Variant report
| Variant | rs12231330 |
|---|---|
| Chromosome Location | chr12:42424360-42424361 |
| 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:25)
| rs_ID | r2[population] |
|---|---|
| rs10492386 | 0.92[JPT][hapmap] |
| rs10492387 | 0.84[JPT][hapmap] |
| rs10785332 | 0.93[JPT][hapmap] |
| rs10880222 | 1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs10880263 | 0.93[JPT][hapmap] |
| rs11181281 | 0.90[EUR][1000 genomes] |
| rs11181282 | 0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes] |
| rs11181283 | 0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs11181317 | 0.93[AFR][1000 genomes];0.93[AMR][1000 genomes] |
| rs11181332 | 1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap] |
| rs11181344 | 1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap] |
| rs11181347 | 0.93[JPT][hapmap] |
| rs11181356 | 0.93[JPT][hapmap] |
| rs11181359 | 0.93[JPT][hapmap] |
| rs12579560 | 0.93[JPT][hapmap] |
| rs17090898 | 0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17091018 | 0.93[JPT][hapmap] |
| rs17494245 | 0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs3852593 | 0.81[JPT][hapmap] |
| rs3852594 | 0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap] |
| rs3864939 | 0.86[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs56085053 | 0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs61942479 | 0.86[AMR][1000 genomes] |
| rs7965273 | 0.86[JPT][hapmap] |
| rs7972986 | 1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 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 |
| 3 | nsv685 | chr12:42420723-42434827 | Enhancers Weak transcription | Chromatin interactive region | n/a | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12231330 | PRICKLE1 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:42421000-42425600 | Weak transcription | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
