Variant report
| Variant | rs3990974 |
|---|---|
| Chromosome Location | chr12:42464967-42464968 |
| allele | A/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:32)
| rs_ID | r2[population] |
|---|---|
| rs11181284 | 0.80[ASN][1000 genomes] |
| rs11610892 | 0.86[AMR][1000 genomes] |
| rs11611399 | 0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs11613623 | 0.90[AMR][1000 genomes] |
| rs12313210 | 0.80[ASN][1000 genomes] |
| rs12812537 | 0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes] |
| rs12813181 | 0.90[AMR][1000 genomes] |
| rs12819127 | 0.86[AMR][1000 genomes] |
| rs12819341 | 0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes] |
| rs12823639 | 0.88[AFR][1000 genomes];0.83[AMR][1000 genomes] |
| rs12824122 | 0.83[ASN][1000 genomes] |
| rs17224170 | 0.86[AMR][1000 genomes];0.80[ASN][1000 genomes] |
| rs17224177 | 0.90[AMR][1000 genomes] |
| rs1872444 | 0.90[AMR][1000 genomes] |
| rs1920699 | 0.80[ASN][1000 genomes] |
| rs34064806 | 0.83[ASN][1000 genomes] |
| rs34329231 | 0.86[AMR][1000 genomes] |
| rs34331898 | 0.90[AMR][1000 genomes] |
| rs34619605 | 0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs34669984 | 0.90[AMR][1000 genomes] |
| rs34827386 | 0.86[AMR][1000 genomes] |
| rs34842994 | 0.86[AMR][1000 genomes] |
| rs35644702 | 0.90[AMR][1000 genomes] |
| rs35682620 | 0.90[AMR][1000 genomes] |
| rs35986152 | 0.90[AMR][1000 genomes] |
| rs4264206 | 0.88[AFR][1000 genomes];0.83[AMR][1000 genomes] |
| rs56142563 | 0.90[AMR][1000 genomes] |
| rs58891308 | 0.83[AMR][1000 genomes] |
| rs61279714 | 0.90[AMR][1000 genomes] |
| rs67788023 | 0.90[AMR][1000 genomes] |
| rs68185827 | 0.83[ASN][1000 genomes] |
| rs7960537 | 0.80[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 | nsv430505 | chr12:42297931-42720773 | Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 38 gene(s) | inside rSNPs | diseases |
| 2 | nsv832387 | chr12:42345541-42465505 | Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3990974 | PRICKLE1 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:42463800-42474600 | Weak transcription | Left Ventricle | heart |
| 2 | chr12:42464400-42465600 | Weak transcription | HSMMtube | muscle |
| 3 | chr12:42464600-42484000 | Weak transcription | HSMM | muscle |
