Variant report

Variant	rs4666828
Chromosome Location	chr2:183113151-183113152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10169895	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10195097	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10204284	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10930991	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10930993	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10930995	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930996	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930997	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930998	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10930999	0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.86[ASN][1000 genomes]
rs11681840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11687469	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12473534	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12475647	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12617420	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13400054	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13420620	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1368216	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1481630	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1594615	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16822886	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16822889	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16822915	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1991766	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2195878	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2368277	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2368278	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568671	0.94[ASN][1000 genomes]
rs2568675	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2623438	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769792	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3769800	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769803	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769810	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3820963	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4666817	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666818	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666827	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57521051	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59215767	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62190507	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62190508	0.86[ASN][1000 genomes]
rs6721984	0.85[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs724851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7567112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567423	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7583421	0.91[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7606428	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9653242	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9711065	0.83[EUR][1000 genomes]
rs9784041	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][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	nsv583913	chr2:183043563-183243313	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv533782	chr2:183059730-183500040	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1008825	chr2:183067339-183228668	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv536066	chr2:183067339-183228668	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4666828	OSBPL6	cis	parietal	SCAN
rs4666828	ZNF804A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183106400-183138400	Weak transcription	Aorta	Aorta
2	chr2:183111000-183113400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:183111600-183117000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:183112200-183114200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:183112800-183113200	Enhancers	HSMMtube	muscle
6	chr2:183112800-183113800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:183112800-183114000	Enhancers	NHDF-Ad	bronchial
8	chr2:183113000-183113200	Enhancers	Right Atrium	heart
9	chr2:183113000-183113600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:183113000-183113800	Enhancers	Osteobl	bone

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