Variant report
| Variant | rs12874106 |
|---|---|
| Chromosome Location | chr13:50379700-50379701 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr13:50365533..50367919-chr13:50378840..50381173,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000102753 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:22)
| rs_ID | r2[population] |
|---|---|
| rs12430539 | 0.92[EUR][1000 genomes] |
| rs12584401 | 0.92[EUR][1000 genomes] |
| rs12853861 | 0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12868235 | 0.87[EUR][1000 genomes] |
| rs12875005 | 0.85[AFR][1000 genomes] |
| rs12876223 | 0.85[AFR][1000 genomes] |
| rs12876889 | 0.85[AFR][1000 genomes] |
| rs2236354 | 0.84[EUR][1000 genomes] |
| rs34423763 | 0.85[AFR][1000 genomes] |
| rs35672544 | 0.89[EUR][1000 genomes] |
| rs4603448 | 0.92[EUR][1000 genomes] |
| rs4941657 | 0.87[EUR][1000 genomes] |
| rs4942870 | 0.92[EUR][1000 genomes] |
| rs4942879 | 0.87[EUR][1000 genomes] |
| rs71428292 | 0.85[AFR][1000 genomes] |
| rs9526607 | 0.87[EUR][1000 genomes] |
| rs9535344 | 0.89[EUR][1000 genomes] |
| rs9535345 | 0.89[EUR][1000 genomes] |
| rs9535347 | 0.92[EUR][1000 genomes] |
| rs9535352 | 0.92[EUR][1000 genomes] |
| rs9535356 | 0.85[EUR][1000 genomes] |
| rs9535365 | 0.86[EUR][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 | nsv900072 | chr13:50266109-50381016 | Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 18 gene(s) | inside rSNPs | diseases |
| 2 | nsv900073 | chr13:50286218-50381016 | Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
| 3 | nsv900074 | chr13:50317104-50381016 | Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 16 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12874106 | KPNA3 | Cis_1M | lymphoblastoid | RTeQTL |
| rs12874106 | EBPL | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr13:50378800-50379800 | Weak transcription | Fetal Adrenal Gland | Adrenal Gland |
| 2 | chr13:50379600-50385200 | Enhancers | HepG2 | liver |
