Variant report
| Variant | rs4388958 |
|---|---|
| Chromosome Location | chr12:43038338-43038339 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:6)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:6 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | EP300 | chr12:43037975-43038416 | SK-N-SH_RA | brain: | n/a | n/a |
| 2 | GATA3 | chr12:43037705-43038361 | SK-N-SH | brain: | n/a | chr12:43038156-43038172 chr12:43038158-43038165 chr12:43038155-43038172 |
| 3 | GATA3 | chr12:43037601-43038380 | SK-N-SH | brain: | n/a | chr12:43038156-43038172 chr12:43038158-43038165 chr12:43038155-43038172 |
| 4 | GATA2 | chr12:43037742-43038405 | SH-SY5Y | brain: | n/a | chr12:43038156-43038172 chr12:43038158-43038165 chr12:43038155-43038172 |
| 5 | EP300 | chr12:43037611-43038506 | SK-N-SH | brain: | n/a | n/a |
| 6 | EP300 | chr12:43037971-43038383 | SK-N-SH_RA | brain: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000257164 | TF binding region |
rSNPs within LD-proxies of this variant (count:14)
| rs_ID | r2[population] |
|---|---|
| rs10748332 | 1.00[AMR][1000 genomes] |
| rs2406859 | 1.00[AMR][1000 genomes] |
| rs4284452 | 1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes] |
| rs4338582 | 1.00[AMR][1000 genomes] |
| rs4768429 | 0.93[LWK][hapmap];0.87[MKK][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes] |
| rs4768434 | 0.91[YRI][hapmap] |
| rs6582407 | 1.00[AMR][1000 genomes] |
| rs6582408 | 1.00[AMR][1000 genomes] |
| rs7302424 | 0.94[YRI][hapmap];0.82[AFR][1000 genomes] |
| rs7308632 | 0.85[AFR][1000 genomes] |
| rs7313926 | 0.93[YRI][hapmap];0.82[AFR][1000 genomes] |
| rs7955138 | 1.00[AMR][1000 genomes] |
| rs7975135 | 1.00[AMR][1000 genomes] |
| rs9988994 | 1.00[AMR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:4 , 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 | nsv1044790 | chr12:42672255-43344184 | Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 29 gene(s) | inside rSNPs | diseases |
| 2 | nsv541483 | chr12:42672255-43344184 | Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 29 gene(s) | inside rSNPs | diseases |
| 3 | nsv832388 | chr12:42878328-43087069 | Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 12 gene(s) | inside rSNPs | diseases |
| 4 | nsv832389 | chr12:43003361-43173896 | Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNA | 11 gene(s) | inside rSNPs | diseases |
| No data |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:43035200-43045800 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |
