Variant report
| Variant | rs354188 |
|---|---|
| Chromosome Location | chr2:54938031-54938032 |
| allele | C/T |
| 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 | chr2:54936799..54938418-chr2:54939824..54941892,2 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:23)
| rs_ID | r2[population] |
|---|---|
| rs1027950 | 0.93[ASN][1000 genomes] |
| rs12611806 | 0.91[ASN][1000 genomes] |
| rs12612665 | 0.89[ASN][1000 genomes] |
| rs12622340 | 0.93[ASN][1000 genomes] |
| rs1510612 | 0.92[ASN][1000 genomes] |
| rs17046153 | 0.90[ASN][1000 genomes] |
| rs2007020 | 0.89[ASN][1000 genomes] |
| rs241662 | 0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes] |
| rs2567837 | 0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2666036 | 0.83[AFR][1000 genomes] |
| rs354191 | 0.85[AFR][1000 genomes] |
| rs354193 | 0.96[AFR][1000 genomes] |
| rs354215 | 0.85[EUR][1000 genomes];0.96[ASN][1000 genomes] |
| rs354239 | 0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs354241 | 0.81[AMR][1000 genomes];0.90[EUR][1000 genomes] |
| rs354242 | 0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes] |
| rs4671966 | 0.80[ASN][1000 genomes] |
| rs4671968 | 0.93[ASN][1000 genomes] |
| rs56898160 | 0.92[ASN][1000 genomes] |
| rs6738725 | 0.91[ASN][1000 genomes] |
| rs72618665 | 0.90[ASN][1000 genomes] |
| rs72618667 | 0.93[ASN][1000 genomes] |
| rs72618668 | 0.92[ASN][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 | esv33638 | chr2:54765256-55109455 | Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 29 gene(s) | inside rSNPs | diseases |
| 2 | nsv582024 | chr2:54894649-54999712 | Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 14 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs354188 | EML6 | cis | Esophagus Muscularis | GTEx |
| rs354188 | EML6 | cis | Artery Tibial | GTEx |
| rs354188 | SPTBN1 | Cis_1M | lymphoblastoid | RTeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:54937200-54939200 | Weak transcription | Foreskin Keratinocyte Primary Cells skin02 | Skin |
