Variant report
| Variant | rs10080593 |
|---|---|
| Chromosome Location | chr6:121710386-121710387 |
| 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:21)
| rs_ID | r2[population] |
|---|---|
| rs10080648 | 0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17083560 | 0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs17647008 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1925219 | 0.98[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs57946868 | 1.00[ASN][1000 genomes] |
| rs62427606 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs67144741 | 1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6901938 | 1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6917166 | 0.87[GIH][hapmap];0.90[TSI][hapmap] |
| rs6933586 | 0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73532213 | 1.00[ASN][1000 genomes] |
| rs73532218 | 1.00[ASN][1000 genomes] |
| rs73532223 | 1.00[ASN][1000 genomes] |
| rs73532226 | 1.00[ASN][1000 genomes] |
| rs73532231 | 1.00[ASN][1000 genomes] |
| rs7738364 | 0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7749457 | 0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9490223 | 0.83[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs9490227 | 0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9490229 | 0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs9490230 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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 | nsv530527 | chr6:121298528-121789855 | ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 10 gene(s) | inside rSNPs | diseases |
| 2 | nsv830789 | chr6:121581450-121732320 | Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 3 | nsv969324 | chr6:121703134-121711366 | Enhancers Weak transcription | TF binding regionlncRNA | 2 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs10080593 | PLSCR4 | trans | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:121709600-121711000 | Enhancers | Fetal Intestine Large | intestine |
| 2 | chr6:121710000-121710800 | Enhancers | Fetal Intestine Small | intestine |
