Variant report

Variant	rs9862534
Chromosome Location	chr3:49598064-49598065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49597065..49598629-chr3:49601574..49603503,2	K562	blood:
2	chr3:49591238..49594235-chr3:49595852..49599097,3	K562	blood:
3	chr3:49597039..49599713-chr3:49710205..49712896,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164061	Chromatin interaction
ENSG00000226913	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10155014	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10452032	1.00[CHD][hapmap];0.90[MKK][hapmap]
rs1078341	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs10865956	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]
rs1106620	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130204	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130208	1.00[CHD][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap]
rs11130211	1.00[CHB][hapmap]
rs11130217	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs11709734	1.00[CHD][hapmap]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs11720705	1.00[CHD][hapmap]
rs11928090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	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];0.99[EUR][1000 genomes]
rs12637313	1.00[CHD][hapmap]
rs12715437	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs13096474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	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];0.96[EUR][1000 genomes]
rs1352889	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap]
rs1464569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap]
rs1982861	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs2131108	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs2140270	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2312462	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329021	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs2329025	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34890793	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap]
rs3866330	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241405	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs4241407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap]
rs4855837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855846	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs4855853	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855858	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.85[EUR][1000 genomes]
rs4855882	1.00[CHD][hapmap]
rs4855885	1.00[CHD][hapmap]
rs56049603	0.83[EUR][1000 genomes]
rs56127630	0.82[EUR][1000 genomes]
rs56324858	0.81[EUR][1000 genomes]
rs57273516	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.86[EUR][1000 genomes]
rs62259943	0.80[EUR][1000 genomes]
rs62259947	0.82[EUR][1000 genomes]
rs62261183	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62261249	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446275	0.86[EUR][1000 genomes]
rs6446285	1.00[CHD][hapmap]
rs6769744	1.00[ASN][1000 genomes]
rs6774202	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap]
rs6783003	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6785045	0.82[EUR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs72934271	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73088137	0.83[EUR][1000 genomes]
rs7355800	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7374731	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7613491	0.90[EUR][1000 genomes]
rs7619789	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625857	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628207	1.00[CHD][hapmap]
rs7644148	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];0.94[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7648995	0.82[EUR][1000 genomes]
rs7651372	0.90[EUR][1000 genomes]
rs7653505	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs8897	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs940045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.84[EUR][1000 genomes]
rs974495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9809237	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9817807	0.80[EUR][1000 genomes]
rs9824435	1.00[CHD][hapmap]
rs9835157	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs9842132	0.80[EUR][1000 genomes]
rs9849038	1.00[CHD][hapmap]
rs9860055	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861027	0.82[EUR][1000 genomes]
rs9870858	1.00[CHD][hapmap]
rs9871024	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];0.96[EUR][1000 genomes]
rs9883000	1.00[CHD][hapmap];0.92[MKK][hapmap]

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:35)

SNP	Gene	Cis/trans	Tissue	Source
rs9862534	AMT	cis	Nerve Tibial	GTEx
rs9862534	AMT	cis	Whole Blood	GTEx
rs9862534	NICN1-AS1	cis	Thyroid	GTEx
rs9862534	WDR6	cis	Muscle Skeletal	GTEx
rs9862534	DALRD3	cis	parietal	SCAN
rs9862534	AMT	cis	Artery Tibial	GTEx
rs9862534	P4HTM	cis	parietal	SCAN
rs9862534	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9862534	WDR6	cis	Nerve Tibial	GTEx
rs9862534	NME6	cis	cerebellum	SCAN
rs9862534	WDR6	cis	cerebellum	SCAN
rs9862534	NICN1	cis	cerebellum	SCAN
rs9862534	AMT	cis	Artery Aorta	GTEx
rs9862534	AMT	cis	Muscle Skeletal	GTEx
rs9862534	DALRD3	cis	cerebellum	SCAN
rs9862534	ZNF589	cis	parietal	SCAN
rs9862534	WDR6	cis	Esophagus Muscularis	GTEx
rs9862534	AMT	cis	Adipose Subcutaneous	GTEx
rs9862534	GNL3	cis	cerebellum	SCAN
rs9862534	WDR6	cis	parietal	SCAN
rs9862534	AMT	cis	parietal	SCAN
rs9862534	AMT	cis	Esophagus Muscularis	GTEx
rs9862534	AMT	cis	Esophagus Mucosa	GTEx
rs9862534	AMT	cis	lung	GTEx
rs9862534	NICN1	cis	Thyroid	GTEx
rs9862534	AMT	cis	cerebellum	SCAN
rs9862534	GMPPB	cis	parietal	SCAN
rs9862534	SEMA3G	cis	cerebellum	SCAN
rs9862534	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9862534	GPX1	cis	parietal	SCAN
rs9862534	WDR6	cis	lung	GTEx
rs9862534	LZTFL1	cis	cerebellum	SCAN
rs9862534	AMT	cis	Thyroid	GTEx
rs9862534	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs9862534	QRICH1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49596000-49599400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:49596000-49600000	Weak transcription	Brain Anterior Caudate	brain
3	chr3:49596000-49615000	Weak transcription	Brain Germinal Matrix	brain
4	chr3:49596000-49616800	Weak transcription	Fetal Brain Female	brain
5	chr3:49596200-49598200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:49596200-49599200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:49596200-49600000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:49596200-49600400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:49597400-49598200	Enhancers	Brain Angular Gyrus	brain
10	chr3:49597800-49600400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:49598000-49602000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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