Variant report
| Variant | rs2215094 |
|---|---|
| Chromosome Location | chr12:1998141-1998142 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:9)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:9 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | MAFK | chr12:1998113-1998471 | HepG2 | liver: | n/a | chr12:1998283-1998298 |
| 2 | MAFF | chr12:1998085-1998491 | HepG2 | liver: | n/a | chr12:1998282-1998300 |
| 3 | MAFK | chr12:1998004-1998662 | GM12878 | blood: | n/a | chr12:1998283-1998298 |
| 4 | MAFK | chr12:1998109-1998470 | Hela-S3 | cervix: | n/a | chr12:1998283-1998298 |
| 5 | MAFK | chr12:1998108-1998467 | H1-hESC | embryonic stem cell: | n/a | chr12:1998283-1998298 |
| 6 | MAFK | chr12:1998101-1998474 | K562 | blood: | n/a | chr12:1998283-1998298 |
| 7 | MAFF | chr12:1998102-1998475 | K562 | blood: | n/a | chr12:1998282-1998300 |
| 8 | MAFK | chr12:1998087-1998487 | IMR90 | lung: | n/a | chr12:1998283-1998298 |
| 9 | MAFK | chr12:1998098-1998481 | HepG2 | liver: | n/a | chr12:1998283-1998298 |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| CACNA2D4 | TF binding region |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs10848584 | 0.86[YRI][hapmap] |
| rs11062017 | 1.00[CEU][hapmap] |
| rs12303402 | 1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes] |
| rs12307771 | 1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs12309518 | 0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs12829901 | 1.00[CEU][hapmap] |
| rs4765647 | 0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs4766420 | 1.00[TSI][hapmap] |
| rs4766423 | 1.00[EUR][1000 genomes] |
| rs6489332 | 1.00[CEU][hapmap] |
| rs7136278 | 1.00[TSI][hapmap] |
| rs7298554 | 1.00[CEU][hapmap] |
| rs7304843 | 1.00[TSI][hapmap] |
| rs7308757 | 1.00[TSI][hapmap] |
| rs740458 | 0.81[YRI][hapmap] |
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 | nsv948480 | chr12:1776217-2284333 | Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 39 gene(s) | inside rSNPs | diseases |
| 2 | nsv832306 | chr12:1847726-2001308 | Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 17 gene(s) | inside rSNPs | diseases |
| 3 | nsv898598 | chr12:1939252-2215448 | Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 15 gene(s) | inside rSNPs | diseases |
| 4 | nsv1046388 | chr12:1964846-2034887 | ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 5 | nsv1043329 | chr12:1986238-2034887 | Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
| 6 | nsv518786 | chr12:1998044-2016322 | Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription | TF binding regionCpG islandChromatin interactive region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2215094 | PPP4R4 | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:1997400-1999400 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
