Variant report
| Variant | rs12406787 |
|---|---|
| Chromosome Location | chr1:91062107-91062108 |
| allele | G/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:25)
| rs_ID | r2[population] |
|---|---|
| rs10922877 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12028695 | 0.82[EUR][1000 genomes] |
| rs12032305 | 0.80[EUR][1000 genomes] |
| rs12035858 | 0.86[EUR][1000 genomes] |
| rs12048611 | 0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs12411027 | 0.85[EUR][1000 genomes] |
| rs12726749 | 0.85[EUR][1000 genomes] |
| rs1336873 | 0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs1336875 | 0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs1336880 | 0.85[EUR][1000 genomes] |
| rs1361009 | 0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1361010 | 0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1415141 | 0.88[EUR][1000 genomes] |
| rs1418783 | 0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1538136 | 0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs17131073 | 0.85[EUR][1000 genomes] |
| rs1832256 | 0.85[EUR][1000 genomes] |
| rs2152729 | 0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs2152730 | 0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes] |
| rs2859908 | 0.84[EUR][1000 genomes] |
| rs35314527 | 0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes] |
| rs4306108 | 0.86[AMR][1000 genomes];0.88[ASN][1000 genomes] |
| rs519486 | 0.98[ASN][1000 genomes] |
| rs6667438 | 0.97[ASN][1000 genomes] |
| rs867434 | 0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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 | nsv870816 | chr1:91018205-91141196 | Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
| 2 | esv3323556 | chr1:91052980-91071967 | Enhancers ZNF genes & repeats Weak transcription | lncRNA | n/a | inside rSNPs | diseases |
mRNA abundance (count:4)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12406787 | DR1 | cis | cerebellum | SCAN |
| rs12406787 | C11orf34 | trans | cerebellum | SCAN |
| rs12406787 | BCAR3 | cis | parietal | SCAN |
| rs12406787 | HSP90B3P | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:91061800-91062800 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
