Variant report

Variant	rs3114653
Chromosome Location	chr5:90218612-90218613
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	chr5:90213363..90215563-chr5:90217273..90219030,2	MCF-7	breast:
2	chr5:90217916..90220914-chr5:90395407..90397788,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10074525	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514342	1.00[ASN][1000 genomes]
rs10514343	1.00[ASN][1000 genomes]
rs10942618	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11738573	1.00[ASN][1000 genomes]
rs11743775	1.00[ASN][1000 genomes]
rs11744005	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs11744033	1.00[ASN][1000 genomes]
rs11744325	1.00[ASN][1000 genomes]
rs11749470	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs11949884	1.00[ASN][1000 genomes]
rs11951675	1.00[ASN][1000 genomes]
rs11952993	1.00[ASN][1000 genomes]
rs11955946	1.00[ASN][1000 genomes]
rs12186968	1.00[ASN][1000 genomes]
rs12187656	1.00[ASN][1000 genomes]
rs12187790	1.00[ASN][1000 genomes]
rs12188068	1.00[ASN][1000 genomes]
rs12188094	1.00[ASN][1000 genomes]
rs12188249	1.00[ASN][1000 genomes]
rs12188655	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189005	1.00[ASN][1000 genomes]
rs17571029	1.00[ASN][1000 genomes]
rs17572843	1.00[ASN][1000 genomes]
rs17633498	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs1976566	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063244	0.88[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2438348	0.89[GIH][hapmap];1.00[ASN][1000 genomes]
rs3105789	0.90[AFR][1000 genomes]
rs3114658	0.85[EUR][1000 genomes]
rs34243354	1.00[ASN][1000 genomes]
rs34381536	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060258	1.00[ASN][1000 genomes]
rs35299092	1.00[ASN][1000 genomes]
rs4415111	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs55792004	1.00[ASN][1000 genomes]
rs55941525	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051320	1.00[ASN][1000 genomes]
rs56099704	1.00[ASN][1000 genomes]
rs56106025	1.00[ASN][1000 genomes]
rs56258383	1.00[ASN][1000 genomes]
rs62374052	1.00[ASN][1000 genomes]
rs62376462	1.00[ASN][1000 genomes]
rs62376463	1.00[ASN][1000 genomes]
rs62376490	1.00[ASN][1000 genomes]
rs62376491	1.00[ASN][1000 genomes]
rs6452927	1.00[ASN][1000 genomes]
rs66509877	1.00[ASN][1000 genomes]
rs6860216	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880626	1.00[ASN][1000 genomes]
rs6886773	1.00[ASN][1000 genomes]
rs6888672	1.00[ASN][1000 genomes]
rs6888979	1.00[ASN][1000 genomes]
rs6889138	1.00[ASN][1000 genomes]
rs72784617	1.00[ASN][1000 genomes]
rs72784624	1.00[ASN][1000 genomes]
rs7711168	1.00[ASN][1000 genomes]
rs7721862	1.00[ASN][1000 genomes]
rs7723305	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729840	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs949789	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv2754394	chr5:90181320-90225796	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90185000-90226600	Weak transcription	K562	blood
2	chr5:90205000-90225000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:90205200-90219200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:90208000-90231000	Weak transcription	Brain Anterior Caudate	brain
5	chr5:90211600-90225000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:90211600-90225000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:90215800-90225000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:90216000-90225000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:90217400-90218800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:90217600-90218800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:90218000-90218800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:90218200-90218800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr5:90218600-90225000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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