Variant report

Variant	rs3779870
Chromosome Location	chr8:65519166-65519167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1007219	0.83[TSI][hapmap]
rs10092618	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs10105184	0.81[JPT][hapmap]
rs10808738	0.81[JPT][hapmap]
rs11986615	0.81[JPT][hapmap]
rs13282866	0.85[ASW][hapmap];0.83[TSI][hapmap]
rs16931334	0.85[ASW][hapmap]
rs28679790	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3779874	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[ASN][1000 genomes]
rs4236934	0.92[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4327886	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4395923	0.81[JPT][hapmap]
rs4452822	0.81[JPT][hapmap]
rs4465006	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4467968	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4486246	0.92[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4507804	0.80[JPT][hapmap]
rs4581093	0.81[JPT][hapmap]
rs6999999	0.81[JPT][hapmap]
rs7004685	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs7005708	0.92[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7817744	0.92[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs8192899	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8192906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9298085	0.94[EUR][1000 genomes]
rs9298087	0.81[JPT][hapmap]
rs9298088	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534001	chr8:64992196-65798776	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	esv1847262	chr8:65509694-65595527	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv611449	chr8:65511032-65543401	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3779870	CYP7B1	cis	cerebellum	SCAN
rs3779870	CYP7B1	cis	parietal	SCAN
rs3779870	CHD7	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:65499800-65553000	Weak transcription	Pancreas	Pancrea
2	chr8:65500600-65526800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:65503600-65538400	Weak transcription	Fetal Kidney	kidney
4	chr8:65505800-65521400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr8:65507400-65526400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr8:65507600-65520200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr8:65507800-65527200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr8:65510000-65525400	Weak transcription	Esophagus	oesophagus
9	chr8:65510400-65527400	Weak transcription	Adipose Nuclei	Adipose
10	chr8:65515600-65528200	Weak transcription	Brain Substantia Nigra	brain
11	chr8:65516600-65521800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr8:65516600-65522000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr8:65517200-65540000	Weak transcription	Fetal Stomach	stomach
14	chr8:65517200-65540200	Weak transcription	Fetal Lung	lung
15	chr8:65517400-65521400	Enhancers	Fetal Brain Male	brain
16	chr8:65517400-65535400	Weak transcription	Brain Anterior Caudate	brain
17	chr8:65517400-65540800	Weak transcription	Fetal Muscle Leg	muscle
18	chr8:65517600-65520400	Weak transcription	Spleen	Spleen
19	chr8:65518000-65521200	Enhancers	Fetal Brain Female	brain
20	chr8:65518200-65519400	Weak transcription	Brain Germinal Matrix	brain
21	chr8:65518200-65522400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:65518200-65522400	Weak transcription	NHEK	skin
23	chr8:65518200-65523400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:65518600-65519400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr8:65518800-65520400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr8:65519000-65525600	Weak transcription	Liver	Liver
27	chr8:65519000-65535200	Weak transcription	Ovary	ovary

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