Variant report
| Variant | rs12998926 |
|---|---|
| Chromosome Location | chr2:114546660-114546661 |
| 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:26)
| rs_ID | r2[population] |
|---|---|
| rs10199515 | 0.81[CEU][hapmap] |
| rs1062074 | 0.80[CEU][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes] |
| rs12329244 | 0.81[CEU][hapmap] |
| rs12711787 | 0.81[CEU][hapmap] |
| rs13401587 | 0.81[CEU][hapmap] |
| rs13409879 | 1.00[AMR][1000 genomes] |
| rs13410586 | 0.81[CEU][hapmap] |
| rs13416738 | 1.00[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs13424899 | 0.81[CEU][hapmap] |
| rs17048299 | 0.81[CEU][hapmap] |
| rs17048506 | 0.81[CEU][hapmap] |
| rs17633451 | 0.81[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes] |
| rs28392566 | 0.86[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs34004564 | 1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs34222823 | 1.00[ASN][1000 genomes] |
| rs35049717 | 0.93[AMR][1000 genomes] |
| rs35192494 | 1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs55878739 | 1.00[ASN][1000 genomes] |
| rs56316177 | 0.92[AMR][1000 genomes] |
| rs72833665 | 1.00[ASN][1000 genomes] |
| rs72835446 | 1.00[ASN][1000 genomes] |
| rs72835471 | 1.00[ASN][1000 genomes] |
| rs72835491 | 1.00[ASN][1000 genomes] |
| rs72835497 | 1.00[ASN][1000 genomes] |
| rs72835498 | 1.00[ASN][1000 genomes] |
| rs998151 | 1.00[AMR][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 | nsv1009509 | chr2:114432965-114557306 | Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
| 2 | nsv535896 | chr2:114432965-114557306 | Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 16 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12998926 | RPL23AP7 | cis | multi-tissue | Pritchard |
| rs12998926 | CHCHD5 | cis | cerebellum | SCAN |
| rs12998926 | RABL2A | cis | Skin Sun Exposed Lower leg | GTEx |
| rs12998926 | SLC35F5 | cis | parietal | SCAN |
| rs12998926 | SLC35F5 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:114543400-114549000 | Weak transcription | HSMM | muscle |
