Variant report

Variant	rs9836340
Chromosome Location	chr3:89405754-89405755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs13316356	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1398534	0.90[CEU][hapmap]
rs1512185	0.85[CHB][hapmap]
rs1512908	0.84[CEU][hapmap]
rs17738248	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17800551	0.85[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17801001	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17801031	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2063590	0.90[CEU][hapmap]
rs2175670	0.90[CEU][hapmap]
rs28623022	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4857497	0.85[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4857502	0.90[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs57670516	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62275015	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62275016	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62275018	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62275019	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6773815	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6782527	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6796339	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6800041	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7373232	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7615949	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7631682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645408	0.88[CEU][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs870898	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs870899	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9310110	1.00[JPT][hapmap]
rs9310112	1.00[JPT][hapmap]
rs9310119	0.87[CHD][hapmap]
rs9821666	0.85[CEU][hapmap]
rs9829401	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9832305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs9836060	0.84[AMR][1000 genomes]
rs9842599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844971	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849029	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9851954	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs9852380	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs9852594	0.87[CHD][hapmap]
rs9852722	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs9854073	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9860266	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862195	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9863058	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs9863107	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs9864984	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9866618	0.85[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs9868782	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs9875278	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs9883541	0.85[CEU][hapmap]
rs993186	0.85[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs993187	0.85[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:83 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv590922	chr3:89314862-89417064	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv590923	chr3:89336417-89417171	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1001345	chr3:89368629-89444995	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1000694	chr3:89373820-89453045	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv590924	chr3:89375433-89417287	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv590925	chr3:89379935-89417171	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv590926	chr3:89379935-89417287	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv590927	chr3:89379935-89418262	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1013893	chr3:89381141-89419369	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1006351	chr3:89384121-89417287	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1011402	chr3:89384121-89444995	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1014091	chr3:89385875-89419369	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv998808	chr3:89385875-89425802	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1013406	chr3:89386462-89419369	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1007183	chr3:89386779-89419369	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv998705	chr3:89387034-89419369	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1008293	chr3:89387089-89417287	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1002312	chr3:89387089-89419369	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv1007800	chr3:89387089-89420476	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv437790	chr3:89389507-89426589	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv590928	chr3:89389507-89442369	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv870256	chr3:89391047-89421451	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv10290	chr3:89391277-89420095	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv590929	chr3:89392778-89418262	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv10816	chr3:89394021-89418291	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
29	esv33126	chr3:89394086-89418273	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv1002414	chr3:89394580-89408423	Active TSS Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv1008568	chr3:89394580-89410117	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv1007123	chr3:89394580-89413307	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv1009903	chr3:89394580-89413458	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
34	nsv1003901	chr3:89394580-89414123	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv1005753	chr3:89394580-89415640	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv1011147	chr3:89394580-89415915	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv1001884	chr3:89394580-89416204	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv1009238	chr3:89394580-89416565	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv1000645	chr3:89394580-89417287	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
40	nsv1013434	chr3:89394580-89419369	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv1006662	chr3:89394580-89419909	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv1010218	chr3:89394580-89420219	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
43	nsv1014916	chr3:89394580-89420476	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
44	nsv1012663	chr3:89394580-89425802	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
45	nsv1012824	chr3:89394580-89431445	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
46	esv2421597	chr3:89394592-89419381	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
47	nsv441832	chr3:89394592-89419381	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
48	esv2760812	chr3:89394592-89420488	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
49	esv2763745	chr3:89394592-89427509	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
50	nsv1004819	chr3:89394639-89415915	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9836340	STX19	trans	multi-tissue	Pritchard
rs9836340	EPHA3	cis	cerebellum	SCAN
rs9836340	CAT	trans	parietal	SCAN
rs9836340	CHMP2B	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89392600-89417400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:89404400-89417600	Weak transcription	Brain Germinal Matrix	brain

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