Variant report

Variant	rs7962863
Chromosome Location	chr12:50060874-50060875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50053639..50056299-chr12:50060265..50061800,2	K562	blood:
2	chr12:50059879..50062225-chr12:50063774..50067547,4	K562	blood:
3	chr12:50059406..50061559-chr12:50099659..50102514,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction
ENSG00000161791	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1049986	0.86[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs10875964	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10875968	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169063	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11169065	1.00[JPT][hapmap]
rs11169069	0.85[JPT][hapmap]
rs11169073	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs11169080	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169081	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs11169082	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs11169092	0.85[JPT][hapmap]
rs11169097	1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs11169101	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169104	0.82[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169106	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169109	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169111	0.89[ASN][1000 genomes]
rs11169112	0.89[ASN][1000 genomes]
rs11169118	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169125	0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs11169127	0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs11169133	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169140	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1150057	1.00[JPT][hapmap]
rs11615488	0.97[ASN][1000 genomes]
rs11833411	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs11834380	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12296586	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12299505	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs12299513	0.80[AMR][1000 genomes]
rs12301824	0.90[ASN][1000 genomes]
rs12303310	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12304796	0.84[ASN][1000 genomes]
rs12305460	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12308256	0.87[ASN][1000 genomes]
rs12309940	0.84[ASN][1000 genomes]
rs12310510	0.85[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12311839	0.84[JPT][hapmap]
rs12314795	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12315224	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12315791	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12316284	0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs12317646	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12321169	0.82[AMR][1000 genomes]
rs12321819	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs13906	0.85[JPT][hapmap]
rs1470906	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1574326	0.86[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17123808	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs17123981	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap]
rs1902329	1.00[JPT][hapmap]
rs1902330	0.82[JPT][hapmap]
rs2278068	1.00[JPT][hapmap]
rs2278069	0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs2303305	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs2336058	0.86[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2878532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35275181	0.85[CHD][hapmap]
rs3815832	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs3887727	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3887728	0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs4073998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4133070	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4563	0.85[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4584654	0.86[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4993294	0.86[CHD][hapmap]
rs57191490	0.87[ASN][1000 genomes]
rs57342147	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58446833	0.80[AMR][1000 genomes]
rs59233136	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59849800	0.80[AMR][1000 genomes]
rs60121503	0.87[ASN][1000 genomes]
rs60402517	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61512987	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61616163	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61620972	0.89[ASN][1000 genomes]
rs61710637	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6580719	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7131915	0.85[JPT][hapmap]
rs7132792	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs7136052	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7137976	0.86[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7295556	0.86[CHD][hapmap]
rs7296281	0.85[JPT][hapmap]
rs7299002	0.89[ASN][1000 genomes]
rs7299609	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7301209	0.85[JPT][hapmap]
rs7306877	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7309607	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312658	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313738	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73305085	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73305098	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73306808	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73309030	0.84[ASN][1000 genomes]
rs74089182	0.87[ASN][1000 genomes]
rs7688	0.86[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs7952734	1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7952938	0.82[ASN][1000 genomes]
rs7953911	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7954994	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7955586	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956089	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7956181	1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7962645	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7963954	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7965658	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7967624	0.87[ASN][1000 genomes]
rs7970241	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7973389	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7975599	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7975712	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs7977389	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7979262	0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7979285	0.91[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7980979	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8626	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs876889	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs897056	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9804749	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9804971	0.82[AMR][1000 genomes];0.84[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	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:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50042400-50067000	Weak transcription	Fetal Brain Male	brain
2	chr12:50052200-50066200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:50052400-50064800	Weak transcription	Fetal Kidney	kidney
4	chr12:50052600-50067000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:50052600-50067400	Weak transcription	Fetal Brain Female	brain
6	chr12:50054400-50069800	Enhancers	Left Ventricle	heart
7	chr12:50054600-50061000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr12:50055400-50061400	Enhancers	Brain Substantia Nigra	brain
9	chr12:50055600-50062400	Enhancers	Psoas Muscle	Psoas
10	chr12:50057400-50063800	Weak transcription	Ovary	ovary
11	chr12:50057400-50066200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:50057600-50063200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr12:50057600-50064400	Weak transcription	Gastric	stomach
14	chr12:50057600-50064400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:50057600-50064400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr12:50057600-50064800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:50057600-50065000	Weak transcription	Pancreas	Pancrea
18	chr12:50057600-50065200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:50057600-50066000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:50057600-50066200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:50057600-50066400	Weak transcription	Aorta	Aorta
22	chr12:50057600-50066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:50057600-50067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:50057600-50067000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:50057600-50067200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:50057800-50063800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr12:50057800-50066200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:50058000-50062600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:50058200-50062000	Genic enhancers	Primary B cells from cord blood	blood
30	chr12:50058400-50061000	Genic enhancers	Thymus	Thymus
31	chr12:50058400-50062000	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr12:50058400-50064400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:50058400-50066000	Weak transcription	Esophagus	oesophagus
34	chr12:50058400-50067200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr12:50058600-50061200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:50058800-50061200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:50058800-50061400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:50058800-50061800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:50058800-50063800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:50058800-50063800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:50058800-50064600	Weak transcription	K562	blood
42	chr12:50058800-50066000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:50059000-50061200	Weak transcription	NHDF-Ad	bronchial
44	chr12:50059000-50061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:50059000-50063000	Weak transcription	Colon Smooth Muscle	Colon
46	chr12:50059000-50063200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:50059000-50063600	Weak transcription	Dnd41	blood
48	chr12:50059000-50063800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:50059000-50064000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr12:50059000-50064200	Weak transcription	Monocytes-CD14+_RO01746	blood

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