Variant report
| Variant | rs354243 |
|---|---|
| Chromosome Location | chr2:54947282-54947283 |
| allele | A/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | STAT3 | chr2:54947192-54947452 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
(count:2 , 50 per page) page:
1
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| EML6 | TF binding region |
| ENSG00000214595 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:27)
| rs_ID | r2[population] |
|---|---|
| rs10191922 | 0.84[ASN][1000 genomes] |
| rs168503 | 0.85[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs168506 | 0.85[ASN][1000 genomes] |
| rs168507 | 0.84[EUR][1000 genomes] |
| rs168508 | 0.88[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs17416806 | 0.88[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs181348 | 0.85[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs1821138 | 0.89[EUR][1000 genomes];0.97[ASN][1000 genomes] |
| rs187124 | 0.86[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs191628 | 0.86[EUR][1000 genomes];0.85[ASN][1000 genomes] |
| rs2567835 | 0.82[EUR][1000 genomes];0.81[ASN][1000 genomes] |
| rs2971889 | 0.91[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs354187 | 0.88[ASN][1000 genomes] |
| rs354195 | 0.82[EUR][1000 genomes] |
| rs354199 | 0.81[EUR][1000 genomes] |
| rs354209 | 0.86[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs354213 | 0.85[ASN][1000 genomes] |
| rs354214 | 0.86[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs354223 | 0.80[ASN][1000 genomes] |
| rs354226 | 0.83[ASN][1000 genomes] |
| rs354228 | 0.82[ASN][1000 genomes] |
| rs354231 | 0.82[ASN][1000 genomes] |
| rs354235 | 0.80[EUR][1000 genomes] |
| rs354236 | 0.88[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs354237 | 0.85[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs354238 | 0.85[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs58175244 | 0.82[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 | 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:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs354243 | EML6 | cis | Thyroid | GTEx |
| rs354243 | EML6 | cis | Artery Tibial | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr2:54945200-54950000 | Weak transcription | Right Atrium | heart |
