Variant report

Variant	rs56176580
Chromosome Location	chr5:41246850-41246851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs28603337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55730142	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57480514	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61115205	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6861061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6882368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73750104	0.94[AFR][1000 genomes]
rs73753120	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73753123	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73753125	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73753127	1.00[AMR][1000 genomes]
rs73753129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73753134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7706509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7728289	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7728387	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427717	chr5:41201377-41369202	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv4808	chr5:41203254-41251985	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830269	chr5:41209113-41393536	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv597879	chr5:41229277-41253853	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41239000-41248000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:41246000-41247200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr5:41246200-41247000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:41246200-41247000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:41246200-41247000	Enhancers	Stomach Mucosa	stomach
6	chr5:41246200-41247000	Enhancers	HMEC	breast
7	chr5:41246200-41247400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:41246200-41247400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr5:41246400-41247000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:41246600-41247000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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