Variant report
| Variant | rs7972739 |
|---|---|
| Chromosome Location | chr12:40958852-40958853 |
| allele | C/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:5)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:5 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | SPI1 | chr12:40958830-40959133 | GM12891 | blood: | n/a | chr12:40959008-40959017 chr12:40959006-40959019 chr12:40959005-40959018 |
| 2 | SPI1 | chr12:40958830-40959126 | GM12891 | blood: | n/a | chr12:40959008-40959017 chr12:40959006-40959019 chr12:40959005-40959018 |
| 3 | SPI1 | chr12:40958675-40959418 | GM12878 | blood: | n/a | chr12:40959008-40959017 chr12:40959006-40959019 chr12:40959005-40959018 |
| 4 | EP300 | chr12:40958054-40959758 | SK-N-SH | brain: | n/a | chr12:40959007-40959021 chr12:40958467-40958481 |
| 5 | GATA2 | chr12:40958784-40959403 | SH-SY5Y | brain: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:40718883..40719693-chr12:40958776..40959283,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| MUC19 | TF binding region |
rSNPs within LD-proxies of this variant (count:19)
| rs_ID | r2[population] |
|---|---|
| rs10083205 | 1.00[CEU][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[EUR][1000 genomes] |
| rs10784705 | 1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes] |
| rs10878851 | 0.92[AFR][1000 genomes];0.89[EUR][1000 genomes] |
| rs10878852 | 0.92[AFR][1000 genomes];0.87[EUR][1000 genomes] |
| rs10878853 | 0.90[AFR][1000 genomes];0.88[EUR][1000 genomes] |
| rs10878854 | 0.92[AFR][1000 genomes];0.89[EUR][1000 genomes] |
| rs11177226 | 1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes] |
| rs11177288 | 0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs11177343 | 0.81[AFR][1000 genomes];0.83[EUR][1000 genomes] |
| rs1492319 | 0.91[YRI][hapmap] |
| rs1602635 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2588399 | 0.91[YRI][hapmap] |
| rs2933352 | 0.91[YRI][hapmap] |
| rs3751173 | 0.92[AFR][1000 genomes];0.93[EUR][1000 genomes] |
| rs56080664 | 0.95[AFR][1000 genomes];0.96[EUR][1000 genomes] |
| rs7303283 | 1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs7304371 | 0.87[JPT][hapmap] |
| rs7971126 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7974188 | 0.93[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv899033 | chr12:40758652-41122288 | Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 23 gene(s) | inside rSNPs | diseases |
| 2 | nsv832378 | chr12:40943111-41132305 | Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 4 gene(s) | inside rSNPs | diseases |
| 3 | nsv683 | chr12:40951473-40996258 | Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:40947400-40967800 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr12:40956000-40963600 | Weak transcription | GM12878-XiMat | blood |
