Variant report
| Variant | rs12665480 |
|---|---|
| Chromosome Location | chr6:27029809-27029810 |
| allele | A/G |
| Outlinks | Ensembl UCSC |
- TF binding region (count:1)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:1 , 50 per page) page:
1
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr6:26121476..26124237-chr6:27029296..27031595,2 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| VN1R13P | TF binding region |
| ENSG00000180596 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs11967487 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11968996 | 1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs11969113 | 0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12661273 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs12663161 | 0.86[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs56824660 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs58678580 | 0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs6921711 | 0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs73384370 | 0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes] |
| rs73384380 | 0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes] |
| rs73399191 | 0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73399199 | 0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73401122 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73401133 | 0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73401144 | 1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7741445 | 0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7765489 | 0.86[EUR][1000 genomes];0.96[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv948921 | chr6:26556890-27443957 | Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 472 gene(s) | inside rSNPs | diseases |
| 2 | esv2758038 | chr6:26695219-27095714 | Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 67 gene(s) | inside rSNPs | diseases |
| 3 | esv2759410 | chr6:26695219-27095714 | Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 67 gene(s) | inside rSNPs | diseases |
| 4 | nsv1029124 | chr6:26825468-27109774 | Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 244 gene(s) | inside rSNPs | diseases |
| 5 | nsv471636 | chr6:26841084-27038175 | Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 27 gene(s) | inside rSNPs | diseases |
| 6 | nsv830616 | chr6:26859097-27030476 | ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 25 gene(s) | inside rSNPs | diseases |
| 7 | nsv469625 | chr6:26893739-27038175 | Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 26 gene(s) | inside rSNPs | diseases |
| 8 | nsv482537 | chr6:26893739-27038175 | Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription | TF binding regionCpG islandChromatin interactive regionlncRNA | 26 gene(s) | inside rSNPs | diseases |
| 9 | nsv965631 | chr6:27007405-27037069 | Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 7 gene(s) | inside rSNPs | diseases |
| 10 | esv3369822 | chr6:27007480-27037513 | Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:11)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12665480 | GUSBP2 | cis | lung | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Thyroid | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Whole Blood | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Adipose Subcutaneous | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Esophagus Mucosa | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Artery Tibial | GTEx |
| rs12665480 | RP11-457M11.5 | cis | lung | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Nerve Tibial | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Muscle Skeletal | GTEx |
| rs12665480 | RP11-457M11.5 | cis | Stomach | GTEx |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr6:27028000-27034200 | Weak transcription | HUES6 Cell Line | embryonic stem cell |
| 2 | chr6:27028800-27032800 | Weak transcription | K562 | blood |
| 3 | chr6:27029600-27034000 | Weak transcription | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
| 4 | chr6:27029600-27034200 | Weak transcription | HepG2 | liver |
| 5 | chr6:27029600-27034400 | Weak transcription | GM12878-XiMat | blood |
