Variant report

Variant	rs1512912
Chromosome Location	chr3:89307931-89307932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1040017	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11128071	0.86[CHB][hapmap]
rs11128072	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11923303	0.80[EUR][1000 genomes]
rs13076853	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13083092	0.84[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs13088663	0.83[EUR][1000 genomes]
rs13100388	0.81[EUR][1000 genomes]
rs1398532	0.83[EUR][1000 genomes]
rs1398535	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1512907	0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1512910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs1567732	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17800641	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28675360	0.81[EUR][1000 genomes]
rs28885734	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35173319	0.81[EUR][1000 genomes]
rs35448293	0.82[EUR][1000 genomes]
rs35511518	0.82[EUR][1000 genomes]
rs4132275	0.88[GIH][hapmap];0.87[YRI][hapmap]
rs4425279	0.85[LWK][hapmap]
rs4449340	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4857496	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6419884	0.84[JPT][hapmap]
rs6551409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6768381	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs6770978	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6771336	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6771477	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6793727	0.90[YRI][hapmap]
rs7428532	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7432948	0.85[CHB][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs7612746	0.91[GIH][hapmap]
rs7619025	0.81[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644070	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs7646842	0.88[GIH][hapmap];0.87[YRI][hapmap]
rs872976	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907712	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9310117	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9310119	0.81[EUR][1000 genomes]
rs9310120	0.80[EUR][1000 genomes]
rs9310121	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs954964	0.85[EUR][1000 genomes]
rs9809011	0.96[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809046	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9811041	0.82[CEU][hapmap]
rs9817310	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9817553	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9833400	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs9833437	0.83[AFR][1000 genomes]
rs9837346	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9838512	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9845870	0.96[CEU][hapmap]
rs9846844	0.89[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs9853389	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866945	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866959	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs9867299	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9873281	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs9877953	0.96[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9879028	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs994129	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9990016	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1512912	EPHA3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89303800-89310000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:89304200-89309800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:89306000-89310000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:89306800-89309800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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