Variant report

Variant	rs7972650
Chromosome Location	chr12:46283997-46283998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46282601..46285658-chr12:46286027..46288801,3	K562	blood:
2	chr12:46283214..46284987-chr12:46286727..46288375,2	MCF-7	breast:
3	chr12:45883996..45884939-chr12:46283903..46284713,3	MCF-7	breast:
4	chr12:46273812..46279067-chr12:46282105..46286818,5	K562	blood:

Variant related genes	Relation type
ENSG00000270429	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10161001	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10161062	0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10161510	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10161536	1.00[CHD][hapmap];0.85[YRI][hapmap]
rs10880858	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs11183171	1.00[MEX][hapmap]
rs11183197	1.00[EUR][1000 genomes]
rs11183199	1.00[EUR][1000 genomes]
rs11183202	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs11183211	1.00[CHB][hapmap]
rs11574971	1.00[CHD][hapmap];0.85[YRI][hapmap]
rs12296933	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs12297214	0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12301665	1.00[EUR][1000 genomes]
rs12302862	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs12305110	1.00[EUR][1000 genomes]
rs12309988	1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs12316361	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs12316726	1.00[EUR][1000 genomes]
rs12321106	1.00[EUR][1000 genomes]
rs28583490	1.00[EUR][1000 genomes]
rs55916269	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56338250	1.00[EUR][1000 genomes]
rs58253063	1.00[EUR][1000 genomes]
rs58782185	1.00[EUR][1000 genomes]
rs59340060	1.00[EUR][1000 genomes]
rs6582575	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7132585	1.00[EUR][1000 genomes]
rs7133123	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs7296694	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs7303119	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7308856	0.85[ASW][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs7308893	1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7309921	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs7310702	0.81[YRI][hapmap]
rs7315365	1.00[EUR][1000 genomes]
rs74081382	1.00[EUR][1000 genomes]
rs74081384	1.00[EUR][1000 genomes]
rs74081401	1.00[EUR][1000 genomes]
rs74084208	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7953515	1.00[EUR][1000 genomes]
rs7964495	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7965539	0.85[YRI][hapmap]
rs7970212	0.86[AFR][1000 genomes]
rs7971936	1.00[CHD][hapmap]
rs7973967	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7975170	0.85[ASW][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7975408	0.85[YRI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv558782	chr12:46254995-46286683	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46245400-46318600	Weak transcription	Small Intestine	intestine
2	chr12:46246000-46285400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:46246600-46285400	Weak transcription	NH-A	brain
4	chr12:46246600-46285600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:46246600-46286000	Weak transcription	HMEC	breast
6	chr12:46246800-46288000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:46259000-46316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:46269000-46287000	Weak transcription	Esophagus	oesophagus
9	chr12:46269000-46319200	Weak transcription	Spleen	Spleen
10	chr12:46269200-46289000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:46269400-46316200	Weak transcription	Brain Angular Gyrus	brain
12	chr12:46269600-46285600	Weak transcription	HSMM	muscle
13	chr12:46269600-46285600	Weak transcription	HSMMtube	muscle
14	chr12:46269600-46285800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:46269600-46287800	Weak transcription	Colonic Mucosa	Colon
16	chr12:46269800-46285800	Weak transcription	Fetal Kidney	kidney
17	chr12:46269800-46285800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:46269800-46285800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:46269800-46315800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:46270000-46287200	Weak transcription	Osteobl	bone
21	chr12:46270200-46285800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:46271200-46285400	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:46271200-46285600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:46271400-46285800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:46272800-46285600	Weak transcription	HUVEC	blood vessel
26	chr12:46273400-46285600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:46273400-46307600	Weak transcription	NHLF	lung
28	chr12:46273400-46310200	Weak transcription	Stomach Mucosa	stomach
29	chr12:46273400-46311200	Weak transcription	Right Ventricle	heart
30	chr12:46273400-46314400	Weak transcription	Brain Substantia Nigra	brain
31	chr12:46273600-46286000	Weak transcription	Brain Anterior Caudate	brain
32	chr12:46273800-46285400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:46274600-46288000	Weak transcription	Brain Germinal Matrix	brain
34	chr12:46274800-46285200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:46275000-46288600	Weak transcription	Fetal Heart	heart
36	chr12:46275200-46290000	Weak transcription	Fetal Brain Male	brain
37	chr12:46275400-46285600	Weak transcription	K562	blood
38	chr12:46275800-46287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:46276000-46285600	Weak transcription	Aorta	Aorta
40	chr12:46277400-46285200	Weak transcription	Hela-S3	cervix
41	chr12:46277800-46292400	Strong transcription	Dnd41	blood
42	chr12:46278200-46285800	Weak transcription	NHDF-Ad	bronchial
43	chr12:46279000-46285800	Weak transcription	NHEK	skin
44	chr12:46279600-46285000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:46279600-46285400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:46279600-46285600	Weak transcription	HepG2	liver
47	chr12:46279800-46285000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:46279800-46285600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:46279800-46285600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:46279800-46287000	Weak transcription	H1 Cell Line	embryonic stem cell

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