Variant report
| Variant | rs11947451 |
|---|---|
| Chromosome Location | chr4:91258025-91258026 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs10025951 | 1.00[MEX][hapmap] |
| rs10026112 | 1.00[MEX][hapmap] |
| rs10031148 | 1.00[MEX][hapmap] |
| rs10452165 | 1.00[AMR][1000 genomes] |
| rs11933080 | 1.00[MEX][hapmap] |
| rs11937852 | 1.00[MEX][hapmap] |
| rs11941084 | 1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs11944787 | 0.86[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs11945084 | 1.00[MEX][hapmap] |
| rs11946053 | 1.00[MEX][hapmap] |
| rs11947703 | 1.00[MEX][hapmap] |
| rs17016811 | 0.84[ASW][hapmap] |
| rs17016824 | 0.84[ASW][hapmap] |
| rs35299649 | 0.86[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs6813228 | 1.00[MEX][hapmap] |
| rs6828199 | 1.00[MEX][hapmap] |
| rs6831098 | 1.00[MEX][hapmap] |
| rs6832140 | 1.00[MEX][hapmap] |
| rs6838438 | 1.00[MEX][hapmap] |
| rs6848616 | 1.00[MEX][hapmap] |
| rs7356145 | 1.00[MEX][hapmap] |
| rs7676938 | 1.00[MEX][hapmap] |
Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv470053 | chr4:90879613-91439573 | Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 2 | nsv931074 | chr4:90970476-91753697 | Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
| 3 | nsv1007826 | chr4:91049593-91438961 | Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 4 | nsv537177 | chr4:91049593-91438961 | Bivalent/Poised TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 5 | nsv999065 | chr4:91049593-91520073 | Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 6 | nsv879542 | chr4:91185206-91287204 | Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS | TF binding regionChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:13)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs11947451 | GEM | trans | lymphoblastoid | seeQTL |
| rs11947451 | ITPKB | trans | lymphoblastoid | seeQTL |
| rs11947451 | TMEM2 | trans | lymphoblastoid | seeQTL |
| rs11947451 | INPP5F | trans | lymphoblastoid | seeQTL |
| rs11947451 | TOX | trans | lymphoblastoid | seeQTL |
| rs11947451 | ARHGAP25 | trans | lymphoblastoid | seeQTL |
| rs11947451 | PTK2 | trans | lymphoblastoid | seeQTL |
| rs11947451 | BANK1 | trans | lymphoblastoid | seeQTL |
| rs11947451 | ADCY1 | trans | lymphoblastoid | seeQTL |
| rs11947451 | TREML3 | trans | lymphoblastoid | seeQTL |
| rs11947451 | CREB5 | trans | lymphoblastoid | seeQTL |
| rs11947451 | ITGAX | trans | lymphoblastoid | seeQTL |
| rs11947451 | TFEC | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr4:91244600-91270200 | Weak transcription | Pancreas | Pancrea |
| 2 | chr4:91250600-91259200 | Weak transcription | Primary hematopoietic stem cells short term culture | blood |
| 3 | chr4:91257800-91261000 | Enhancers | Primary neutrophils fromperipheralblood | blood |
| 4 | chr4:91258000-91259200 | Weak transcription | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
