Variant report
| Variant | rs6666937 |
|---|---|
| Chromosome Location | chr1:170286843-170286844 |
| 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:19)
| rs_ID | r2[population] |
|---|---|
| rs10494485 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs10919355 | 0.82[AFR][1000 genomes];0.85[AMR][1000 genomes] |
| rs12085525 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs12085537 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs12089288 | 0.81[AFR][1000 genomes];0.85[AMR][1000 genomes] |
| rs12094851 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs16863271 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs16863272 | 0.85[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs2779706 | 1.00[MEX][hapmap] |
| rs2806492 | 1.00[MEX][hapmap] |
| rs28595176 | 0.97[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs28643534 | 0.94[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs6666779 | 0.88[AFR][1000 genomes];0.85[AMR][1000 genomes] |
| rs6667169 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs6690817 | 0.88[AFR][1000 genomes];0.85[AMR][1000 genomes] |
| rs6691470 | 0.88[AFR][1000 genomes];0.85[AMR][1000 genomes] |
| rs6700231 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs6703181 | 0.95[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs6703200 | 0.86[AFR][1000 genomes];1.00[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1014033 | chr1:169968488-170453021 | Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 18 gene(s) | inside rSNPs | diseases |
| 2 | nsv535200 | chr1:169968488-170453021 | Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 18 gene(s) | inside rSNPs | diseases |
| 3 | nsv872543 | chr1:170171083-170674903 | Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 4 | nsv533915 | chr1:170258766-170725296 | Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 14 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:22)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs6666937 | GPR3 | trans | brain | seeQTL |
| rs6666937 | LBH | trans | brain | seeQTL |
| rs6666937 | NPAS4 | trans | brain | seeQTL |
| rs6666937 | TRIB1 | trans | brain | seeQTL |
| rs6666937 | EGR2 | trans | brain | seeQTL |
| rs6666937 | RGS2 | trans | brain | seeQTL |
| rs6666937 | CCL4 | trans | brain | seeQTL |
| rs6666937 | ARC | trans | brain | seeQTL |
| rs6666937 | LAMB3 | trans | brain | seeQTL |
| rs6666937 | ADAD2 | trans | brain | seeQTL |
| rs6666937 | DUSP5 | trans | brain | seeQTL |
| rs6666937 | PDYN | trans | brain | seeQTL |
| rs6666937 | EGR1 | trans | brain | seeQTL |
| rs6666937 | SERTAD1 | trans | brain | seeQTL |
| rs6666937 | SLC2A3 | trans | brain | seeQTL |
| rs6666937 | EGR4 | trans | brain | seeQTL |
| rs6666937 | PTGS2 | trans | brain | seeQTL |
| rs6666937 | CSRNP1 | trans | brain | seeQTL |
| rs6666937 | SLC25A25 | trans | brain | seeQTL |
| rs6666937 | FOSB | trans | brain | seeQTL |
| rs6666937 | FCER2 | trans | brain | seeQTL |
| rs6666937 | DUSP2 | trans | brain | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:170282400-170287800 | Weak transcription | NHDF-Ad | bronchial |
| 2 | chr1:170285600-170287000 | Weak transcription | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
| 3 | chr1:170285600-170287200 | Weak transcription | Osteobl | bone |
| 4 | chr1:170286000-170287200 | Weak transcription | Bone Marrow Derived Cultured Mesenchymal Stem Cells | Bone marrow |
| 5 | chr1:170286000-170287400 | Weak transcription | Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells | embryonic stem cell |
