Variant report

Variant	rs56334239
Chromosome Location	chr5:9166642-9166643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10039094	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10039096	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10044766	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10475457	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10475458	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11948082	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11952859	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11960524	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354182	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13356945	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13362456	0.83[EUR][1000 genomes]
rs13436248	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13436321	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1806077	0.93[EUR][1000 genomes]
rs1806089	0.83[EUR][1000 genomes]
rs1806110	0.93[EUR][1000 genomes]
rs1806125	0.83[EUR][1000 genomes]
rs2074608	0.83[EUR][1000 genomes]
rs3026340	0.83[EUR][1000 genomes]
rs3777276	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777277	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777278	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777279	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777280	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777282	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797916	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797917	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797918	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797919	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797922	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797923	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797924	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797925	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797929	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3797931	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797932	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797933	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797934	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797936	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822769	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822770	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822773	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822774	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55980672	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56043446	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56705339	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62343367	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62343370	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6555595	0.83[EUR][1000 genomes]
rs72643788	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72643790	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72643791	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72643792	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72643793	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72643794	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv880683	chr5:9091164-9170323	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9136800-9176400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:9136800-9189000	Weak transcription	Pancreas	Pancrea
3	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:9151000-9169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:9151200-9168800	Weak transcription	NH-A	brain
6	chr5:9152400-9171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:9153800-9183400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:9154000-9226200	Weak transcription	Fetal Intestine Large	intestine
9	chr5:9154800-9170200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:9154800-9173400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:9154800-9176200	Weak transcription	Fetal Intestine Small	intestine
12	chr5:9154800-9176400	Weak transcription	Aorta	Aorta
13	chr5:9155000-9174200	Weak transcription	Liver	Liver
14	chr5:9156800-9171400	Weak transcription	Fetal Stomach	stomach
15	chr5:9157400-9167000	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:9157600-9176400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:9157800-9168200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:9158000-9167400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:9162200-9172000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:9163800-9189200	Weak transcription	Fetal Heart	heart
21	chr5:9164000-9168800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:9164600-9170200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:9164800-9166800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:9165200-9185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:9165400-9167200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:9165600-9167000	Enhancers	Brain Substantia Nigra	brain
27	chr5:9165600-9167800	Enhancers	Dnd41	blood
28	chr5:9165600-9168000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:9165600-9170400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:9165600-9170400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:9165800-9167200	Enhancers	Fetal Lung	lung
32	chr5:9166200-9167600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:9166400-9166800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:9166400-9166800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:9166400-9167400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:9166400-9167400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr5:9166400-9167600	Enhancers	Osteobl	bone
38	chr5:9166400-9167800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:9166400-9168600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:9166400-9170000	Enhancers	Brain Germinal Matrix	brain
41	chr5:9166600-9166800	Weak transcription	Fetal Brain Male	brain
42	chr5:9166600-9167200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:9166600-9167600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:9166600-9167600	Enhancers	NHDF-Ad	bronchial
45	chr5:9166600-9168000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:9166600-9176800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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