Variant report

Variant	rs2005195
Chromosome Location	chr12:49983479-49983480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49981751..49983968-chr5:66846722..66848370,2	MCF-7	breast:
2	chr12:49982198..49984699-chr12:49997127..49999143,2	MCF-7	breast:
3	chr12:49977137..49979191-chr12:49981991..49984278,2	MCF-7	breast:
4	chr12:49982217..49984243-chr12:50003590..50006014,2	MCF-7	breast:
5	chr12:49964375..49969334-chr12:49981796..49986330,5	MCF-7	breast:
6	chr12:49961312..49963172-chr12:49981340..49984293,2	K562	blood:

Variant related genes	Relation type
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1049986	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875964	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875968	0.81[ASN][1000 genomes]
rs11169063	0.86[ASN][1000 genomes]
rs11169065	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169069	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169070	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169073	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169076	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169080	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169081	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169092	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169097	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169104	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169106	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169109	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169111	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169112	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169113	0.82[EUR][1000 genomes]
rs11169118	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169125	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11169127	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169133	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11833411	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11834380	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12296586	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12299505	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299513	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12301824	0.82[EUR][1000 genomes]
rs12303310	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12304796	0.83[EUR][1000 genomes]
rs12308256	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12309940	0.84[EUR][1000 genomes]
rs12310510	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12311527	0.94[ASN][1000 genomes]
rs12311839	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314795	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12314878	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315224	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12315791	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12316284	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12317646	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12320556	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321169	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12321819	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13906	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470906	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1574326	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17123808	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902329	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902330	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241418	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278068	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278069	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278070	0.97[ASN][1000 genomes]
rs2303305	0.97[ASN][1000 genomes]
rs2336058	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2878532	0.84[ASN][1000 genomes]
rs3815832	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887727	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3887728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4045193	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4073998	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4133070	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4563	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4584654	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs52824916	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55853522	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57191490	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57342147	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57463238	0.82[EUR][1000 genomes]
rs57916875	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58278271	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58446833	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59233136	0.81[ASN][1000 genomes]
rs59849800	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59940006	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60121503	0.80[ASN][1000 genomes]
rs60402517	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61512987	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61620972	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61710637	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6580719	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7131915	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132792	0.94[ASN][1000 genomes]
rs7136052	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7137976	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7296281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299002	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7301209	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306877	0.83[AMR][1000 genomes]
rs7309607	0.81[ASN][1000 genomes]
rs7312658	0.81[ASN][1000 genomes]
rs7313738	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73305008	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305012	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305085	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73305098	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73306808	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73309030	0.83[EUR][1000 genomes]
rs74089182	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7688	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7952734	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7952938	0.86[ASN][1000 genomes]
rs7953911	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954994	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7955586	0.81[ASN][1000 genomes]
rs7956089	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7956181	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7962645	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7965658	0.97[ASN][1000 genomes]
rs7967624	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7970241	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973389	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975599	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977389	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979262	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7979285	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7980979	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8626	0.84[ASN][1000 genomes]
rs876889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897056	0.81[ASN][1000 genomes]
rs933738	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9804749	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9804971	0.84[AMR][1000 genomes];0.83[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	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
2	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
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-49984800	Weak transcription	Small Intestine	intestine
2	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
3	chr12:49963200-49986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:49963400-49984800	Weak transcription	Primary B cells from cord blood	blood
5	chr12:49967800-49987400	Weak transcription	Hela-S3	cervix
6	chr12:49971200-49984800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:49974800-49984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:49974800-49984800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:49974800-49984800	Weak transcription	Fetal Thymus	thymus
10	chr12:49974800-49985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:49974800-49985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:49974800-49986200	Weak transcription	K562	blood
13	chr12:49974800-49986600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:49974800-49986600	Weak transcription	NH-A	brain
15	chr12:49975000-49984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:49975000-49986200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:49975000-49986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:49975000-49987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:49976800-49984200	Weak transcription	Fetal Intestine Large	intestine
20	chr12:49976800-49994000	Weak transcription	Liver	Liver
21	chr12:49977600-49996200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:49977800-49984200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:49978000-49985000	Weak transcription	Dnd41	blood
24	chr12:49978000-49985400	Weak transcription	Thymus	Thymus
25	chr12:49978000-49988000	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:49978600-49984800	Weak transcription	Ovary	ovary
27	chr12:49978800-49994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:49979200-49984600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:49979600-49986600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:49979600-50002600	Weak transcription	HepG2	liver
31	chr12:49979800-49992000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:49979800-49995600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:49979800-49998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:49980000-49984800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:49980000-49988200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:49980200-49984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:49980200-49985400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:49980400-49984000	Weak transcription	Fetal Lung	lung
39	chr12:49980400-49987000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:49980400-50000200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:49980600-49984400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:49980800-49984800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:49981000-49984800	Weak transcription	Lung	lung
44	chr12:49981000-49994000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:49981400-49984200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr12:49981600-49984600	Weak transcription	Primary T cells from cord blood	blood
47	chr12:49982200-49985000	Weak transcription	Fetal Brain Female	brain
48	chr12:49982200-49991800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:49982200-49993600	Weak transcription	Brain Germinal Matrix	brain
50	chr12:49982200-49993800	Weak transcription	Stomach Smooth Muscle	stomach

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