Variant report
| Variant | rs62365866 |
|---|---|
| Chromosome Location | chr5:80623588-80623589 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000247572 | Chromatin interaction |
| ENSG00000131732 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:24)
| rs_ID | r2[population] |
|---|---|
| rs10514218 | 0.81[AFR][1000 genomes];0.84[EUR][1000 genomes] |
| rs10942946 | 0.80[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11739833 | 0.83[EUR][1000 genomes] |
| rs11739834 | 0.81[AFR][1000 genomes];0.84[EUR][1000 genomes] |
| rs11740916 | 1.00[ASN][1000 genomes] |
| rs11743842 | 0.84[EUR][1000 genomes] |
| rs11743849 | 0.81[AFR][1000 genomes];0.84[EUR][1000 genomes] |
| rs11745275 | 0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11953113 | 0.80[EUR][1000 genomes] |
| rs11957137 | 0.80[EUR][1000 genomes] |
| rs12516089 | 0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12517538 | 0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12518716 | 0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12523578 | 0.82[EUR][1000 genomes] |
| rs16878594 | 0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs16878597 | 0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56067803 | 1.00[ASN][1000 genomes] |
| rs62365031 | 1.00[ASN][1000 genomes] |
| rs62365032 | 0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62365035 | 0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62365038 | 0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs62365867 | 0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs72771170 | 0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7731320 | 0.82[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1024844 | chr5:79862428-80860430 | Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 42 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:10)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs62365866 | CTC-281B15.1 | cis | Esophagus Muscularis | GTEx |
| rs62365866 | CTC-281B15.1 | cis | Nerve Tibial | GTEx |
| rs62365866 | CTC-281B15.1 | cis | Adipose Subcutaneous | GTEx |
| rs62365866 | CTC-281B15.1 | cis | Thyroid | GTEx |
| rs62365866 | CTC-281B15.1 | cis | Artery Tibial | GTEx |
| rs62365866 | CTC-281B15.1 | cis | lung | GTEx |
| rs62365866 | LOC100131067 | cis | brain | BrainEAC |
| rs62365866 | LOC100131067 | cis | intralobular white matter | BrainEAC |
| rs62365866 | CTC-281B15.1 | cis | Esophagus Mucosa | GTEx |
| rs62365866 | CTC-281B15.1 | cis | Skin Sun Exposed Lower leg | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr5:80611600-80623600 | Weak transcription | iPS-20b Cell Line | embryonic stem cell |
| 2 | chr5:80612200-80623600 | Weak transcription | ES-I3 Cell Line | embryonic stem cell |
| 3 | chr5:80622400-80632400 | Strong transcription | Liver | Liver |
