Variant report
| Variant | rs1840827 |
|---|---|
| Chromosome Location | chr19:52021743-52021744 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:5)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:5 , 50 per page) page:
1
| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | SETDB1 | chr19:52021213-52021908 | K562 | blood: | n/a | n/a |
| 2 | ZNF143 | chr19:52021355-52021751 | K562 | blood: | n/a | n/a |
| 3 | CBX3 | chr19:52021324-52021762 | K562 | blood: | n/a | n/a |
| 4 | TRIM28 | chr19:52021244-52021805 | K562 | blood: | n/a | n/a |
| 5 | KAP1 | chr19:52020685-52022098 | K562 | blood: | n/a | n/a |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr19:52016872..52019391-chr19:52020928..52022569,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000268777 | TF binding region |
rSNPs within LD-proxies of this variant (count:11)
| rs_ID | r2[population] |
|---|---|
| rs10221457 | 0.82[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs10853836 | 0.82[ASN][1000 genomes] |
| rs1973096 | 0.83[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs2168643 | 0.94[ASN][1000 genomes] |
| rs2864105 | 0.81[ASN][1000 genomes] |
| rs2902665 | 0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs4801874 | 0.94[ASN][1000 genomes] |
| rs6509547 | 1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6509548 | 1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs8101241 | 0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes] |
| rs8101465 | 0.82[EUR][1000 genomes];0.82[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1066308 | chr19:51680133-52103974 | Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 71 gene(s) | inside rSNPs | diseases |
| 2 | nsv544049 | chr19:51680133-52103974 | Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 71 gene(s) | inside rSNPs | diseases |
| 3 | nsv544051 | chr19:51944903-52147459 | Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 26 gene(s) | inside rSNPs | diseases |
| 4 | esv2758504 | chr19:51991896-52266700 | Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 542 gene(s) | inside rSNPs | diseases |
| 5 | esv2758767 | chr19:51991896-52604625 | Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 578 gene(s) | inside rSNPs | diseases |
| 6 | nsv469584 | chr19:52001381-52151821 | Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 25 gene(s) | inside rSNPs | diseases |
| 7 | nsv482654 | chr19:52001381-52151821 | Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 25 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:5)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1840827 | SIGLEC12 | cis | Whole Blood | GTEx |
| rs1840827 | SIGLEC12 | cis | Adipose Subcutaneous | GTEx |
| rs1840827 | SIGLEC12 | cis | Nerve Tibial | GTEx |
| rs1840827 | SIGLEC12 | cis | Artery Tibial | GTEx |
| rs1840827 | SIGLEC12 | cis | lung | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr19:52020200-52023000 | Weak transcription | Placenta | Placenta |
| 2 | chr19:52021200-52022000 | ZNF genes & repeats | Primary B cells from peripheral blood | blood |
| 3 | chr19:52021400-52022200 | ZNF genes & repeats | Primary hematopoietic stem cells short term culture | blood |
