Variant report

Variant	rs7652946
Chromosome Location	chr3:178704949-178704950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11711320	0.94[EUR][1000 genomes]
rs11720081	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13072825	1.00[ASN][1000 genomes]
rs13094954	1.00[ASN][1000 genomes]
rs4245914	0.94[EUR][1000 genomes]
rs4279147	0.94[EUR][1000 genomes]
rs4280676	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4377525	0.93[EUR][1000 genomes]
rs4395442	0.94[EUR][1000 genomes]
rs4417911	0.94[EUR][1000 genomes]
rs4469018	0.91[EUR][1000 genomes]
rs4501160	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4505756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522816	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4525914	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4552405	0.94[EUR][1000 genomes]
rs4579062	0.89[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs4607155	0.87[EUR][1000 genomes]
rs4626139	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632588	0.81[EUR][1000 genomes]
rs4637331	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs4955796	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955802	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955807	0.94[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4955810	0.94[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs56115013	0.94[EUR][1000 genomes]
rs56154408	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6443607	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6443611	0.95[ASN][1000 genomes]
rs6443614	0.94[EUR][1000 genomes]
rs6443617	0.80[EUR][1000 genomes]
rs6772028	0.94[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6789706	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6790867	0.94[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs6793769	0.94[EUR][1000 genomes]
rs6793893	0.89[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs6794956	0.87[EUR][1000 genomes]
rs6795238	0.87[EUR][1000 genomes]
rs6800015	0.89[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap]
rs6804084	0.94[CEU][hapmap]
rs7429173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612363	0.94[EUR][1000 genomes]
rs7633318	0.94[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap]
rs7639391	0.94[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs7643052	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7651510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7652668	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846511	0.94[EUR][1000 genomes]
rs9860318	0.91[EUR][1000 genomes]
rs9860749	0.91[EUR][1000 genomes]
rs9879637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880749	0.91[EUR][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7652946	KCNMB3	cis	parietal	SCAN
rs7652946	YEATS2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178685200-178705200	Weak transcription	HSMMtube	muscle
2	chr3:178697200-178705000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:178703200-178705800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:178704000-178705400	Strong transcription	HSMM	muscle
5	chr3:178704000-178710000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr3:178704200-178708600	ZNF genes & repeats	Liver	Liver
7	chr3:178704200-178710600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
8	chr3:178704400-178705200	Weak transcription	Aorta	Aorta
9	chr3:178704800-178705400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:178704800-178708200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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