Variant report

Variant	rs9833400
Chromosome Location	chr3:89389507-89389508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1040017	0.93[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs11128072	0.93[CEU][hapmap];0.81[CHB][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11923303	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13076853	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13088663	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13100388	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1398532	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1398535	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1512907	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1512910	0.93[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs1512912	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1567732	0.93[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs17800641	0.83[EUR][1000 genomes]
rs28675360	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28885734	0.81[EUR][1000 genomes]
rs35173319	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35448293	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35511518	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4449340	0.93[CEU][hapmap];0.81[CHB][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs4857496	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs6551409	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs6551410	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6768381	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6770978	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs6771336	0.81[EUR][1000 genomes]
rs6771477	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7428532	0.80[EUR][1000 genomes]
rs7619025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7644070	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs907712	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs9310117	0.89[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs9310119	1.00[ASW][hapmap];0.95[LWK][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9310120	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9310121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9310122	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs954964	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9809011	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9811041	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9817310	0.89[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs9817553	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838512	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9845870	0.93[CEU][hapmap]
rs9846844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853389	0.82[EUR][1000 genomes]
rs9866945	0.93[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs9866959	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9877953	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs994129	0.93[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs9990016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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
16	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
17	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
18	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
19	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
20	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
21	nsv1008293	chr3:89387089-89417287	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
22	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
23	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
24	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
25	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9833400	EPHA3	cis	cerebellum	SCAN

Chromatin state (count:6 , 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	chr3:89386800-89393200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:89389200-89390400	Enhancers	Fetal Lung	lung
6	chr3:89389400-89390400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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