Variant report
| Variant | rs7979115 |
|---|---|
| Chromosome Location | chr12:9365280-9365281 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 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 | chr12:9365182-9365312 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| PZP | TF binding region |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs11612110 | 0.91[EUR][1000 genomes] |
| rs2195209 | 0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs2195211 | 0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs34363 | 1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs34364 | 0.80[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs34369 | 0.91[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes] |
| rs34370 | 0.91[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes] |
| rs4454768 | 1.00[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs4883222 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs7301988 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs7955045 | 0.85[EUR][1000 genomes] |
| rs7956661 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes] |
| rs7959360 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes] |
| rs972110 | 0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:6 , 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 | nsv1045317 | chr12:9113216-9544655 | Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 38 gene(s) | inside rSNPs | diseases |
| 2 | nsv1048491 | chr12:9208806-9544655 | Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 35 gene(s) | inside rSNPs | diseases |
| 3 | nsv527404 | chr12:9250601-9435244 | Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 18 gene(s) | inside rSNPs | diseases |
| 4 | nsv523958 | chr12:9303440-9549072 | Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 23 gene(s) | inside rSNPs | diseases |
| 5 | nsv557355 | chr12:9309995-9529015 | Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 23 gene(s) | inside rSNPs | diseases |
| 6 | nsv1035953 | chr12:9314481-9544655 | Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 22 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7979115 | RBP5 | cis | cerebellum | SCAN |
| rs7979115 | C1RL | cis | cerebellum | SCAN |
| rs7979115 | CLEC4D | cis | cerebellum | SCAN |
| rs7979115 | RPL13P5 | cis | parietal | SCAN |
| rs7979115 | CLEC2D | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:9357400-9384800 | Weak transcription | Primary Natural Killer cells fromperipheralblood | blood |
| 2 | chr12:9365000-9365600 | Weak transcription | Esophagus | oesophagus |
