Variant report
| Variant | rs240565 |
|---|---|
| Chromosome Location | chr11:64731049-64731050 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:8)
- CpG islands (count:0)
- Chromatin interactive region (count:2)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:8 , 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 | chr11:64730811-64731123 | K562 | blood: | n/a | n/a |
| 2 | TEAD4 | chr11:64730452-64731133 | K562 | blood: | n/a | n/a |
| 3 | MAFK | chr11:64730873-64731113 | HepG2 | liver: | n/a | n/a |
| 4 | MAFK | chr11:64730890-64731054 | K562 | blood: | n/a | n/a |
| 5 | PML | chr11:64730694-64731057 | K562 | blood: | n/a | n/a |
| 6 | RCOR1 | chr11:64730619-64731096 | K562 | blood: | n/a | n/a |
| 7 | TAL1 | chr11:64730741-64731101 | K562 | blood: | n/a | chr11:64730947-64730965 |
| 8 | CEBPB | chr11:64730777-64731139 | K562 | blood: | n/a | n/a |
| No data |
(count:2 , 50 per page) page:
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| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| C11orf85 | TF binding region |
| ENSG00000168070 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs11231913 | 0.90[AMR][1000 genomes];0.87[ASN][1000 genomes] |
| rs240567 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs240571 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs240572 | 0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs2518909 | 0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs2670908 | 0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
| rs35131180 | 0.81[EUR][1000 genomes] |
| rs470511 | 0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes] |
| rs519796 | 0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs594392 | 0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs610130 | 0.83[EUR][1000 genomes];0.90[ASN][1000 genomes] |
| rs675090 | 0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes] |
| rs688749 | 0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:3 , 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 | nsv526181 | chr11:64638041-65257329 | Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 1539 gene(s) | inside rSNPs | diseases |
| 2 | nsv555208 | chr11:64645119-64771179 | Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 1029 gene(s) | inside rSNPs | diseases |
| 3 | nsv976460 | chr11:64727780-64743097 | Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats | TF binding regionCpG islandChromatin interactive region | 7 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:1)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs240565 | SPDYC | cis | Whole Blood | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr11:64728600-64736400 | Weak transcription | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast |
| 2 | chr11:64730200-64738400 | Weak transcription | Stomach Mucosa | stomach |
