Variant report
| Variant | rs4638844 |
|---|---|
| Chromosome Location | chr2:48654584-48654585 |
| allele | A/C |
| 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 |
|---|---|
| ENSG00000162869 | Chromatin interaction |
| ENSG00000272663 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:34)
| rs_ID | r2[population] |
|---|---|
| rs10211336 | 0.90[ASN][1000 genomes] |
| rs10454133 | 0.90[ASN][1000 genomes] |
| rs10454134 | 0.90[ASN][1000 genomes] |
| rs10454143 | 0.81[EUR][1000 genomes] |
| rs11680719 | 0.92[ASN][1000 genomes] |
| rs11683639 | 0.92[ASN][1000 genomes] |
| rs11683708 | 0.92[ASN][1000 genomes] |
| rs11689622 | 0.90[ASN][1000 genomes] |
| rs13399936 | 0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes] |
| rs13400909 | 0.92[ASN][1000 genomes] |
| rs13401749 | 0.92[ASN][1000 genomes] |
| rs13401752 | 0.92[ASN][1000 genomes] |
| rs4274640 | 0.92[ASN][1000 genomes] |
| rs4316980 | 0.91[ASN][1000 genomes] |
| rs4438532 | 0.88[ASN][1000 genomes] |
| rs4494796 | 0.91[ASN][1000 genomes] |
| rs4606978 | 0.89[ASN][1000 genomes] |
| rs55640438 | 0.88[ASN][1000 genomes] |
| rs55744465 | 0.82[EUR][1000 genomes] |
| rs55757090 | 0.87[ASN][1000 genomes] |
| rs55971719 | 0.87[ASN][1000 genomes] |
| rs56391806 | 0.82[EUR][1000 genomes] |
| rs58020097 | 0.92[ASN][1000 genomes] |
| rs58969359 | 0.92[ASN][1000 genomes] |
| rs60988618 | 0.88[ASN][1000 genomes] |
| rs62137041 | 0.89[ASN][1000 genomes] |
| rs6732196 | 0.86[ASN][1000 genomes] |
| rs72820474 | 0.90[ASN][1000 genomes] |
| rs72820479 | 0.92[ASN][1000 genomes] |
| rs72820484 | 0.93[ASN][1000 genomes] |
| rs72820492 | 0.91[ASN][1000 genomes] |
| rs72820494 | 0.92[ASN][1000 genomes] |
| rs72820499 | 0.92[ASN][1000 genomes] |
| rs7565792 | 0.85[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 | esv2762252 | chr2:48554150-48741093 | Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 20 gene(s) | inside rSNPs | diseases |
| 2 | nsv581775 | chr2:48619869-48714938 | Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 17 gene(s) | inside rSNPs | diseases |
| 3 | nsv524919 | chr2:48649738-48658779 | Enhancers Weak transcription Bivalent Enhancer | Chromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs4638844 | PPP1R21 | cis | Thyroid | GTEx |
| rs4638844 | GTF2A1L | cis | Esophagus Muscularis | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:48648000-48655000 | Weak transcription | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
| 2 | chr2:48652000-48660200 | Weak transcription | Foreskin Keratinocyte Primary Cells skin03 | Skin |
| 3 | chr2:48653600-48661200 | Weak transcription | Brain Dorsolateral Prefrontal Cortex | brain |
