Variant report

Variant	rs11564153
Chromosome Location	chr12:40634991-40634992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10506143	1.00[JPT][hapmap]
rs10506144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs10506146	1.00[JPT][hapmap]
rs10506147	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506154	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10878244	1.00[JPT][hapmap]
rs11175186	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11175593	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564107	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564108	1.00[JPT][hapmap]
rs11564123	1.00[JPT][hapmap]
rs11564131	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs11564145	1.00[CEU][hapmap]
rs11564152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11564185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564196	1.00[JPT][hapmap]
rs11564199	0.87[EUR][1000 genomes]
rs11564209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564212	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564216	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11564218	1.00[JPT][hapmap]
rs11564253	1.00[CEU][hapmap]
rs11564255	1.00[CEU][hapmap]
rs11564256	1.00[CEU][hapmap]
rs11564266	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs11564271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12422278	0.83[AMR][1000 genomes]
rs12422390	1.00[CEU][hapmap]
rs12422527	0.83[AMR][1000 genomes]
rs12422544	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12422796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423419	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs12423551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12423566	1.00[CHB][hapmap]
rs12423986	1.00[CEU][hapmap]
rs12424040	0.93[EUR][1000 genomes]
rs12424294	1.00[JPT][hapmap]
rs12424424	1.00[CEU][hapmap]
rs12425561	1.00[JPT][hapmap]
rs12425677	1.00[CEU][hapmap]
rs12425678	1.00[CEU][hapmap]
rs12426378	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12426639	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12426903	1.00[CEU][hapmap]
rs12427022	1.00[JPT][hapmap]
rs12427134	1.00[CEU][hapmap]
rs12427245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1365768	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs1365769	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs1388585	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1388597	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491945	0.82[AMR][1000 genomes]
rs17442924	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443078	0.86[EUR][1000 genomes]
rs17443178	0.80[EUR][1000 genomes]
rs17443185	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443206	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17443656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17443909	0.87[EUR][1000 genomes]
rs17444028	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17444054	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17444103	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17444646	1.00[CEU][hapmap]
rs17444667	1.00[CEU][hapmap]
rs17444688	1.00[CEU][hapmap]
rs17444744	1.00[CEU][hapmap]
rs17444751	1.00[CEU][hapmap]
rs17458549	0.93[EUR][1000 genomes]
rs17458808	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17461575	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17461664	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461692	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17465610	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17465946	0.87[EUR][1000 genomes]
rs17466016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17466626	1.00[CEU][hapmap]
rs17466907	1.00[CEU][hapmap]
rs17466969	1.00[CEU][hapmap]
rs17467039	1.00[CEU][hapmap]
rs17467081	1.00[CEU][hapmap]
rs17467088	1.00[CEU][hapmap]
rs17467102	1.00[CEU][hapmap]
rs17467116	1.00[CEU][hapmap]
rs17467137	1.00[CEU][hapmap]
rs17467144	1.00[CEU][hapmap]
rs17484003	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17484141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17484342	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17484493	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17484541	0.81[AMR][1000 genomes]
rs17492152	1.00[CEU][hapmap]
rs2017917	1.00[CEU][hapmap]
rs2131081	1.00[JPT][hapmap]
rs2638223	0.86[EUR][1000 genomes]
rs2708460	0.86[EUR][1000 genomes]
rs28365169	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs28365173	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs28365206	0.82[AMR][1000 genomes]
rs28365229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28365689	0.93[EUR][1000 genomes]
rs34567498	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs36212067	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36220738	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789329	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs3899331	1.00[CEU][hapmap]
rs4628750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4767965	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768213	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4768226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768248	1.00[CEU][hapmap]
rs4768249	1.00[CEU][hapmap]
rs4768251	1.00[CEU][hapmap]
rs4768254	1.00[CEU][hapmap]
rs72547977	0.87[EUR][1000 genomes]
rs729215	0.93[EUR][1000 genomes]
rs7485401	1.00[CEU][hapmap]
rs7487209	1.00[CEU][hapmap]

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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
4	nsv1042967	chr12:40629636-40710319	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619400-40644400	Weak transcription	Gastric	stomach
2	chr12:40619600-40636400	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
5	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:40620400-40644200	Weak transcription	Brain Angular Gyrus	brain
7	chr12:40620800-40644200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:40620800-40648000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:40620800-40659200	Weak transcription	Brain Anterior Caudate	brain
10	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
11	chr12:40621000-40643800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
16	chr12:40629200-40635600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:40630600-40643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:40631200-40646600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:40631600-40636200	Weak transcription	NHLF	lung
22	chr12:40632000-40655200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:40632000-40656000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr12:40632400-40635200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:40632600-40635200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:40632600-40635400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:40632600-40635400	Weak transcription	A549	lung
28	chr12:40632600-40635800	Weak transcription	Osteobl	bone
29	chr12:40632800-40635400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:40632800-40635600	Weak transcription	NHDF-Ad	bronchial
31	chr12:40633200-40635400	Weak transcription	Hela-S3	cervix
32	chr12:40633200-40643800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:40633400-40635400	Weak transcription	Adipose Nuclei	Adipose
34	chr12:40633400-40646600	Weak transcription	Ovary	ovary
35	chr12:40633400-40654200	Weak transcription	Aorta	Aorta
36	chr12:40633600-40636200	Weak transcription	Liver	Liver
37	chr12:40634400-40635800	Enhancers	Primary B cells from peripheral blood	blood
38	chr12:40634400-40636200	Genic enhancers	Primary B cells from cord blood	blood
39	chr12:40634600-40635000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:40634600-40635000	Enhancers	Spleen	Spleen
41	chr12:40634800-40635000	ZNF genes & repeats	Lung	lung
42	chr12:40634800-40635000	ZNF genes & repeats	Pancreas	Pancrea
43	chr12:40634800-40635200	Enhancers	Right Atrium	heart

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