Variant report
| Variant | rs2046143 |
|---|---|
| Chromosome Location | chr15:79040223-79040224 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:9)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:9 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | MAX | chr15:79040208-79040502 | K562 | blood: | n/a | n/a |
| 2 | MYC | chr15:79040184-79040507 | K562 | blood: | n/a | n/a |
| 3 | ZBTB33 | chr15:79040070-79040375 | GM12878 | blood: | n/a | n/a |
| 4 | ZBTB33 | chr15:79040077-79040417 | GM12878 | blood: | n/a | n/a |
| 5 | ETS1 | chr15:79040129-79040351 | GM12878 | blood: | n/a | n/a |
| 6 | ZBTB33 | chr15:79040053-79040440 | K562 | blood: | n/a | n/a |
| 7 | ZBTB33 | chr15:79040128-79040305 | HepG2 | liver: | n/a | n/a |
| 8 | ZBTB33 | chr15:79039991-79040498 | K562 | blood: | n/a | n/a |
| 9 | CHD2 | chr15:79040115-79040485 | K562 | blood: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000238166 | TF binding region |
rSNPs within LD-proxies of this variant (count:16)
| rs_ID | r2[population] |
|---|---|
| rs1045130 | 0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes] |
| rs11072800 | 0.81[ASN][1000 genomes] |
| rs11632672 | 0.81[ASN][1000 genomes] |
| rs12906835 | 0.81[ASN][1000 genomes] |
| rs1964562 | 0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2005263 | 0.86[AMR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2017295 | 0.84[AMR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2929154 | 0.83[EUR][1000 genomes] |
| rs34019568 | 0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs34816637 | 0.90[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs4887091 | 0.81[ASN][1000 genomes] |
| rs4887092 | 0.81[ASN][1000 genomes] |
| rs59414039 | 0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7182567 | 0.81[ASN][1000 genomes] |
| rs7182694 | 0.81[ASN][1000 genomes] |
| rs7182993 | 0.81[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 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 | nsv917303 | chr15:78491050-79205255 | Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 122 gene(s) | inside rSNPs | diseases |
| 2 | nsv974606 | chr15:78996783-79048337 | Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 3 | nsv904431 | chr15:79006442-79155088 | Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 4 | esv3310945 | chr15:79036897-79041395 | Weak transcription Enhancers | TF binding regionCpG island | 1 gene(s) | inside rSNPs | diseases |
| 5 | esv3310944 | chr15:79037922-79040770 | Weak transcription Enhancers | TF binding region | 1 gene(s) | inside rSNPs | diseases |
| 6 | esv3310946 | chr15:79037922-79040770 | Weak transcription Enhancers | TF binding region | 1 gene(s) | inside rSNPs | diseases |
| 7 | esv3378980 | chr15:79038147-79040545 | Weak transcription Enhancers | TF binding region | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs2046143 | CHRNA3 | cis | Muscle Skeletal | GTEx |
| rs2046143 | CHRNA5 | cis | Muscle Skeletal | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr15:79033000-79045000 | Weak transcription | iPS DF 19.11 Cell Line | embryonic stem cell |
| 2 | chr15:79033400-79040400 | Weak transcription | iPS DF 6.9 Cell Line | embryonic stem cell |
