Variant report

Variant	rs11128072
Chromosome Location	chr3:89317917-89317918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:89313859..89316197-chr3:89316268..89318290,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1040017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11128071	0.86[CHB][hapmap]
rs11923303	0.81[EUR][1000 genomes]
rs13076853	0.83[EUR][1000 genomes]
rs13083092	0.84[CHB][hapmap];0.82[YRI][hapmap]
rs13088663	0.84[EUR][1000 genomes]
rs13100388	0.82[EUR][1000 genomes]
rs1398532	0.84[EUR][1000 genomes]
rs1398535	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512907	0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1512910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1512912	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]
rs1567732	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17800641	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28675360	0.82[EUR][1000 genomes]
rs28885734	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35173319	0.82[EUR][1000 genomes]
rs35448293	0.83[EUR][1000 genomes]
rs35511518	0.83[EUR][1000 genomes]
rs4132275	0.85[GIH][hapmap]
rs4425279	0.84[LWK][hapmap]
rs4449340	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4857496	0.96[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6551409	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6768381	0.93[CEU][hapmap];0.81[CHB][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs6770978	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771336	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6771477	0.96[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793727	0.81[YRI][hapmap]
rs7428532	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7432948	0.85[CHB][hapmap]
rs7612746	0.88[GIH][hapmap]
rs7619025	0.93[CEU][hapmap];0.81[CHB][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644070	0.93[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap]
rs7646842	0.85[GIH][hapmap]
rs872976	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907712	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9310117	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9310119	0.82[EUR][1000 genomes]
rs9310120	0.81[EUR][1000 genomes]
rs9310121	0.93[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs954964	0.87[EUR][1000 genomes]
rs9809011	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9809046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9811041	0.85[CEU][hapmap]
rs9817310	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9817553	0.93[CEU][hapmap];0.81[CHB][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs9833400	0.93[CEU][hapmap];0.81[CHB][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9837346	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9838512	0.96[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845870	1.00[CEU][hapmap]
rs9846844	0.93[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs9853389	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866959	0.93[CEU][hapmap];0.81[CHB][hapmap];0.86[TSI][hapmap]
rs9867299	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9877953	0.92[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879028	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs994129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9990016	0.93[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11128072	EPHA3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89316200-89318000	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:89317400-89319400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:89317800-89325400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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