Variant report
| Variant | rs532141 |
|---|---|
| Chromosome Location | chr1:170139508-170139509 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:2)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:2 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | CEBPB | chr1:170139313-170139599 | Hela-S3 | cervix: | n/a | chr1:170139436-170139447 |
| 2 | CEBPB | chr1:170139393-170139576 | A549 | lung: | n/a | chr1:170139436-170139447 |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000233985 | TF binding region |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs10800496 | 0.81[CEU][hapmap] |
| rs10800501 | 0.80[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs1411464 | 0.80[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs471155 | 0.81[ASN][1000 genomes] |
| rs471569 | 0.83[ASN][1000 genomes] |
| rs482571 | 0.86[AMR][1000 genomes];0.99[ASN][1000 genomes] |
| rs495524 | 0.80[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs514257 | 0.80[AMR][1000 genomes];0.86[ASN][1000 genomes] |
| rs550297 | 0.91[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes] |
| rs551042 | 0.80[AMR][1000 genomes];0.87[ASN][1000 genomes] |
| rs575119 | 0.80[JPT][hapmap];0.87[MEX][hapmap] |
| rs576152 | 0.80[JPT][hapmap] |
| rs579438 | 0.80[JPT][hapmap];0.83[ASN][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 | nsv1014033 | chr1:169968488-170453021 | Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 18 gene(s) | inside rSNPs | diseases |
| 2 | nsv535200 | chr1:169968488-170453021 | Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 18 gene(s) | inside rSNPs | diseases |
| 3 | nsv999310 | chr1:170065943-170223350 | Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA | 8 gene(s) | inside rSNPs | diseases |
| 4 | nsv3454 | chr1:170134880-170149447 | Weak transcription Enhancers Active TSS Flanking Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 1 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:3)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs532141 | BRP44 | cis | parietal | SCAN |
| rs532141 | BLZF1 | cis | cerebellum | SCAN |
| rs532141 | DPT | cis | parietal | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:170132400-170140200 | Weak transcription | Right Ventricle | heart |
| 2 | chr1:170132800-170140600 | Weak transcription | Fetal Heart | heart |
