Variant report

Variant	rs10865956
Chromosome Location	chr3:49581559-49581560
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49581218..49583706-chr3:49709789..49712577,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 34 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10155014	0.82[EUR][1000 genomes]
rs10452032	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs1078341	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs1106620	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130204	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130207	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11130208	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	0.80[YRI][hapmap]
rs11130217	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11719762	1.00[CEU][hapmap]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs11720705	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11928090	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[CHD][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs12715437	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096474	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs13096480	0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs13322887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352889	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs1491983	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs1982861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2029591	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs2131108	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs2140270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2329021	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs2329025	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3020779	0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs3448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs34890793	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs3866330	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3870341	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3905330	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4052546	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4241405	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855833	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs4855837	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855838	0.87[AFR][1000 genomes]
rs4855845	0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs4855846	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855858	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4855869	0.84[EUR][1000 genomes]
rs4855882	1.00[CHD][hapmap]
rs4855885	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs56049603	0.84[EUR][1000 genomes]
rs56127630	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56324858	0.82[EUR][1000 genomes]
rs57273516	0.88[EUR][1000 genomes]
rs62259933	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62261249	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446275	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446284	0.83[AFR][1000 genomes]
rs6446285	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6774202	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs6778080	1.00[ASN][1000 genomes]
rs6783003	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6785045	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797299	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs72934271	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7613491	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619789	0.88[EUR][1000 genomes]
rs7620024	0.84[EUR][1000 genomes]
rs7622786	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7625857	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628207	1.00[CHD][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653505	1.00[CHD][hapmap];0.84[MKK][hapmap]
rs8897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs9654010	0.84[EUR][1000 genomes]
rs974495	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap]
rs9757181	1.00[CEU][hapmap]
rs9809237	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9817807	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9842132	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849038	1.00[CHD][hapmap]
rs9860055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870858	1.00[CHD][hapmap]
rs9871024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	1.00[ASN][1000 genomes]
rs9883000	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs10865956	GPX1	cis	parietal	SCAN
rs10865956	AMT	cis	Nerve Tibial	GTEx
rs10865956	SEMA3G	cis	cerebellum	SCAN
rs10865956	WDR6	cis	parietal	SCAN
rs10865956	WDR6	cis	Muscle Skeletal	GTEx
rs10865956	AMT	cis	Whole Blood	GTEx
rs10865956	AMT	cis	Esophagus Mucosa	GTEx
rs10865956	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs10865956	WDR6	cis	Esophagus Muscularis	GTEx
rs10865956	NICN1	cis	cerebellum	SCAN
rs10865956	AMT	cis	cerebellum	SCAN
rs10865956	AMT	cis	Esophagus Muscularis	GTEx
rs10865956	AMT	cis	Thyroid	GTEx
rs10865956	NICN1	cis	Thyroid	GTEx
rs10865956	AMT	cis	lymphoblastoid	seeQTL
rs10865956	AMT	cis	parietal	SCAN
rs10865956	P4HTM	cis	parietal	SCAN
rs10865956	ZNF589	cis	parietal	SCAN
rs10865956	LZTFL1	cis	cerebellum	SCAN
rs10865956	AMT	cis	Artery Tibial	GTEx
rs10865956	WDR6	cis	cerebellum	SCAN
rs10865956	GMPPB	cis	parietal	SCAN
rs10865956	WDR6	cis	Nerve Tibial	GTEx
rs10865956	QRICH1	cis	cerebellum	SCAN
rs10865956	AMT	cis	Muscle Skeletal	GTEx
rs10865956	NME6	cis	cerebellum	SCAN
rs10865956	DALRD3	cis	parietal	SCAN
rs10865956	AMT	cis	lung	GTEx
rs10865956	NICN1-AS1	cis	Thyroid	GTEx
rs10865956	AMT	cis	Artery Aorta	GTEx
rs10865956	AMT	cis	Adipose Subcutaneous	GTEx
rs10865956	GNL3	cis	cerebellum	SCAN
rs10865956	DALRD3	cis	cerebellum	SCAN
rs10865956	AMT	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49578200-49581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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