Variant report

Variant	rs11169065
Chromosome Location	chr12:49939645-49939646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49931658..49934528-chr12:49938714..49943333,4	MCF-7	breast:
2	chr12:49938158..49941104-chr12:49951037..49955376,3	K562	blood:
3	chr12:49939604..49941296-chr12:49942002..49944105,2	K562	blood:
4	chr12:49939089..49944852-chr12:49945260..49949994,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187778	Chromatin interaction
ENSG00000135519	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10219602	1.00[CHB][hapmap]
rs1078216	1.00[CHB][hapmap]
rs10875964	0.81[EUR][1000 genomes]
rs11169063	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11169069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169070	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169076	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169080	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11169081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169097	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169101	1.00[JPT][hapmap]
rs11169104	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169106	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs11169109	0.82[EUR][1000 genomes]
rs11169118	0.82[EUR][1000 genomes]
rs11169125	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs11169127	0.88[CEU][hapmap];0.90[YRI][hapmap]
rs11169128	1.00[CHB][hapmap]
rs11169130	1.00[CHB][hapmap]
rs1150057	1.00[JPT][hapmap]
rs11833411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11834380	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs12299505	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12299513	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12303310	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12306114	1.00[CHB][hapmap]
rs12309940	0.81[EUR][1000 genomes]
rs12310510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs12311527	0.94[ASN][1000 genomes]
rs12311839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12314878	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12315224	0.82[EUR][1000 genomes]
rs12315791	0.81[EUR][1000 genomes]
rs12317646	0.82[EUR][1000 genomes]
rs12320556	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12321819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13066	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574326	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs17123808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005195	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241418	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278070	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2303305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2336058	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs2878532	1.00[JPT][hapmap]
rs35275181	1.00[CHB][hapmap]
rs3815832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3887727	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3887728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4045193	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4073998	1.00[JPT][hapmap]
rs4133070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4584654	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs4993294	1.00[CHB][hapmap]
rs52824916	0.91[ASN][1000 genomes]
rs55853522	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57916875	0.91[ASN][1000 genomes]
rs58278271	0.86[ASN][1000 genomes]
rs59940006	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60402517	0.81[EUR][1000 genomes]
rs61620972	0.81[EUR][1000 genomes]
rs61710637	0.82[EUR][1000 genomes]
rs7131915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7132792	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7136772	1.00[CHB][hapmap]
rs7137976	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs7296281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7299609	0.82[JPT][hapmap]
rs7301209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7313738	0.82[EUR][1000 genomes]
rs73305008	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73305012	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73306808	0.82[EUR][1000 genomes]
rs7952734	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7952938	0.86[ASN][1000 genomes]
rs7953911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7956181	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7962863	1.00[JPT][hapmap]
rs7963954	1.00[JPT][hapmap]
rs7965658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7970241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7975599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979262	0.87[CEU][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs7979285	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs8626	1.00[JPT][hapmap]
rs876889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs933738	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9804749	0.82[EUR][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	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49933000-49942600	Weak transcription	Pancreas	Pancrea
2	chr12:49933400-49942000	Weak transcription	Right Ventricle	heart
3	chr12:49933400-49942400	Weak transcription	Right Atrium	heart
4	chr12:49934200-49942000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:49934600-49942200	Weak transcription	Brain Angular Gyrus	brain
6	chr12:49937400-49940200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:49937400-49942000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:49938800-49942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:49939000-49940200	Enhancers	HepG2	liver
10	chr12:49939400-49940600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:49939600-49939800	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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