Variant report

Variant	rs11960268
Chromosome Location	chr5:108303131-108303132
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:108300744..108303743-chr5:108308321..108310024,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10043207	0.82[EUR][1000 genomes]
rs10061582	0.86[ASN][1000 genomes]
rs10447249	0.80[EUR][1000 genomes]
rs10515399	1.00[ASN][1000 genomes]
rs11948270	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948684	0.83[EUR][1000 genomes]
rs11950165	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11951285	0.86[EUR][1000 genomes]
rs11951595	0.85[EUR][1000 genomes]
rs11953198	0.81[AFR][1000 genomes]
rs11955924	0.86[EUR][1000 genomes]
rs11956572	0.86[EUR][1000 genomes]
rs11956900	0.91[EUR][1000 genomes]
rs11958129	0.86[EUR][1000 genomes]
rs11960336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960400	0.85[EUR][1000 genomes]
rs12153527	0.85[EUR][1000 genomes]
rs12153646	0.85[EUR][1000 genomes]
rs12188521	0.83[EUR][1000 genomes]
rs17534347	0.83[EUR][1000 genomes]
rs17534396	0.83[EUR][1000 genomes]
rs28733366	0.89[ASN][1000 genomes]
rs3797818	0.91[ASN][1000 genomes]
rs3797819	0.90[ASN][1000 genomes]
rs3797820	0.90[ASN][1000 genomes]
rs3797821	0.91[ASN][1000 genomes]
rs3797823	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3797825	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797827	0.83[EUR][1000 genomes]
rs3797830	0.83[EUR][1000 genomes]
rs3822684	0.84[EUR][1000 genomes]
rs4404726	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4957793	1.00[ASN][1000 genomes]
rs55899933	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56121551	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56382548	0.86[EUR][1000 genomes]
rs57158292	0.81[AFR][1000 genomes]
rs57221554	0.86[EUR][1000 genomes]
rs57814250	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58255942	0.82[EUR][1000 genomes]
rs58499805	0.86[EUR][1000 genomes]
rs58647764	1.00[ASN][1000 genomes]
rs58729959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59409290	0.83[EUR][1000 genomes]
rs60584949	0.86[EUR][1000 genomes]
rs60834821	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66623856	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66851282	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67053762	0.94[ASN][1000 genomes]
rs67586696	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6861439	0.85[ASN][1000 genomes]
rs6867147	0.91[EUR][1000 genomes]
rs6872299	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882759	1.00[ASN][1000 genomes]
rs6884648	1.00[ASN][1000 genomes]
rs6893501	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893984	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72789336	0.91[EUR][1000 genomes]
rs72789338	0.91[EUR][1000 genomes]
rs72789339	0.91[EUR][1000 genomes]
rs72790513	0.91[EUR][1000 genomes]
rs72790518	0.87[EUR][1000 genomes]
rs72790537	0.86[EUR][1000 genomes]
rs72790543	0.86[EUR][1000 genomes]
rs72790544	0.86[EUR][1000 genomes]
rs72790554	0.85[EUR][1000 genomes]
rs72790558	0.85[EUR][1000 genomes]
rs72790564	0.85[EUR][1000 genomes]
rs72790571	0.83[EUR][1000 genomes]
rs72790572	0.83[EUR][1000 genomes]
rs72793921	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73209364	0.97[ASN][1000 genomes]
rs73209368	0.96[ASN][1000 genomes]
rs73209370	0.98[ASN][1000 genomes]
rs73211527	0.98[ASN][1000 genomes]
rs73211528	0.98[ASN][1000 genomes]
rs73211549	1.00[ASN][1000 genomes]
rs73211553	1.00[ASN][1000 genomes]
rs73211559	1.00[ASN][1000 genomes]
rs73211560	1.00[ASN][1000 genomes]
rs73778332	0.97[ASN][1000 genomes]
rs73778336	0.98[ASN][1000 genomes]
rs73778344	1.00[ASN][1000 genomes]
rs73778358	1.00[ASN][1000 genomes]
rs73778371	0.91[EUR][1000 genomes]
rs73778394	0.86[EUR][1000 genomes]
rs73779112	0.83[EUR][1000 genomes]
rs73780406	0.85[EUR][1000 genomes]
rs73781924	0.85[EUR][1000 genomes]
rs7719638	0.98[ASN][1000 genomes]
rs7723942	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7725708	0.83[EUR][1000 genomes]
rs7726922	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7731116	0.97[ASN][1000 genomes]
rs7731221	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7732335	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7732510	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7734092	0.96[ASN][1000 genomes]
rs7734110	0.96[ASN][1000 genomes]
rs7735749	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
3	chr5:108254000-108311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:108277600-108322400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:108278000-108308200	Weak transcription	Fetal Kidney	kidney
6	chr5:108279200-108325600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:108281000-108313400	Weak transcription	Adipose Nuclei	Adipose
8	chr5:108282200-108324600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:108282400-108327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:108283400-108319000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:108287800-108310000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:108289200-108309200	Weak transcription	Hela-S3	cervix
13	chr5:108289200-108318600	Weak transcription	NHDF-Ad	bronchial
14	chr5:108290000-108313600	Weak transcription	Aorta	Aorta
15	chr5:108290000-108322000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:108290000-108328800	Weak transcription	Esophagus	oesophagus
17	chr5:108293400-108303400	Weak transcription	Fetal Lung	lung
18	chr5:108293400-108325600	Weak transcription	NHEK	skin
19	chr5:108294400-108329400	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:108295200-108319400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:108295800-108316600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:108296600-108307800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:108296600-108311800	Weak transcription	HSMMtube	muscle
24	chr5:108297000-108313400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:108298000-108316400	Weak transcription	Brain Substantia Nigra	brain
26	chr5:108298200-108315800	Weak transcription	HepG2	liver
27	chr5:108299600-108328800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:108300400-108314200	Weak transcription	NH-A	brain
29	chr5:108301400-108328600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:108301600-108361200	Weak transcription	Primary T cells from cord blood	blood
31	chr5:108301800-108318600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:108302200-108330200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:108302400-108303200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:108302400-108303200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:108302400-108303200	ZNF genes & repeats	Dnd41	blood
36	chr5:108302600-108303200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:108302600-108303200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:108302600-108303200	ZNF genes & repeats	Liver	Liver
39	chr5:108302600-108303200	ZNF genes & repeats	Fetal Stomach	stomach
40	chr5:108302600-108303200	ZNF genes & repeats	Ovary	ovary
41	chr5:108302600-108303200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:108302600-108303400	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr5:108302600-108303600	Strong transcription	HMEC	breast
44	chr5:108302600-108303800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr5:108302800-108303200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:108302800-108304000	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr5:108303000-108303200	Strong transcription	Pancreas	Pancrea
48	chr5:108303000-108310000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:108303000-108313600	Weak transcription	Lung	lung
50	chr5:108303000-108318800	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links