Variant report

Variant	rs11128068
Chromosome Location	chr3:89207222-89207223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:89207136..89210104-chr3:89214868..89216855,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10779990	0.83[JPT][hapmap]
rs11128067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11128069	0.83[JPT][hapmap]
rs12633482	0.83[JPT][hapmap]
rs12638746	0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs12714732	0.82[JPT][hapmap]
rs13069582	1.00[YRI][hapmap]
rs13075167	0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs35712958	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4128782	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs55849666	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792104	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797260	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs7428438	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7428598	0.83[JPT][hapmap]
rs7429534	0.83[JPT][hapmap]
rs7610407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835094	0.83[JPT][hapmap]
rs9868686	0.81[GIH][hapmap]
rs9883199	0.83[JPT][hapmap]

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	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	nsv1005603	chr3:89174152-89223459	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	nsv1008916	chr3:89206065-89241915	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11128068	EPHA3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89205800-89210200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:89206000-89211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:89206800-89208200	Weak transcription	Fetal Brain Female	brain
4	chr3:89207200-89208600	Weak transcription	Fetal Brain Male	brain

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