Variant report

Variant	rs7963954
Chromosome Location	chr12:50064928-50064929
allele	A/G
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	CTCF	chr12:50064900-50065050	GM12872	blood:	n/a	chr12:50064947-50064956
2	TCF3	chr12:50064767-50064995	GM12878	blood:	n/a	n/a
3	TCF12	chr12:50064786-50065080	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:50064688-50066106	GM12892	blood:	n/a	n/a
5	RELA	chr12:50064449-50065738	GM18951	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
6	CTCF	chr12:50064880-50065030	GM12870	blood:	n/a	chr12:50064947-50064956
7	SPI1	chr12:50064701-50065134	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:50064812-50064980	GM12878	blood:	n/a	n/a
9	CTCF	chr12:50064800-50064950	GM12867	blood:	n/a	n/a
10	RELA	chr12:50064647-50067064	GM12891	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
11	SPI1	chr12:50064717-50065076	GM12878	blood:	n/a	n/a
12	CEBPB	chr12:50064689-50065637	GM12878	blood:	n/a	n/a
13	MYC	chr12:50064690-50065057	NB4	blood:	n/a	chr12:50064845-50064855
14	MTA3	chr12:50064628-50065529	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:50064581-50065171	HL-60	blood:	n/a	n/a
16	STAT5A	chr12:50064565-50065220	GM12878	blood:	n/a	chr12:50064901-50064909
17	TCF3	chr12:50064673-50065091	GM12878	blood:	n/a	n/a
18	SPI1	chr12:50064698-50065046	HL-60	blood:	n/a	n/a
19	CTCF	chr12:50064820-50064970	GM12864	blood:	n/a	chr12:50064947-50064956
20	CTCF	chr12:50064820-50064970	GM12866	blood:	n/a	chr12:50064947-50064956
21	CTCF	chr12:50064900-50065050	GM12873	blood:	n/a	chr12:50064947-50064956
22	RELA	chr12:50064419-50067389	GM19193	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
23	EBF1	chr12:50064722-50065484	GM12878	blood:	n/a	n/a
24	SPI1	chr12:50064703-50065083	GM12891	blood:	n/a	n/a
25	CTCF	chr12:50064920-50065070	GM12868	blood:	n/a	chr12:50064947-50064956
26	POLR2A	chr12:50064578-50066098	GM12892	blood:	n/a	n/a
27	CTCF	chr12:50064840-50064990	GM12865	blood:	n/a	chr12:50064947-50064956
28	RUNX3	chr12:50064659-50065444	GM12878	blood:	n/a	n/a
29	EBF1	chr12:50064894-50065539	GM12878	blood:	n/a	n/a
30	MTA3	chr12:50064454-50065721	GM12878	blood:	n/a	n/a
31	EBF1	chr12:50064628-50065502	GM12878	blood:	n/a	n/a
32	MAX	chr12:50064733-50065072	NB4	blood:	n/a	chr12:50064845-50064855
33	SPI1	chr12:50064766-50064942	GM12878	blood:	n/a	n/a
34	RELA	chr12:50064591-50067007	GM19099	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
35	CTCF	chr12:50064800-50064950	GM12864	blood:	n/a	n/a
36	NFATC1	chr12:50064618-50065741	GM12878	blood:	n/a	n/a
37	RUNX3	chr12:50064648-50065421	GM12878	blood:	n/a	n/a
38	SPI1	chr12:50064611-50065207	HL-60	blood:	n/a	n/a
39	CTCF	chr12:50064860-50065010	GM12873	blood:	n/a	chr12:50064947-50064956
40	RELA	chr12:50064676-50065769	GM10847	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
41	RELA	chr12:50064783-50065602	GM12878	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
42	CTCF	chr12:50064860-50065010	GM12872	blood:	n/a	chr12:50064947-50064956
43	RELA	chr12:50064715-50065761	GM18505	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255

No.	Distal block	Cell Line	Cell type
1	chr12:50062633..50068951-chr12:50134385..50140154,8	K562	blood:
2	chr12:50059879..50062225-chr12:50063774..50067547,4	K562	blood:
3	chr12:50064210..50067102-chr12:50135101..50137236,3	K562	blood:
4	chr12:50016535..50018168-chr12:50064664..50066809,2	K562	blood:
5	chr12:50055936..50058449-chr12:50062400..50065896,4	K562	blood:
6	chr12:50058474..50062820-chr12:50063991..50067805,5	MCF-7	breast:

Variant related genes	Relation type
FMNL3	TF binding region
ENSG00000110844	Chromatin interaction
ENSG00000161791	Chromatin interaction
ENSG00000139644	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1049986	0.92[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1078216	0.85[CHD][hapmap]
rs10875964	0.89[ASN][1000 genomes]
rs10875968	0.84[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11169048	0.87[GIH][hapmap]
rs11169058	0.84[GIH][hapmap]
rs11169059	0.83[GIH][hapmap]
rs11169063	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs11169065	1.00[JPT][hapmap]
rs11169069	0.85[JPT][hapmap]
rs11169073	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs11169080	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11169081	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs11169082	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs11169092	0.85[JPT][hapmap]
rs11169097	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs11169101	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169104	0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169106	0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169109	0.89[ASN][1000 genomes]
rs11169111	0.89[ASN][1000 genomes]
rs11169112	0.89[ASN][1000 genomes]
rs11169118	0.89[ASN][1000 genomes]
rs11169128	0.85[CHD][hapmap]
rs11169130	0.85[CHD][hapmap]
rs11169133	0.89[ASN][1000 genomes]
rs11169140	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs1150057	1.00[JPT][hapmap]
rs11615488	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11833411	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs11834380	0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12296440	0.84[GIH][hapmap]
rs12296586	0.89[ASN][1000 genomes]
rs12299505	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs12301824	0.90[ASN][1000 genomes]
rs12303310	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12304796	0.84[ASN][1000 genomes]
rs12308256	0.87[ASN][1000 genomes]
rs12309940	0.84[ASN][1000 genomes]
rs12310510	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12311839	0.84[JPT][hapmap]
rs12314795	0.89[ASN][1000 genomes]
rs12315224	0.89[ASN][1000 genomes]
rs12315791	0.89[ASN][1000 genomes]
rs12315996	0.84[GIH][hapmap]
rs12316284	0.85[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12317646	0.89[ASN][1000 genomes]
rs12321819	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs13906	0.85[JPT][hapmap]
rs1470906	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1574326	0.92[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17123808	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs17123981	0.84[CEU][hapmap]
rs1902329	1.00[JPT][hapmap]
rs1902330	0.82[JPT][hapmap]
rs2272478	0.84[GIH][hapmap]
rs2278068	1.00[JPT][hapmap]
rs2278069	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2303305	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2336058	0.92[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2878532	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3815832	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs3887727	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3887728	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs4073998	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4133070	0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4563	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4584654	0.92[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs57191490	0.87[ASN][1000 genomes]
rs57342147	0.89[ASN][1000 genomes]
rs59233136	0.92[ASN][1000 genomes]
rs60121503	0.87[ASN][1000 genomes]
rs60402517	0.84[ASN][1000 genomes]
rs61512987	0.90[ASN][1000 genomes]
rs61616163	1.00[ASN][1000 genomes]
rs61620972	0.89[ASN][1000 genomes]
rs61710637	0.89[ASN][1000 genomes]
rs6580719	0.89[ASN][1000 genomes]
rs7131915	0.85[JPT][hapmap]
rs7132792	0.86[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs7136052	0.89[ASN][1000 genomes]
rs7137976	0.92[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7294648	0.84[GIH][hapmap]
rs7295556	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs7296281	0.85[JPT][hapmap]
rs7299002	0.89[ASN][1000 genomes]
rs7299609	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7301209	0.85[JPT][hapmap]
rs7306877	0.93[ASN][1000 genomes]
rs7309607	0.92[ASN][1000 genomes]
rs7312658	0.92[ASN][1000 genomes]
rs7313738	0.89[ASN][1000 genomes]
rs73305085	0.87[ASN][1000 genomes]
rs73305098	0.89[ASN][1000 genomes]
rs73306808	0.89[ASN][1000 genomes]
rs73309030	0.84[ASN][1000 genomes]
rs74089182	0.87[ASN][1000 genomes]
rs7688	0.92[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7952734	0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7952938	0.82[ASN][1000 genomes]
rs7953911	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs7954994	0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7955586	0.92[ASN][1000 genomes]
rs7956089	0.89[ASN][1000 genomes]
rs7956181	0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7962645	0.89[ASN][1000 genomes]
rs7962863	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	0.82[ASW][hapmap];0.92[CEU][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7967624	0.87[ASN][1000 genomes]
rs7970241	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs7973389	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs7975599	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs7975712	1.00[CHB][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap]
rs7977389	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs7979262	0.89[ASN][1000 genomes]
rs7979285	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7980979	0.89[ASN][1000 genomes]
rs8626	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs876889	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs897056	0.92[ASN][1000 genomes]
rs9804749	0.89[ASN][1000 genomes]
rs9804971	0.84[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	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
2	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
3	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:117 , 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	chr12:50052600-50067000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:50052600-50067400	Weak transcription	Fetal Brain Female	brain
5	chr12:50054400-50069800	Enhancers	Left Ventricle	heart
6	chr12:50057400-50066200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:50057600-50065000	Weak transcription	Pancreas	Pancrea
8	chr12:50057600-50065200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:50057600-50066000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:50057600-50066200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:50057600-50066400	Weak transcription	Aorta	Aorta
12	chr12:50057600-50066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:50057600-50067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:50057600-50067000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:50057600-50067200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:50057800-50066200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:50058400-50066000	Weak transcription	Esophagus	oesophagus
18	chr12:50058400-50067200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:50058800-50066000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:50059000-50065000	Weak transcription	HMEC	breast
21	chr12:50059000-50065400	Weak transcription	NHLF	lung
22	chr12:50059000-50066200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:50059000-50066200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:50059600-50065000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:50060000-50065400	Weak transcription	Fetal Intestine Small	intestine
26	chr12:50060000-50066000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:50060000-50066600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:50060400-50069400	Enhancers	Fetal Thymus	thymus
29	chr12:50060800-50065400	Weak transcription	Brain Germinal Matrix	brain
30	chr12:50061000-50065000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:50061600-50065400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:50061800-50065000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:50061800-50065600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:50062000-50065600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:50062000-50069600	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:50062200-50065600	Weak transcription	Osteobl	bone
37	chr12:50062200-50067000	Enhancers	Brain Anterior Caudate	brain
38	chr12:50062400-50065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:50063000-50065800	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr12:50063000-50066400	Enhancers	Brain Angular Gyrus	brain
41	chr12:50063200-50065000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr12:50063200-50065600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:50063200-50066400	Enhancers	Brain Cingulate Gyrus	brain
44	chr12:50063200-50066800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:50063200-50069200	Enhancers	Thymus	Thymus
46	chr12:50063200-50069400	Enhancers	Lung	lung
47	chr12:50063200-50069800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:50063400-50068200	Enhancers	Spleen	Spleen
49	chr12:50063600-50065800	Enhancers	Colon Smooth Muscle	Colon
50	chr12:50063600-50066200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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