Variant report
| Variant | rs4306279 |
|---|---|
| Chromosome Location | chr11:6084153-6084154 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:50)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:50 , 50 per page) page:
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| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| OR52L2P | TF binding region |
rSNPs within LD-proxies of this variant (count:28)
| rs_ID | r2[population] |
|---|---|
| rs10500654 | 1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs10742949 | 0.84[ASN][1000 genomes] |
| rs10839353 | 0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs10839362 | 0.83[AMR][1000 genomes] |
| rs11040512 | 0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs11040550 | 0.87[AFR][1000 genomes] |
| rs11040551 | 0.89[AFR][1000 genomes] |
| rs11040552 | 0.84[AFR][1000 genomes] |
| rs11040558 | 0.85[AFR][1000 genomes] |
| rs11040594 | 0.85[AFR][1000 genomes] |
| rs11040648 | 0.85[AFR][1000 genomes] |
| rs11040650 | 0.82[AFR][1000 genomes] |
| rs11040652 | 0.82[AFR][1000 genomes] |
| rs11040653 | 0.82[AFR][1000 genomes] |
| rs11511999 | 0.81[AFR][1000 genomes] |
| rs35755858 | 0.81[AFR][1000 genomes] |
| rs4310587 | 0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs4332504 | 0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs4353251 | 0.87[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes] |
| rs4570555 | 0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes] |
| rs4604856 | 0.82[AFR][1000 genomes] |
| rs4758074 | 0.84[AFR][1000 genomes] |
| rs4758077 | 0.85[AFR][1000 genomes] |
| rs4758079 | 0.85[AFR][1000 genomes] |
| rs4758080 | 0.83[AFR][1000 genomes] |
| rs4758379 | 0.82[AFR][1000 genomes] |
| rs7479778 | 0.92[AFR][1000 genomes] |
| rs7948696 | 0.84[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:8 , 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 | nsv553241 | chr11:5506034-6203685 | Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 74 gene(s) | inside rSNPs | diseases |
| 2 | nsv530216 | chr11:5614439-6468232 | Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 90 gene(s) | inside rSNPs | diseases |
| 3 | nsv1036389 | chr11:5695451-6177680 | Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 55 gene(s) | inside rSNPs | diseases |
| 4 | nsv540943 | chr11:5695451-6177680 | Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 55 gene(s) | inside rSNPs | diseases |
| 5 | nsv1052156 | chr11:6003428-6107778 | Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS | TF binding regionCpG islandChromatin interactive region | 11 gene(s) | inside rSNPs | diseases |
| 6 | nsv1047794 | chr11:6003428-6116105 | Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive region | 11 gene(s) | inside rSNPs | diseases |
| 7 | nsv1038674 | chr11:6058703-6090372 | Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats | TF binding regionChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 8 | esv19708 | chr11:6076999-6117545 | Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS | TF binding regionChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4306279 | EXOC1 | trans | cerebellum | SCAN |
| rs4306279 | OR52N2 | cis | parietal | SCAN |
| rs4306279 | OVCH2 | cis | parietal | SCAN |
| rs4306279 | TMEM9B | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr11:6083000-6084400 | Enhancers | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
| 2 | chr11:6084000-6085200 | Enhancers | Primary monocytes fromperipheralblood | blood |
