Variant report
Variant | rs1562908 |
---|---|
Chromosome Location | chr6:56857665-56857666 |
allele | A/C |
Outlinks | Ensembl   UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:3)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
No data |
No data |
(count:3 , 50 per page) page:
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No data |
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Variant related genes | Relation type |
---|---|
ENSG00000151917 | Chromatin interaction |
ENSG00000151914 | Chromatin interaction |
rs_ID | r2[population] |
---|---|
rs1007417 | 0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs1016048 | 0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes] |
rs12154043 | 0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs13193465 | 0.84[TSI][hapmap] |
rs13220575 | 0.84[TSI][hapmap] |
rs1451709 | 0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs1597694 | 0.90[AMR][1000 genomes];0.99[EUR][1000 genomes] |
rs16888222 | 0.82[JPT][hapmap] |
rs17685277 | 0.84[TSI][hapmap] |
rs17685356 | 0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs2006930 | 0.85[AMR][1000 genomes];0.99[EUR][1000 genomes] |
rs2008698 | 0.82[AMR][1000 genomes];0.95[EUR][1000 genomes] |
rs2122958 | 0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes] |
rs2167460 | 0.87[ASW][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes] |
rs2397227 | 0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes] |
rs2817573 | 0.84[TSI][hapmap] |
rs34589109 | 0.83[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs34703235 | 0.90[AMR][1000 genomes];0.99[EUR][1000 genomes] |
rs34896907 | 0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs35553446 | 0.82[AMR][1000 genomes];0.97[EUR][1000 genomes] |
rs62417384 | 0.88[AMR][1000 genomes];0.99[EUR][1000 genomes] |
rs62417410 | 0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs6901192 | 0.91[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs6901660 | 0.85[AMR][1000 genomes];0.99[EUR][1000 genomes] |
rs6901944 | 0.84[TSI][hapmap] |
rs6904172 | 0.93[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap] |
rs6915492 | 0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs6924882 | 0.93[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs6925107 | 0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs6935636 | 0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs720884 | 0.84[TSI][hapmap] |
rs720885 | 0.93[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes] |
rs7741507 | 0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs7760435 | 0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes] |
rs9296855 | 0.82[JPT][hapmap];0.81[MEX][hapmap] |
rs9296857 | 0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes] |
rs9296859 | 0.81[AMR][1000 genomes];0.84[EUR][1000 genomes] |
rs9357934 | 0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs9370550 | 0.85[CHD][hapmap] |
rs9370552 | 0.93[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs9382669 | 0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes] |
rs9382670 | 0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes] |
rs9382672 | 0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes] |
rs9382674 | 0.93[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs9382675 | 0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs9382676 | 0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes] |
rs9396240 | 0.85[CHD][hapmap] |
rs9396245 | 0.85[CHD][hapmap] |
rs9396246 | 0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs9396249 | 0.85[AMR][1000 genomes];1.00[EUR][1000 genomes] |
rs9396250 | 0.83[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes] |
rs9396253 | 0.81[AMR][1000 genomes];0.84[EUR][1000 genomes] |
rs9475758 | 0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes] |
rs9475760 | 1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes] |
rs9475763 | 0.92[CEU][hapmap];0.85[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes] |

No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | nsv491933 | chr6:56177722-57171010 | Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 51 gene(s) | inside rSNPs | diseases |
2 | nsv934026 | chr6:56382056-57184218 | Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 49 gene(s) | inside rSNPs | diseases |
3 | nsv533050 | chr6:56504480-57297586 | Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNAmiRNA target site | 44 gene(s) | inside rSNPs | diseases |
4 | nsv1021651 | chr6:56569444-56966319 | Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
5 | nsv538228 | chr6:56569444-56966319 | Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 28 gene(s) | inside rSNPs | diseases |
6 | esv3430228 | chr6:56830972-57079281 | Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 26 gene(s) | inside rSNPs | diseases |
SNP | Gene | Cis/trans | Tissue | Source |
---|---|---|---|---|
rs1562908 | BEND6 | cis | cerebellum | SCAN |
rs1562908 | BEND6 | cis | Esophagus Mucosa | GTEx |
rs1562908 | BEND6 | cis | Esophagus Muscularis | GTEx |
rs1562908 | DST | cis | cerebellum | SCAN |
rs1562908 | C6orf65 | cis | multi-tissue | Pritchard |
rs1562908 | BEND6 | cis | Artery Tibial | GTEx |
rs1562908 | BEND6 | cis | Heart Left Ventricle | GTEx |
rs1562908 | BEND6 | cis | Muscle Skeletal | GTEx |
rs1562908 | BEND6 | cis | lung | GTEx |
rs1562908 | BEND6 | cis | lymphoblastoid | seeQTL |
rs1562908 | BEND6 | cis | parietal | SCAN |
rs1562908 | BEND6 | cis | Thyroid | GTEx |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr6:56844800-56863800 | Weak transcription | Brain Inferior Temporal Lobe | brain |
2 | chr6:56846400-56865800 | Weak transcription | Brain Cingulate Gyrus | brain |
3 | chr6:56849800-56860200 | Weak transcription | Osteobl | bone |
4 | chr6:56850200-56863800 | Weak transcription | Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells | embryonic stem cell |
5 | chr6:56853400-56863800 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
6 | chr6:56856800-56858200 | Enhancers | Adipose Derived Mesenchymal Stem Cell Cultured Cells | ES cell derived |
7 | chr6:56856800-56863800 | Weak transcription | Foreskin Fibroblast Primary Cells skin01 | Skin |
8 | chr6:56856800-56863800 | Weak transcription | Brain Dorsolateral Prefrontal Cortex | brain |
9 | chr6:56857200-56858400 | Enhancers | NHDF-Ad | bronchial |
10 | chr6:56857400-56858400 | Weak transcription | A549 | lung |