Variant report

Variant	rs4857497
Chromosome Location	chr3:89294149-89294150
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	chr3:89290113..89292001-chr3:89293257..89295439,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs13316356	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13323078	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1398531	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398534	0.95[CEU][hapmap]
rs1512908	0.89[CEU][hapmap]
rs1567731	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17738248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17800347	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17800551	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17801001	0.80[CEU][hapmap];0.93[CHD][hapmap]
rs17801031	0.80[CEU][hapmap]
rs2063590	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2137487	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2137488	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2175670	0.95[CEU][hapmap]
rs28620812	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28834186	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4857502	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57468276	0.91[ASN][1000 genomes]
rs62274634	0.85[ASN][1000 genomes]
rs62274635	0.82[ASN][1000 genomes]
rs62274654	0.91[ASN][1000 genomes]
rs62274656	0.91[ASN][1000 genomes]
rs62274657	0.91[ASN][1000 genomes]
rs62274981	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274982	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274984	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62274986	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62278161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62278163	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62278164	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62278166	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278168	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278170	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278172	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419884	0.87[MEX][hapmap]
rs6773815	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776281	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782527	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs6786204	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786328	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794975	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796339	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73146387	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7373232	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7374904	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7615949	0.81[CEU][hapmap];0.93[CHD][hapmap]
rs7631682	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs870898	0.80[CEU][hapmap];0.93[CHD][hapmap]
rs870899	0.80[CEU][hapmap];0.93[CHD][hapmap]
rs9310110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9310112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9310119	0.86[CHD][hapmap]
rs9809894	0.91[ASN][1000 genomes]
rs9821666	0.90[CEU][hapmap];0.88[CHB][hapmap]
rs9829401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832305	0.86[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9836340	0.85[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9842599	0.85[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9844971	0.83[CEU][hapmap]
rs9847087	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848971	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852380	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9852594	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs9852722	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9852981	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs9854073	0.81[CEU][hapmap];0.93[CHD][hapmap]
rs9860266	0.85[CEU][hapmap]
rs9862195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863058	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863107	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9863971	0.91[ASN][1000 genomes]
rs9864984	0.81[CEU][hapmap]
rs9866618	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9868782	0.90[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs9875278	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9883541	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs993186	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs993187	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	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	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
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4857497	EPHA3	cis	cerebellum	SCAN
rs4857497	CHMP2B	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89289600-89294600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:89293800-89296400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:89293800-89297400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:89294000-89294200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:89294000-89294400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:89294000-89296200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:89294000-89296200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:89294000-89296400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:89294000-89296800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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