Variant report

Variant	rs9868782
Chromosome Location	chr3:89384121-89384122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs13316356	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1398534	0.95[CEU][hapmap]
rs1512908	0.94[CEU][hapmap]
rs1567731	0.83[ASN][1000 genomes]
rs17738248	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs17800551	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17801001	0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17801031	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2063590	0.95[CEU][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2137487	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2137488	0.83[ASN][1000 genomes]
rs2175670	0.95[CEU][hapmap]
rs4857497	0.90[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4857502	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57670516	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62274981	0.81[ASN][1000 genomes]
rs62274982	0.81[ASN][1000 genomes]
rs62274984	0.81[ASN][1000 genomes]
rs62274986	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62275015	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62275016	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62275018	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62275019	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773815	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6782527	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap]
rs6796339	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6800041	0.80[EUR][1000 genomes]
rs7373232	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7615949	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7631682	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7645408	0.81[EUR][1000 genomes]
rs870898	0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs870899	0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9310110	1.00[JPT][hapmap]
rs9310112	1.00[JPT][hapmap]
rs9310119	0.93[CHD][hapmap];0.82[GIH][hapmap]
rs9821666	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs9829401	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9832305	0.85[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9836340	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]
rs9842599	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]
rs9844971	0.85[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9849029	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9851954	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs9852380	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9852594	0.93[CHD][hapmap]
rs9852722	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9854073	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9860266	0.85[CEU][hapmap];0.92[ASN][1000 genomes]
rs9862195	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs9863058	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9863107	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9864984	0.80[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9866618	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9875278	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9883541	0.90[CEU][hapmap]
rs993186	0.90[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs993187	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

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	nsv590921	chr3:89294149-89392778	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv590922	chr3:89314862-89417064	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv590923	chr3:89336417-89417171	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	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
6	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
7	nsv590924	chr3:89375433-89417287	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv590925	chr3:89379935-89417171	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv590926	chr3:89379935-89417287	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	nsv1006351	chr3:89384121-89417287	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9868782	EPHA3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89382400-89391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:89382800-89391000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:89383000-89390200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:89383200-89384200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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