Variant report

Variant	rs11716079
Chromosome Location	chr3:178706028-178706029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804875	0.85[ASN][1000 genomes]
rs10936987	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936988	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715852	0.93[EUR][1000 genomes]
rs11918186	0.93[EUR][1000 genomes]
rs11926798	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245916	0.85[ASN][1000 genomes]
rs4254707	0.88[ASN][1000 genomes]
rs4328857	0.85[ASN][1000 genomes]
rs4583702	0.85[ASN][1000 genomes]
rs4955797	0.87[ASN][1000 genomes]
rs4955799	0.87[ASN][1000 genomes]
rs57935620	0.84[EUR][1000 genomes]
rs59942474	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61179484	0.93[EUR][1000 genomes]
rs61626196	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6443608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761999	0.87[ASN][1000 genomes]
rs6778195	0.86[ASN][1000 genomes]
rs6780631	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794243	0.85[ASN][1000 genomes]
rs6794279	0.93[EUR][1000 genomes]
rs6797848	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611854	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7638121	0.84[EUR][1000 genomes]
rs9815772	0.87[ASN][1000 genomes]
rs9816837	0.88[ASN][1000 genomes]
rs9832291	0.86[ASN][1000 genomes]
rs9841497	0.85[ASN][1000 genomes]
rs9862902	0.85[ASN][1000 genomes]
rs9871126	0.87[ASN][1000 genomes]

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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178704000-178710000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr3:178704200-178708600	ZNF genes & repeats	Liver	Liver
3	chr3:178704200-178710600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
4	chr3:178704800-178708200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:178705000-178706200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:178705200-178706400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
7	chr3:178705200-178707000	ZNF genes & repeats	HSMMtube	muscle
8	chr3:178705200-178708400	ZNF genes & repeats	Aorta	Aorta
9	chr3:178705400-178707000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr3:178705400-178707000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr3:178705400-178707000	ZNF genes & repeats	HSMM	muscle
12	chr3:178705400-178709200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:178705600-178706800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
14	chr3:178705600-178708200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:178705800-178706800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
16	chr3:178705800-178707000	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr3:178705800-178707200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
18	chr3:178706000-178707000	ZNF genes & repeats	Brain Substantia Nigra	brain
19	chr3:178706000-178707400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:178706000-178708600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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