Variant report

Variant	rs2454686
Chromosome Location	chr3:98661092-98661093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 194 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:189)

rs_ID	r²[population]
rs1062196	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs1123293	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054181	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12107050	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12490832	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1383902	0.81[EUR][1000 genomes]
rs1383904	0.81[EUR][1000 genomes]
rs1383905	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1383910	0.83[ASN][1000 genomes]
rs14310	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1440150	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1440151	0.83[JPT][hapmap]
rs1440153	0.92[GIH][hapmap]
rs1481634	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1481635	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1481636	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1481637	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1580376	0.81[EUR][1000 genomes]
rs1585984	0.81[EUR][1000 genomes]
rs1585985	0.81[EUR][1000 genomes]
rs17270986	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs1837500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1866677	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1866678	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1875086	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1905015	0.81[EUR][1000 genomes]
rs1905016	0.81[EUR][1000 genomes]
rs1905017	0.81[EUR][1000 genomes]
rs1905018	0.81[EUR][1000 genomes]
rs1905019	0.81[EUR][1000 genomes]
rs1905020	0.81[EUR][1000 genomes]
rs1905021	0.81[EUR][1000 genomes]
rs1967009	0.94[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028393	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062059	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs2119187	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs2119188	0.82[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2128050	0.81[EUR][1000 genomes]
rs2128051	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2128054	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246861	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249740	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2262597	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2262598	0.81[EUR][1000 genomes]
rs2262599	0.81[EUR][1000 genomes]
rs2262603	0.81[EUR][1000 genomes]
rs2290067	0.82[ASW][hapmap];0.87[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs2334230	0.92[GIH][hapmap];0.86[JPT][hapmap]
rs2439215	0.81[ASN][1000 genomes]
rs2439218	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439220	0.85[ASN][1000 genomes]
rs2439222	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439223	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439224	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2439225	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439226	0.89[ASN][1000 genomes]
rs2439228	0.80[EUR][1000 genomes]
rs2439231	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs2439236	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439237	0.83[CHB][hapmap]
rs2449001	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2449011	0.81[EUR][1000 genomes]
rs2449012	0.81[EUR][1000 genomes]
rs2449014	0.81[EUR][1000 genomes]
rs2449016	0.81[EUR][1000 genomes]
rs2449017	0.81[EUR][1000 genomes]
rs2449019	0.81[EUR][1000 genomes]
rs2449020	0.81[EUR][1000 genomes]
rs2449021	0.81[EUR][1000 genomes]
rs2449022	0.81[EUR][1000 genomes]
rs2449023	0.81[EUR][1000 genomes]
rs2449026	0.81[EUR][1000 genomes]
rs2449027	0.81[EUR][1000 genomes]
rs2449028	0.81[EUR][1000 genomes]
rs2449029	0.81[EUR][1000 genomes]
rs2449030	0.81[EUR][1000 genomes]
rs2449031	0.81[EUR][1000 genomes]
rs2449034	0.81[EUR][1000 genomes]
rs2449035	0.81[EUR][1000 genomes]
rs2449036	0.81[EUR][1000 genomes]
rs2449038	0.80[EUR][1000 genomes]
rs2449039	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2449040	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2449041	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2449042	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2449063	1.00[JPT][hapmap]
rs2454673	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs2454677	0.81[ASN][1000 genomes]
rs2454680	0.87[ASN][1000 genomes]
rs2454682	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2454684	0.85[ASN][1000 genomes]
rs2454685	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2454691	0.90[ASN][1000 genomes]
rs2462234	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2462235	1.00[JPT][hapmap]
rs2462237	1.00[JPT][hapmap]
rs2462239	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2470750	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2470751	0.81[EUR][1000 genomes]
rs2470752	0.81[EUR][1000 genomes]
rs2470753	0.81[EUR][1000 genomes]
rs2470754	0.80[EUR][1000 genomes]
rs2470756	0.81[EUR][1000 genomes]
rs2470758	0.81[EUR][1000 genomes]
rs2470759	1.00[JPT][hapmap]
rs2470761	1.00[JPT][hapmap]
rs2470769	0.81[EUR][1000 genomes]
rs2470776	0.81[EUR][1000 genomes]
rs2470815	0.81[EUR][1000 genomes]
rs2470816	0.81[EUR][1000 genomes]
rs2470818	0.81[EUR][1000 genomes]
rs2470821	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470822	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470823	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470824	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470825	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470826	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470829	0.81[EUR][1000 genomes]
rs2470830	0.81[EUR][1000 genomes]
rs2470831	0.81[EUR][1000 genomes]
rs2470833	0.81[EUR][1000 genomes]
rs2470836	0.81[EUR][1000 genomes]
rs2470840	0.81[EUR][1000 genomes]
rs2470842	0.81[EUR][1000 genomes]
rs2470843	0.81[EUR][1000 genomes]
rs2470844	0.81[EUR][1000 genomes]
rs2470845	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2470846	0.81[EUR][1000 genomes]
rs2470851	0.97[ASN][1000 genomes]
rs2470854	0.83[ASN][1000 genomes]
rs2470857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs2470859	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470860	0.85[ASN][1000 genomes]
rs2470861	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs2470867	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs2470869	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs2470876	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470879	0.80[EUR][1000 genomes]
rs2470881	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2470885	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs28608112	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2929489	0.81[EUR][1000 genomes]
rs2929490	0.93[EUR][1000 genomes]
rs2960190	0.83[EUR][1000 genomes]
rs3755574	0.87[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs3755576	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs3772099	0.84[JPT][hapmap]
rs3772102	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3821359	0.86[JPT][hapmap]
rs4425200	0.82[ASW][hapmap];0.87[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs4425201	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs4426625	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4426626	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4450736	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4494869	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs62276887	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440280	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6782630	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6785935	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6804850	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs704585	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs7431448	0.94[GIH][hapmap]
rs7611929	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7612036	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7630800	0.85[ASN][1000 genomes]
rs7631624	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633464	0.81[ASN][1000 genomes]
rs828609	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs844160	0.86[JPT][hapmap]
rs9289683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9289685	0.90[ASN][1000 genomes]
rs9811305	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9811449	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs9811860	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9814819	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9815226	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs9821965	0.83[ASN][1000 genomes]
rs9823430	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9835142	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843214	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs9843864	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849048	0.91[ASN][1000 genomes]
rs9852950	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860264	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9866570	0.86[JPT][hapmap]
rs9873932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9883516	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9883537	0.87[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs999147	0.82[ASW][hapmap];0.87[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2454686	ZBTB11	cis	cerebellum	SCAN
rs2454686	ST3GAL6	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98643000-98663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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