Variant report
| Variant | rs354193 |
|---|---|
| Chromosome Location | chr2:54942878-54942879 |
| allele | G/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:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr2:54942542..54944647-chr2:54947416..54949799,3 | K562 | blood: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs241662 | 0.91[AFR][1000 genomes] |
| rs2666036 | 0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs2971888 | 0.89[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs354188 | 0.96[AFR][1000 genomes] |
| rs354190 | 0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs354191 | 0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs354192 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs354196 | 0.83[EUR][1000 genomes] |
| rs354239 | 0.96[AFR][1000 genomes] |
| rs354242 | 0.96[AFR][1000 genomes] |
| rs6545438 | 0.85[ASN][1000 genomes] |
| rs66686261 | 0.88[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page:
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| 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 |
| 3 | nsv1005449 | chr2:54938633-55129503 | Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 13 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs354193 | SPTBN1 | Cis_1M | lymphoblastoid | RTeQTL |
| rs354193 | EML6 | cis | Esophagus Muscularis | GTEx |
| rs354193 | EML6 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:54942200-54943000 | Enhancers | HSMMtube | muscle |
