Variant report

Variant	rs4465006
Chromosome Location	chr8:65525439-65525440
allele	C/T
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]
rs10081461	0.81[CEU][hapmap]
rs10092618	0.96[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs10105184	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs10808738	0.81[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs10957321	0.83[MEX][hapmap]
rs11986615	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs11998077	0.81[CEU][hapmap]
rs28679790	0.88[EUR][1000 genomes]
rs3779870	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]
rs3779874	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4236934	0.91[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs4327886	0.91[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4395923	0.81[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs4406437	0.81[CEU][hapmap]
rs4452822	0.81[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs4467968	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486246	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4581093	0.81[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs6999999	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7004685	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs7005708	0.91[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs7817744	0.96[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs8192899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192906	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9298085	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9298087	0.81[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs9298088	0.81[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][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
rs4465006	CHD7	cis	cerebellum	SCAN
rs4465006	CYP7B1	cis	cerebellum	SCAN
rs4465006	CYP7B1	cis	parietal	SCAN

Chromatin state (count:17 , 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	chr8:65507400-65526400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr8:65507800-65527200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:65510400-65527400	Weak transcription	Adipose Nuclei	Adipose
7	chr8:65515600-65528200	Weak transcription	Brain Substantia Nigra	brain
8	chr8:65517200-65540000	Weak transcription	Fetal Stomach	stomach
9	chr8:65517200-65540200	Weak transcription	Fetal Lung	lung
10	chr8:65517400-65535400	Weak transcription	Brain Anterior Caudate	brain
11	chr8:65517400-65540800	Weak transcription	Fetal Muscle Leg	muscle
12	chr8:65519000-65525600	Weak transcription	Liver	Liver
13	chr8:65519000-65535200	Weak transcription	Ovary	ovary
14	chr8:65521200-65526800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:65521400-65526600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr8:65521400-65527000	Weak transcription	Fetal Brain Male	brain
17	chr8:65523200-65542400	Weak transcription	Primary hematopoietic stem cells	blood

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