Variant report

Variant	rs9852594
Chromosome Location	chr3:89262358-89262359
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs13316356	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs13323078	0.88[CEU][hapmap];0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs1398531	0.96[ASN][1000 genomes]
rs1398534	0.87[YRI][hapmap]
rs1512908	0.87[YRI][hapmap]
rs1567731	0.87[ASN][1000 genomes]
rs17026816	0.89[ASN][1000 genomes]
rs17738248	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs17800347	0.82[ASN][1000 genomes]
rs17800551	0.88[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs17801001	0.93[CHD][hapmap]
rs2063590	0.87[ASN][1000 genomes]
rs2137487	0.87[ASN][1000 genomes]
rs2137488	0.87[ASN][1000 genomes]
rs28620812	0.87[ASN][1000 genomes]
rs28834186	0.91[ASN][1000 genomes]
rs4857497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs4857502	0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs57468276	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274619	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62274634	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62274635	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62274654	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274656	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274657	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274981	0.89[ASN][1000 genomes]
rs62274982	0.89[ASN][1000 genomes]
rs62274984	0.85[ASN][1000 genomes]
rs62274986	0.87[ASN][1000 genomes]
rs62278161	0.96[ASN][1000 genomes]
rs62278163	0.96[ASN][1000 genomes]
rs62278164	0.91[ASN][1000 genomes]
rs62278166	0.91[ASN][1000 genomes]
rs62278168	0.91[ASN][1000 genomes]
rs62278170	0.91[ASN][1000 genomes]
rs62278171	0.91[ASN][1000 genomes]
rs62278172	0.91[ASN][1000 genomes]
rs6551407	0.91[MEX][hapmap]
rs6773815	0.84[CHB][hapmap];0.91[ASN][1000 genomes]
rs6776281	0.96[ASN][1000 genomes]
rs6782527	0.87[CHD][hapmap]
rs6786204	0.91[ASN][1000 genomes]
rs6786328	0.91[ASN][1000 genomes]
rs6794975	0.96[ASN][1000 genomes]
rs6796339	1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[ASN][1000 genomes]
rs73146387	0.96[ASN][1000 genomes]
rs7373232	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615949	0.93[CHD][hapmap]
rs870898	0.93[CHD][hapmap]
rs870899	0.93[CHD][hapmap]
rs9310110	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9310112	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310119	0.86[CHD][hapmap]
rs9809894	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821666	0.88[CHB][hapmap];0.94[YRI][hapmap]
rs9829401	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9832305	0.86[CHD][hapmap]
rs9836340	0.87[CHD][hapmap]
rs9839323	0.82[EUR][1000 genomes]
rs9842599	0.87[CHD][hapmap]
rs9847087	0.91[ASN][1000 genomes]
rs9848971	0.96[ASN][1000 genomes]
rs9851954	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9852380	0.88[CHB][hapmap];0.94[YRI][hapmap]
rs9852722	0.88[CHB][hapmap];0.94[YRI][hapmap]
rs9852981	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9854073	0.93[CHD][hapmap]
rs9862195	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9863058	0.88[CHB][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs9863107	0.88[CHB][hapmap]
rs9863971	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866618	0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs9868782	0.93[CHD][hapmap]
rs9875278	0.86[CHB][hapmap];0.84[YRI][hapmap]
rs9883541	0.91[ASN][1000 genomes]
rs993186	0.93[CHD][hapmap];0.82[LWK][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs993187	0.88[CHB][hapmap];0.87[ASN][1000 genomes]

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	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv997874	chr3:89188275-89279573	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	esv2757001	chr3:89260495-89271087	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv2759160	chr3:89260495-89271087	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9852594	EPHA3	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89250200-89263200	Weak transcription	Fetal Brain Female	brain
2	chr3:89259800-89263200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:89259800-89266200	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:89259800-89266600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:89260400-89265800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:89261400-89262600	Enhancers	Fetal Stomach	stomach
7	chr3:89261600-89262400	Enhancers	Rectal Smooth Muscle	rectum
8	chr3:89261800-89262400	Enhancers	Colon Smooth Muscle	Colon
9	chr3:89262000-89263600	Weak transcription	Fetal Brain Male	brain
10	chr3:89262000-89264000	Enhancers	Fetal Lung	lung

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