Variant report
| Variant | rs16847771 |
|---|---|
| Chromosome Location | chr1:227602770-227602771 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:227597318..227599124-chr1:227602083..227603955,3 | K562 | blood: | |
| 2 | chr1:227601371..227603853-chr1:227605380..227608209,2 | K562 | blood: | |
| 3 | chr1:227598952..227600473-chr1:227602065..227604996,2 | K562 | blood: | |
| 4 | chr1:227583675..227585639-chr1:227602382..227605024,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000232864 | Chromatin interaction |
| ENSG00000234277 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:15)
| rs_ID | r2[population] |
|---|---|
| rs11799772 | 0.85[AMR][1000 genomes] |
| rs11802810 | 0.85[AMR][1000 genomes] |
| rs11808370 | 0.85[AMR][1000 genomes] |
| rs11811413 | 1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes] |
| rs4495663 | 1.00[MEX][hapmap];0.85[AMR][1000 genomes] |
| rs56232962 | 1.00[EUR][1000 genomes] |
| rs56897207 | 0.85[AMR][1000 genomes] |
| rs6688385 | 0.85[AMR][1000 genomes] |
| rs6696713 | 1.00[MEX][hapmap];0.85[AMR][1000 genomes] |
| rs6699740 | 0.85[AMR][1000 genomes] |
| rs73102326 | 0.85[AMR][1000 genomes] |
| rs73102327 | 0.85[AMR][1000 genomes] |
| rs73102341 | 0.85[AMR][1000 genomes] |
| rs73102365 | 0.85[AMR][1000 genomes] |
| rs73102377 | 0.85[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 | 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:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs16847771 | PSEN2 | cis | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:227599200-227603200 | Weak transcription | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
| 2 | chr1:227602600-227604000 | Enhancers | Primary hematopoietic stem cells G-CSF-mobilized Male | -- |
