Variant report

Variant	rs7301209
Chromosome Location	chr12:49946051-49946052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:49945854-49946146	IMR90	lung:	n/a	n/a
2	CEBPB	chr12:49945769-49946220	MCF-7	breast:	n/a	n/a
3	MYC	chr12:49945912-49946159	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr12:49945861-49946103	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr12:49945793-49946151	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:49945943-49946202	HepG2	liver:	n/a	n/a
7	CEBPB	chr12:49945784-49946138	HepG2	liver:	n/a	n/a
8	CEBPB	chr12:49945812-49946125	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49931274..49936005-chr12:49943051..49946094,6	K562	blood:
2	chr12:49758090..49761584-chr12:49941577..49946568,5	K562	blood:
3	chr12:49751652..49753249-chr12:49945364..49947473,2	MCF-7	breast:

Variant related genes	Relation type
KCNH3	TF binding region
ENSG00000135519	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10219602	1.00[CHB][hapmap]
rs1049986	0.81[ASN][1000 genomes]
rs1078216	1.00[CHB][hapmap]
rs10875964	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875968	0.81[ASN][1000 genomes]
rs11169063	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11169065	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]
rs11169069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169070	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169076	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169080	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169097	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169101	0.86[JPT][hapmap]
rs11169104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11169106	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169109	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169111	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169112	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169113	0.80[EUR][1000 genomes]
rs11169118	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169125	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs11169127	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs11169128	1.00[CHB][hapmap]
rs11169130	1.00[CHB][hapmap]
rs11169133	0.83[ASN][1000 genomes]
rs1150057	0.85[JPT][hapmap]
rs11833411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11834380	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12296586	0.83[ASN][1000 genomes]
rs12299505	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299513	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12303310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12306114	1.00[CHB][hapmap]
rs12308256	0.81[ASN][1000 genomes]
rs12309940	0.83[EUR][1000 genomes]
rs12310510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12311527	0.94[ASN][1000 genomes]
rs12311839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314795	0.83[ASN][1000 genomes]
rs12314878	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315224	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12315791	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12316284	0.81[ASN][1000 genomes]
rs12317646	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12320556	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470906	0.83[ASN][1000 genomes]
rs1574326	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17123808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2005195	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241418	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278070	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2336058	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2878532	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs35275181	1.00[CHB][hapmap]
rs3815832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887727	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3887728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4045193	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4073998	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4133070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4563	0.83[ASN][1000 genomes]
rs4584654	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4993294	1.00[CHB][hapmap]
rs52824916	0.97[ASN][1000 genomes]
rs55853522	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57191490	0.80[ASN][1000 genomes]
rs57342147	0.83[ASN][1000 genomes]
rs57916875	0.97[ASN][1000 genomes]
rs58278271	0.91[ASN][1000 genomes]
rs59233136	0.81[ASN][1000 genomes]
rs59940006	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60121503	0.80[ASN][1000 genomes]
rs60402517	0.83[EUR][1000 genomes]
rs61512987	0.84[ASN][1000 genomes]
rs61620972	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61710637	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6580719	0.83[ASN][1000 genomes]
rs7131915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132792	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7136052	0.83[ASN][1000 genomes]
rs7136772	1.00[CHB][hapmap]
rs7137976	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7296281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299002	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7309607	0.81[ASN][1000 genomes]
rs7312658	0.81[ASN][1000 genomes]
rs7313738	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73305008	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305012	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305085	0.81[ASN][1000 genomes]
rs73305098	0.83[ASN][1000 genomes]
rs73306808	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74089182	0.80[ASN][1000 genomes]
rs7688	0.81[ASN][1000 genomes]
rs7952734	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7952938	0.86[ASN][1000 genomes]
rs7953911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7955586	0.81[ASN][1000 genomes]
rs7956089	0.83[ASN][1000 genomes]
rs7956181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7962645	0.83[ASN][1000 genomes]
rs7962863	0.85[JPT][hapmap]
rs7963954	0.85[JPT][hapmap]
rs7965658	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs7967624	0.81[ASN][1000 genomes]
rs7970241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979262	0.87[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7979285	0.89[ASN][1000 genomes]
rs7980979	0.83[ASN][1000 genomes]
rs8626	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs876889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897056	0.81[ASN][1000 genomes]
rs933738	0.94[ASN][1000 genomes]
rs9804749	0.82[EUR][1000 genomes];0.83[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	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	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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49942600-49946600	Enhancers	Pancreas	Pancrea
2	chr12:49943000-49950400	Weak transcription	GM12878-XiMat	blood
3	chr12:49943200-49947200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:49943200-49951000	Weak transcription	Aorta	Aorta
5	chr12:49943200-49959600	Weak transcription	Right Atrium	heart
6	chr12:49943400-49949400	Weak transcription	Gastric	stomach
7	chr12:49943400-49949400	Weak transcription	Spleen	Spleen
8	chr12:49943400-49950000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:49943400-49950200	Weak transcription	Primary B cells from cord blood	blood
10	chr12:49943400-49952600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:49943600-49946200	Enhancers	Fetal Intestine Large	intestine
12	chr12:49943600-49946400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr12:49943600-49947600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:49943600-49949800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:49943600-49949800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:49943600-49949800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:49943600-49949800	Weak transcription	Fetal Lung	lung
18	chr12:49943600-49950000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:49943600-49950000	Weak transcription	Ovary	ovary
20	chr12:49943600-49950200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:49943600-49950200	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:49943600-49950400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:49944200-49952200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:49944400-49946800	Enhancers	Liver	Liver
25	chr12:49944800-49947600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:49944800-49949800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:49944800-49952400	Weak transcription	Fetal Kidney	kidney
28	chr12:49945000-49949400	Weak transcription	Thymus	Thymus
29	chr12:49945000-49952400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:49945200-49947200	Enhancers	HepG2	liver
31	chr12:49945200-49949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:49945400-49946200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:49945400-49946200	Enhancers	Esophagus	oesophagus
34	chr12:49945400-49946200	Enhancers	Lung	lung
35	chr12:49945400-49946400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:49945400-49947000	Enhancers	Left Ventricle	heart
37	chr12:49945400-49947000	Enhancers	Right Ventricle	heart
38	chr12:49945400-49947000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr12:49945600-49946200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:49945600-49946200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:49945600-49946200	Enhancers	Fetal Brain Female	brain
42	chr12:49945600-49946200	Enhancers	Fetal Muscle Trunk	muscle
43	chr12:49945600-49946200	Enhancers	HMEC	breast
44	chr12:49945600-49946200	Enhancers	HSMMtube	muscle
45	chr12:49945600-49946400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:49945600-49946400	Enhancers	Brain Anterior Caudate	brain
47	chr12:49945600-49946400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:49945600-49946400	Enhancers	Brain Substantia Nigra	brain
49	chr12:49945600-49946400	Enhancers	Placenta	Placenta
50	chr12:49945600-49946600	Enhancers	Brain Angular Gyrus	brain

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