Variant report

Variant	rs56020009
Chromosome Location	chr6:4220867-4220868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs55645023	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55954036	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56163885	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56221707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56928713	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58316736	1.00[AMR][1000 genomes]
rs58511621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58922374	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59787593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60324766	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61258183	1.00[AMR][1000 genomes]
rs61707542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71555845	1.00[AMR][1000 genomes]
rs73717464	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717466	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717469	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717483	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717487	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73717493	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73723635	1.00[AMR][1000 genomes]
rs9504023	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4211000-4225400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:4220200-4221600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:4220400-4221400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:4220400-4221600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:4220400-4222000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:4220800-4221000	Flanking Active TSS	HSMMtube	muscle
7	chr6:4220800-4221200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr6:4220800-4221200	Enhancers	Stomach Mucosa	stomach
9	chr6:4220800-4221400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:4220800-4221400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:4220800-4221400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:4220800-4221400	Enhancers	Right Atrium	heart
13	chr6:4220800-4221400	Enhancers	NHEK	skin
14	chr6:4220800-4221400	Enhancers	NHLF	lung
15	chr6:4220800-4221600	Enhancers	Hela-S3	cervix

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