Variant report

Variant	rs11960400
Chromosome Location	chr5:108363903-108363904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10043207	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10062069	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10447249	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11240990	0.84[ASN][1000 genomes]
rs11948270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11948684	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951285	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11951595	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]
rs11954988	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11955924	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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11956572	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11956900	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11958129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11960268	0.85[EUR][1000 genomes]
rs11960336	0.85[EUR][1000 genomes]
rs12152788	0.95[ASN][1000 genomes]
rs12153527	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]
rs12153646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186663	0.91[ASN][1000 genomes]
rs12188107	0.95[ASN][1000 genomes]
rs12188521	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366081	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17534347	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534396	0.85[CHB][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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]
rs3797823	0.82[CEU][hapmap]
rs3797825	0.83[CEU][hapmap]
rs3797827	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797830	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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];0.82[ASN][1000 genomes]
rs3797837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3797847	1.00[JPT][hapmap]
rs3822684	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822685	1.00[JPT][hapmap]
rs4404726	0.88[EUR][1000 genomes]
rs4957795	1.00[YRI][hapmap]
rs55899933	0.90[EUR][1000 genomes]
rs56083128	1.00[ASN][1000 genomes]
rs56382548	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57221554	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57814250	0.85[EUR][1000 genomes]
rs58255942	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58499805	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58729959	0.85[EUR][1000 genomes]
rs59409290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60584949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60834821	0.89[EUR][1000 genomes]
rs61304250	0.91[ASN][1000 genomes]
rs66623856	0.81[EUR][1000 genomes]
rs6865572	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6867147	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6869929	0.91[ASN][1000 genomes]
rs6872299	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6882698	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6884133	1.00[JPT][hapmap]
rs6886017	0.91[ASN][1000 genomes]
rs6889213	0.91[ASN][1000 genomes]
rs6893501	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs72789336	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72789338	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72789339	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72790513	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72790518	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790522	0.95[ASN][1000 genomes]
rs72790537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72790554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790569	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790570	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73778341	0.91[ASN][1000 genomes]
rs73778362	0.91[ASN][1000 genomes]
rs73778371	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73778393	0.91[ASN][1000 genomes]
rs73778394	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73779105	1.00[ASN][1000 genomes]
rs73779109	1.00[ASN][1000 genomes]
rs73779112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73779120	1.00[ASN][1000 genomes]
rs73780404	0.95[ASN][1000 genomes]
rs73780405	0.95[ASN][1000 genomes]
rs73780406	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73781919	1.00[ASN][1000 genomes]
rs73781924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702557	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7709840	0.84[JPT][hapmap]
rs7714599	1.00[JPT][hapmap]
rs7718925	1.00[JPT][hapmap]
rs7719229	0.95[ASN][1000 genomes]
rs7723580	0.95[ASN][1000 genomes]
rs7723942	0.80[EUR][1000 genomes]
rs7725708	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7726922	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs7729380	1.00[JPT][hapmap]
rs7732335	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs7732510	0.80[EUR][1000 genomes]
rs7733971	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7734437	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9688204	0.95[ASN][1000 genomes]
rs9688214	0.95[ASN][1000 genomes]
rs9885203	0.85[CHB][hapmap];0.86[JPT][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	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	nsv4952	chr5:108324146-108369353	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830443	chr5:108326491-108496723	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108350800-108390400	Weak transcription	HSMMtube	muscle
2	chr5:108352400-108365000	Weak transcription	Fetal Intestine Large	intestine
3	chr5:108352400-108381400	Weak transcription	Fetal Lung	lung
4	chr5:108356000-108399000	Weak transcription	HSMM	muscle
5	chr5:108356400-108364200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:108356400-108389200	Weak transcription	Primary B cells from cord blood	blood
7	chr5:108358000-108366400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:108358400-108366600	Weak transcription	Esophagus	oesophagus
9	chr5:108360200-108364000	Weak transcription	HepG2	liver
10	chr5:108360200-108364200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:108360200-108374000	Weak transcription	HUVEC	blood vessel
12	chr5:108360400-108364200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:108360400-108364200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:108360400-108364400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:108360400-108366000	Weak transcription	Fetal Heart	heart
16	chr5:108360400-108366200	Weak transcription	Left Ventricle	heart
17	chr5:108360400-108366600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:108360400-108367400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:108360400-108369000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:108360400-108371400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:108360400-108373400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:108360400-108381200	Weak transcription	Adipose Nuclei	Adipose
23	chr5:108360400-108389000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:108360400-108389400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:108360400-108389600	Weak transcription	Brain Angular Gyrus	brain
26	chr5:108360400-108389800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:108360400-108389800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:108360400-108400400	Weak transcription	NHEK	skin
29	chr5:108360400-108404800	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:108360400-108425200	Weak transcription	Aorta	Aorta
31	chr5:108360600-108364200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:108360600-108365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:108360600-108366200	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:108360600-108382400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:108360600-108385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:108363200-108367000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:108363400-108365200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:108363400-108366000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:108363600-108364800	Enhancers	NHDF-Ad	bronchial
40	chr5:108363800-108364600	Enhancers	A549	lung
41	chr5:108363800-108364800	Enhancers	Muscle Satellite Cultured Cells	--

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