Variant report

Variant	rs875443
Chromosome Location	chr3:23566076-23566077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23563683..23566443-chr3:23573278..23576217,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10510539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129120	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706875	0.94[ASN][1000 genomes]
rs11712991	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11713090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715736	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717508	0.96[ASN][1000 genomes]
rs11718111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13323077	0.85[CEU][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.92[TSI][hapmap]
rs1391756	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498810	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1692619	0.94[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap]
rs1692621	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1692646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1692647	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1692648	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1692649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1695180	0.94[CEU][hapmap]
rs1695183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1695185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1695192	0.84[CEU][hapmap]
rs1695197	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1695203	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs17013268	0.94[CEU][hapmap];0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs17013425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17194751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874234	0.94[CEU][hapmap]
rs1874502	0.94[CEU][hapmap]
rs1874503	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs1995173	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995174	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995175	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2036044	0.94[CEU][hapmap]
rs2055307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2173057	0.94[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs2359761	0.94[CEU][hapmap]
rs28367247	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4858070	0.94[CEU][hapmap]
rs4858499	0.88[CEU][hapmap]
rs4858507	0.94[CEU][hapmap]
rs4858517	0.94[ASN][1000 genomes]
rs56034809	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58130044	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58618629	0.94[ASN][1000 genomes]
rs58718028	0.83[EUR][1000 genomes]
rs59012069	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60028742	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60137984	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62255784	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255785	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255789	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62256025	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62256972	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62256973	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62256975	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62256976	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62256977	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62256982	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs62256990	0.96[ASN][1000 genomes]
rs62256991	0.94[ASN][1000 genomes]
rs6550760	0.92[CEU][hapmap]
rs66864142	0.92[ASN][1000 genomes]
rs6774454	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6780388	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs6801824	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs6807859	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68093882	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73139773	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73140507	0.93[ASN][1000 genomes]
rs73140523	0.97[ASN][1000 genomes]
rs73140544	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7430428	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7614195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7636705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643705	0.94[CEU][hapmap]
rs7646541	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs778463	0.94[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs778465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778473	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs778483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778492	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs778497	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs778502	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs778511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778512	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778515	0.85[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs778516	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778520	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs778522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778524	0.85[CEU][hapmap]
rs778525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801277	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs809640	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931609	0.94[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs9631541	0.85[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs9757330	0.94[CEU][hapmap]
rs9758590	0.94[CEU][hapmap]
rs9862734	0.85[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.92[TSI][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	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs875443	ZNF385D	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23550800-23572000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:23550800-23598600	Weak transcription	HSMMtube	muscle
3	chr3:23553000-23589600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:23560200-23567200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:23560600-23567200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:23561600-23570800	Weak transcription	GM12878-XiMat	blood
7	chr3:23565200-23572200	Weak transcription	Primary B cells from peripheral blood	blood

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