Variant report
| Variant | rs12283559 |
|---|---|
| Chromosome Location | chr11:5505149-5505150 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:6)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:6 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | POLR2A | chr11:5505011-5505500 | K562 | blood: | n/a | n/a |
| 2 | POLR2A | chr11:5504973-5508441 | K562 | blood: | n/a | n/a |
| 3 | POLR2A | chr11:5505056-5506158 | K562 | blood: | n/a | n/a |
| 4 | POLR2A | chr11:5504855-5512186 | K562 | blood: | n/a | n/a |
| 5 | POLR2A | chr11:5504830-5505808 | K562 | blood: | n/a | n/a |
| 6 | POLR2A | chr11:5504972-5505496 | K562 | blood: | n/a | n/a |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| OR52D1 | TF binding region |
| ENSG00000175520 | Chromatin interaction |
| ENSG00000132274 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:10)
| rs_ID | r2[population] |
|---|---|
| rs11821912 | 0.89[CHB][hapmap] |
| rs12577059 | 0.83[CHB][hapmap] |
| rs2340353 | 1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs365943 | 0.81[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap] |
| rs366533 | 0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs404280 | 0.81[TSI][hapmap] |
| rs430252 | 0.85[EUR][1000 genomes] |
| rs435810 | 0.83[CHB][hapmap] |
| rs438996 | 0.81[CEU][hapmap] |
| rs449825 | 0.85[CEU][hapmap] |
Variant overlapped rSNPs/rCNVs (count:10 , 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 | nsv1048608 | chr11:5328516-5645179 | Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 60 gene(s) | inside rSNPs | diseases |
| 2 | nsv1046068 | chr11:5335943-6063742 | Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 89 gene(s) | inside rSNPs | diseases |
| 3 | nsv896931 | chr11:5357881-5505149 | Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 41 gene(s) | inside rSNPs | diseases |
| 4 | nsv832057 | chr11:5375585-5576200 | Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 51 gene(s) | inside rSNPs | diseases |
| 5 | nsv896938 | chr11:5484249-5505149 | Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats | TF binding regionChromatin interactive region | 17 gene(s) | inside rSNPs | diseases |
| 6 | nsv1047754 | chr11:5489195-5506034 | Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers | TF binding regionChromatin interactive region | 8 gene(s) | inside rSNPs | diseases |
| 7 | nsv896939 | chr11:5497799-5809548 | Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 48 gene(s) | inside rSNPs | diseases |
| 8 | nsv1039285 | chr11:5504861-5519672 | Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
| 9 | nsv1042308 | chr11:5504861-5520062 | Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS | TF binding regionCpG islandChromatin interactive region | 5 gene(s) | inside rSNPs | diseases |
| 10 | nsv971925 | chr11:5505050-5505658 | ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12283559 | OR51I2 | cis | cerebellum | SCAN |
| rs12283559 | OR52I1 | cis | cerebellum | SCAN |
| rs12283559 | C11orf42 | cis | parietal | SCAN |
| rs12283559 | UBQLNL | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr11:5504800-5505400 | Genic enhancers | K562 | blood |
