Variant report

Variant	rs11948270
Chromosome Location	chr5:108304246-108304247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10043207	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs10061582	0.86[ASN][1000 genomes]
rs10062069	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10447249	0.80[EUR][1000 genomes]
rs10515399	1.00[ASN][1000 genomes]
rs11948684	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11950165	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11951285	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs11951595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11953198	0.92[YRI][hapmap]
rs11955924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11956572	0.86[EUR][1000 genomes]
rs11956900	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11958129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11960268	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960336	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12153527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12153646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12188521	0.83[EUR][1000 genomes]
rs1366081	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17534347	0.83[EUR][1000 genomes]
rs17534396	0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs1896582	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2416196	1.00[CHB][hapmap]
rs2416197	1.00[CHB][hapmap];0.91[JPT][hapmap]
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	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3797825	0.81[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[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]
rs3797832	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3797833	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3797834	1.00[JPT][hapmap]
rs3797837	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3797847	1.00[JPT][hapmap]
rs3822684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3822685	1.00[JPT][hapmap]
rs4404726	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4957793	1.00[ASN][1000 genomes]
rs55899933	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56121551	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56382548	0.86[EUR][1000 genomes]
rs57221554	0.86[EUR][1000 genomes]
rs57814250	0.91[AFR][1000 genomes];0.94[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	0.97[AFR][1000 genomes];0.94[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	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66851282	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67053762	0.94[ASN][1000 genomes]
rs67586696	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6861439	0.85[ASN][1000 genomes]
rs6865572	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6867147	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6872299	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882698	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6882759	1.00[ASN][1000 genomes]
rs6884133	1.00[JPT][hapmap]
rs6884648	1.00[ASN][1000 genomes]
rs6893501	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893984	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72789336	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72789338	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72789339	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72790513	0.80[AMR][1000 genomes];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	0.94[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	0.80[AMR][1000 genomes];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]
rs7702557	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7709840	0.84[JPT][hapmap]
rs7714599	1.00[JPT][hapmap]
rs7719638	0.98[ASN][1000 genomes]
rs7723942	0.92[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]
rs7729380	1.00[JPT][hapmap]
rs7731116	0.97[ASN][1000 genomes]
rs7731221	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7732335	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7732510	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7733971	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7734092	0.96[ASN][1000 genomes]
rs7734110	0.96[ASN][1000 genomes]
rs7734437	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7735749	1.00[ASN][1000 genomes]
rs9885203	0.85[CHB][hapmap];0.86[JPT][hapmap]

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	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
3	esv3423505	chr5:108304153-108307151	Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:53 , 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	chr5:108293400-108325600	Weak transcription	NHEK	skin
18	chr5:108294400-108329400	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:108295200-108319400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:108295800-108316600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:108296600-108307800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:108296600-108311800	Weak transcription	HSMMtube	muscle
23	chr5:108297000-108313400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:108298000-108316400	Weak transcription	Brain Substantia Nigra	brain
25	chr5:108298200-108315800	Weak transcription	HepG2	liver
26	chr5:108299600-108328800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:108300400-108314200	Weak transcription	NH-A	brain
28	chr5:108301400-108328600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:108301600-108361200	Weak transcription	Primary T cells from cord blood	blood
30	chr5:108301800-108318600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:108302200-108330200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:108303000-108310000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:108303000-108313600	Weak transcription	Lung	lung
34	chr5:108303000-108318800	Weak transcription	Brain Angular Gyrus	brain
35	chr5:108303000-108319400	Weak transcription	HSMM	muscle
36	chr5:108303000-108329000	Weak transcription	Gastric	stomach
37	chr5:108303200-108304800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:108303200-108305200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:108303200-108309200	Weak transcription	Liver	Liver
40	chr5:108303200-108311000	Weak transcription	Dnd41	blood
41	chr5:108303200-108315400	Weak transcription	Fetal Stomach	stomach
42	chr5:108303200-108318800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:108303200-108321200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:108303200-108322200	Weak transcription	Pancreas	Pancrea
45	chr5:108303200-108322400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:108303200-108331800	Weak transcription	Ovary	ovary
47	chr5:108303400-108312400	Weak transcription	Fetal Muscle Leg	muscle
48	chr5:108303600-108304800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:108303600-108315600	Weak transcription	HMEC	breast
50	chr5:108303800-108321000	Weak transcription	Fetal Lung	lung

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