Variant report

Variant	rs11936580
Chromosome Location	chr4:100955687-100955688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1044044	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10516458	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097679	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11097680	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11097681	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097682	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097683	0.89[ASN][1000 genomes]
rs11097685	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097686	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11723286	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11736218	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11736750	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11931053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11931551	0.92[ASN][1000 genomes]
rs11932783	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11935458	0.81[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs11935615	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11936309	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11937848	0.80[ASN][1000 genomes]
rs11937985	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11938952	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11939538	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11941520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941799	0.81[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs11942532	0.87[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11944405	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11944656	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11945303	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11947295	0.82[CEU][hapmap];0.84[ASN][1000 genomes]
rs11947412	0.81[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1365492	0.81[LWK][hapmap]
rs17029573	0.81[CHB][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs17029662	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17029673	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17029724	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1896166	0.81[LWK][hapmap]
rs2017707	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2070738	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2081626	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2081627	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276939	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2298735	0.86[LWK][hapmap]
rs2866179	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34453741	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs36109329	0.80[ASN][1000 genomes]
rs3733463	0.81[GIH][hapmap];0.92[JPT][hapmap]
rs3737484	0.82[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3775512	0.84[JPT][hapmap]
rs4320141	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4343735	0.81[ASN][1000 genomes]
rs4492010	0.80[ASN][1000 genomes]
rs4536938	0.84[ASN][1000 genomes]
rs5015717	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55726736	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55797991	0.83[ASN][1000 genomes]
rs55888547	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56007968	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56140620	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56159765	0.80[ASN][1000 genomes]
rs56311063	0.80[ASN][1000 genomes]
rs57315614	0.80[ASN][1000 genomes]
rs57322716	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58304154	0.84[ASN][1000 genomes]
rs58385517	0.80[ASN][1000 genomes]
rs60070547	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61191235	0.84[ASN][1000 genomes]
rs61203457	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61351569	0.80[ASN][1000 genomes]
rs62305038	0.84[ASN][1000 genomes]
rs62306101	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6532834	0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6532837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532839	0.93[ASN][1000 genomes]
rs6532840	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532841	0.80[ASN][1000 genomes]
rs6532842	0.80[ASN][1000 genomes]
rs66903712	0.80[ASN][1000 genomes]
rs67594720	0.80[ASN][1000 genomes]
rs6813794	0.80[ASN][1000 genomes]
rs6814140	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6816635	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6824513	0.95[ASN][1000 genomes]
rs6825579	0.80[ASN][1000 genomes]
rs6829912	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6830286	0.80[ASN][1000 genomes]
rs6831193	0.92[ASN][1000 genomes]
rs6832726	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6838495	0.93[ASN][1000 genomes]
rs6842840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6843247	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6848337	0.81[LWK][hapmap]
rs6848666	0.81[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs72686215	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732386	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7340772	0.80[ASN][1000 genomes]
rs7340886	0.80[ASN][1000 genomes]
rs73832925	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7660185	0.95[ASN][1000 genomes]
rs7660479	0.80[ASN][1000 genomes]
rs7662195	0.80[ASN][1000 genomes]
rs7665301	0.80[ASN][1000 genomes]
rs7666156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7668076	0.80[ASN][1000 genomes]
rs7676564	0.81[LWK][hapmap]
rs7676597	0.80[ASN][1000 genomes]
rs7686428	0.83[LWK][hapmap]
rs7686565	0.92[JPT][hapmap]
rs7687287	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs890486	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs919132	0.81[LWK][hapmap]
rs919133	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000173	chr4:100928002-100964404	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv427689	chr4:100931741-101216531	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11936580	MAPKSP1	cis	parietal	SCAN
rs11936580	H2AFZ	cis	cerebellum	SCAN
rs11936580	MAPKSP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100955200-100957000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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