Variant report
| Variant | rs3000790 |
|---|---|
| Chromosome Location | chr1:227599079-227599080 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:7)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:7 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | STAT3 | chr1:227598765-227599119 | MCF10A-Er-Src | breast: | n/a | n/a |
| 2 | CEBPB | chr1:227598785-227599091 | IMR90 | lung: | n/a | n/a |
| 3 | STAT3 | chr1:227598791-227599143 | MCF10A-Er-Src | breast: | n/a | n/a |
| 4 | RCOR1 | chr1:227598769-227599109 | K562 | blood: | n/a | n/a |
| 5 | FOS | chr1:227598799-227599117 | MCF10A-Er-Src | breast: | n/a | n/a |
| 6 | STAT3 | chr1:227598797-227599122 | MCF10A-Er-Src | breast: | n/a | n/a |
| 7 | STAT3 | chr1:227598797-227599123 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:227596112..227598714-chr1:227598810..227600667,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000232864 | TF binding region |
| ENSG00000234277 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:5)
| rs_ID | r2[population] |
|---|---|
| rs3000780 | 0.91[CHB][hapmap] |
| rs3000801 | 0.86[CHB][hapmap];0.82[CHD][hapmap] |
| rs3000803 | 0.86[CHB][hapmap];0.85[CHD][hapmap] |
| rs3014289 | 0.80[ASN][1000 genomes] |
| rs3014294 | 0.90[CHB][hapmap] |
Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv534002 | chr1:227315186-228047108 | Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 54 gene(s) | inside rSNPs | diseases |
| 2 | nsv1001353 | chr1:227474785-227660691 | Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 19 gene(s) | inside rSNPs | diseases |
| 3 | nsv1003278 | chr1:227563126-227678464 | Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 10 gene(s) | inside rSNPs | diseases |
| 4 | nsv873243 | chr1:227581017-227617519 | Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNA | 6 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs3000790 | TRIM17 | cis | cerebellum | SCAN |
| rs3000790 | ZNF678 | cis | cerebellum | SCAN |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:227598200-227599200 | Enhancers | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
