SH | brain: | n/a | n/a |
| 10 | GATA3 | chr16:55685924-55686878 | SK-N-SH | brain: | n/a | chr16:55686483-55686492 chr16:55685997-55686005 |
| 11 | EP300 | chr16:55685949-55686835 | SK-N-SH_RA | brain: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr16:55684943..55687258-chr16:55695232..55697470,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| SLC6A2 | TF binding region |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs11076111 | 0.91[EUR][1000 genomes] |
| rs13333066 | 0.92[EUR][1000 genomes] |
| rs1362620 | 0.97[EUR][1000 genomes] |
| rs1362621 | 0.97[EUR][1000 genomes] |
| rs17307291 | 0.89[EUR][1000 genomes] |
| rs2242446 | 0.97[EUR][1000 genomes] |
| rs28501300 | 0.90[EUR][1000 genomes] |
| rs28665972 | 0.97[EUR][1000 genomes] |
| rs28693487 | 0.89[EUR][1000 genomes] |
| rs3760019 | 0.97[EUR][1000 genomes] |
| rs3785147 | 0.89[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
1
| 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 |
| 6 | esv2557814 | chr16:55686817-55686818 | Enhancers Flanking Active TSS | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
| 7 | esv2046929 | chr16:55686818-55686820 | Enhancers Flanking Active TSS | TF binding regionChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs28386840 | SLC6A2 | cis | Skin Sun Exposed Lower leg | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr16:55686200-55687000 | Enhancers | Primary hematopoietic stem cells G-CSF-mobilized Female | -- |
| 2 | chr16:55686600-55687000 | Flanking Active TSS | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
