Variant report
| Variant | rs17131472 |
|---|---|
| Chromosome Location | chr1:91962967-91962968 |
| allele | C/T |
| 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:7)
| rs_ID | r2[population] |
|---|---|
| rs10874743 | 0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes] |
| rs1508589 | 1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs2135604 | 0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6668360 | 0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs7522550 | 0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes] |
| rs7542090 | 0.83[CHB][hapmap];0.88[ASN][1000 genomes] |
| rs7544732 | 0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv949516 | chr1:91644418-92109261 | Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
| 2 | nsv1009560 | chr1:91897078-92270781 | Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 14 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:51)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs17131472 | MRC2 | trans | brain | seeQTL |
| rs17131472 | KLK1 | trans | brain | seeQTL |
| rs17131472 | LAMA4 | trans | brain | seeQTL |
| rs17131472 | SCGB1D2 | trans | brain | seeQTL |
| rs17131472 | OLFML2A | trans | brain | seeQTL |
| rs17131472 | PKP2 | trans | brain | seeQTL |
| rs17131472 | ABI3BP | trans | brain | seeQTL |
| rs17131472 | COCH | trans | brain | seeQTL |
| rs17131472 | TNFRSF11B | trans | brain | seeQTL |
| rs17131472 | UPK1B | trans | brain | seeQTL |
| rs17131472 | GJB2 | trans | brain | seeQTL |
| rs17131472 | SLPI | trans | brain | seeQTL |
| rs17131472 | SFRP2 | trans | brain | seeQTL |
| rs17131472 | FGL2 | trans | brain | seeQTL |
| rs17131472 | NHEDC2 | trans | brain | seeQTL |
| rs17131472 | PRELP | trans | brain | seeQTL |
| rs17131472 | ENPP6 | trans | brain | seeQTL |
| rs17131472 | ANXA2 | trans | brain | seeQTL |
| rs17131472 | DEFB1 | trans | brain | seeQTL |
| rs17131472 | PRRX2 | trans | brain | seeQTL |
| rs17131472 | PDGFD | trans | brain | seeQTL |
| rs17131472 | SLC47A1 | trans | brain | seeQTL |
| rs17131472 | TMEM99 | trans | brain | seeQTL |
| rs17131472 | MXRA8 | trans | brain | seeQTL |
| rs17131472 | PTGDR | trans | brain | seeQTL |
| rs17131472 | CRABP1 | trans | brain | seeQTL |
| rs17131472 | CLIC6 | trans | brain | seeQTL |
| rs17131472 | MLPH | trans | brain | seeQTL |
| rs17131472 | GAS1 | trans | brain | seeQTL |
| rs17131472 | OMD | trans | brain | seeQTL |
| rs17131472 | TMEM100 | trans | brain | seeQTL |
| rs17131472 | BMP5 | trans | brain | seeQTL |
| rs17131472 | COL6A2 | trans | brain | seeQTL |
| rs17131472 | C19orf33 | trans | brain | seeQTL |
| rs17131472 | FXYD5 | trans | brain | seeQTL |
| rs17131472 | ECEL1 | trans | brain | seeQTL |
| rs17131472 | SLC26A2 | trans | brain | seeQTL |
| rs17131472 | SCGB2A2 | trans | brain | seeQTL |
| rs17131472 | SERPIND1 | trans | brain | seeQTL |
| rs17131472 | PHLDB2 | trans | brain | seeQTL |
| rs17131472 | PDGFRL | trans | brain | seeQTL |
| rs17131472 | LRRN4CL | trans | brain | seeQTL |
| rs17131472 | KLF2 | trans | brain | seeQTL |
| rs17131472 | CYP4B1 | trans | brain | seeQTL |
| rs17131472 | ITGBL1 | trans | brain | seeQTL |
| rs17131472 | TMEM30B | trans | brain | seeQTL |
| rs17131472 | KLF5 | trans | brain | seeQTL |
| rs17131472 | C2orf40 | trans | brain | seeQTL |
| rs17131472 | JAM2 | trans | brain | seeQTL |
| rs17131472 | CPXM2 | trans | brain | seeQTL |
| rs17131472 | FMOD | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:91956600-91965800 | Weak transcription | Mesenchymal Stem Cell Derived Adipocyte Cultured Cells | ES cell derived |
| 2 | chr1:91962000-91965600 | Weak transcription | H9 Derived Neuron Cultured Cells | ES cell derived |
