Variant report

Variant	rs9447871
Chromosome Location	chr6:77595543-77595544
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10943391	0.98[EUR][1000 genomes]
rs12205747	0.98[EUR][1000 genomes]
rs2315639	0.95[EUR][1000 genomes]
rs323224	0.81[EUR][1000 genomes]
rs323226	0.82[EUR][1000 genomes]
rs4706637	0.96[EUR][1000 genomes]
rs4706638	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4708296	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6453951	0.82[EUR][1000 genomes]
rs6915022	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7453913	0.85[AFR][1000 genomes]
rs9341611	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9343521	0.95[EUR][1000 genomes]
rs9361163	0.97[EUR][1000 genomes]
rs9447874	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019520	chr6:77355212-77875164	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538321	chr6:77355212-77875164	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830701	chr6:77509152-77678602	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv432924	chr6:77566201-77617213	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
5	nsv886222	chr6:77577055-77734250	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
6	nsv1017082	chr6:77585310-78258237	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv603806	chr6:77587889-77787815	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1021812	chr6:77589219-77792085	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9447871	KCNQ5	cis	cerebellum	SCAN
rs9447871	MYO6	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:77591400-77596600	Weak transcription	Pancreas	Pancrea
2	chr6:77595200-77595600	Enhancers	Ovary	ovary
3	chr6:77595200-77595600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr6:77595200-77595600	Enhancers	NHDF-Ad	bronchial
5	chr6:77595200-77595800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:77595200-77596200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:77595200-77596200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:77595200-77596200	Enhancers	Osteobl	bone
9	chr6:77595200-77596800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:77595200-77597000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:77595400-77595600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:77595400-77595800	Enhancers	Aorta	Aorta
13	chr6:77595400-77595800	Enhancers	Liver	Liver
14	chr6:77595400-77595800	Enhancers	Psoas Muscle	Psoas
15	chr6:77595400-77595800	Enhancers	HMEC	breast
16	chr6:77595400-77596000	Enhancers	Adipose Nuclei	Adipose

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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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