Variant report

Variant	rs60485189
Chromosome Location	chr5:179208132-179208133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179206337..179209276-chr5:179211151..179214245,3	K562	blood:
2	chr5:179207473..179209466-chr5:179245089..179247994,2	MCF-7	breast:
3	chr5:179207715..179210288-chr5:179217795..179219761,2	MCF-7	breast:
4	chr5:179201375..179203959-chr5:179207512..179210271,2	MCF-7	breast:
5	chr5:179207543..179209811-chr5:179227923..179230897,2	MCF-7	breast:
6	chr5:179207814..179210287-chr5:179215624..179217168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs2291417	0.91[AMR][1000 genomes]
rs2291418	0.91[AMR][1000 genomes]
rs55800082	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55815501	1.00[EUR][1000 genomes]
rs55915939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55952102	0.94[EUR][1000 genomes]
rs55967209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56093222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56719864	0.91[AFR][1000 genomes]
rs57463529	0.96[AFR][1000 genomes]
rs58722253	0.96[AFR][1000 genomes]
rs58826518	0.91[AMR][1000 genomes]
rs59108011	0.84[AFR][1000 genomes]
rs59566858	0.96[AFR][1000 genomes]
rs59651103	0.96[AFR][1000 genomes]
rs59721505	0.96[AFR][1000 genomes]
rs59745533	0.96[AFR][1000 genomes]
rs59824837	0.96[AFR][1000 genomes]
rs60716268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60910702	0.87[AFR][1000 genomes]
rs61682673	0.96[AFR][1000 genomes]
rs66465242	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66685266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66686562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66995745	0.91[AMR][1000 genomes]
rs67211456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67637906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67832593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67879510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67952129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865507	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807319	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807328	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807332	1.00[EUR][1000 genomes]
rs72807337	1.00[EUR][1000 genomes]
rs72809763	0.94[EUR][1000 genomes]
rs72809769	0.94[EUR][1000 genomes]
rs72809771	0.94[EUR][1000 genomes]
rs72809773	0.94[EUR][1000 genomes]
rs72809775	1.00[EUR][1000 genomes]
rs72809781	1.00[EUR][1000 genomes]
rs72809782	1.00[EUR][1000 genomes]
rs72809783	1.00[EUR][1000 genomes]
rs72809785	1.00[EUR][1000 genomes]
rs72809787	1.00[EUR][1000 genomes]
rs72809790	1.00[EUR][1000 genomes]
rs72809792	1.00[EUR][1000 genomes]
rs72809794	1.00[EUR][1000 genomes]
rs72809795	1.00[EUR][1000 genomes]
rs72809796	1.00[EUR][1000 genomes]
rs72809798	1.00[EUR][1000 genomes]
rs72809802	1.00[EUR][1000 genomes]
rs73338115	0.88[AFR][1000 genomes]
rs73342167	0.96[AFR][1000 genomes]
rs73347986	0.96[AFR][1000 genomes]
rs73349908	0.96[AFR][1000 genomes]
rs73351620	0.84[AFR][1000 genomes]
rs73351626	0.84[AFR][1000 genomes]
rs73351628	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179191200-179210400	Strong transcription	Thymus	Thymus
2	chr5:179192200-179210400	Strong transcription	Brain Germinal Matrix	brain
3	chr5:179192600-179209800	Strong transcription	Primary T cells from cord blood	blood
4	chr5:179192800-179209800	Strong transcription	Fetal Brain Female	brain
5	chr5:179193000-179210400	Strong transcription	Fetal Stomach	stomach
6	chr5:179193600-179209600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:179193800-179208400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:179193800-179209400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179193800-179209600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:179194600-179210400	Strong transcription	Fetal Intestine Small	intestine
11	chr5:179195800-179208600	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:179196000-179209800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:179196000-179210400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:179196600-179208600	Weak transcription	Fetal Heart	heart
15	chr5:179199800-179214000	Weak transcription	Fetal Brain Male	brain
16	chr5:179200800-179208600	Weak transcription	Stomach Mucosa	stomach
17	chr5:179201400-179210400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:179201600-179209200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:179202000-179221800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:179202600-179209000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:179203400-179209200	Weak transcription	Hela-S3	cervix
22	chr5:179203400-179209400	Weak transcription	NHEK	skin
23	chr5:179203400-179211800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:179203400-179213400	Weak transcription	Psoas Muscle	Psoas
25	chr5:179203400-179218200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:179203400-179221600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:179203600-179208800	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:179203600-179209400	Weak transcription	K562	blood
29	chr5:179203600-179211600	Weak transcription	NHDF-Ad	bronchial
30	chr5:179203600-179219600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr5:179203600-179220400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:179203600-179222000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:179204000-179221200	Weak transcription	Small Intestine	intestine
34	chr5:179204600-179210400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:179205000-179218800	Weak transcription	Right Atrium	heart
36	chr5:179205200-179208600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:179205200-179210400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr5:179205200-179220600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:179205200-179221800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr5:179205400-179209400	Weak transcription	HUVEC	blood vessel
41	chr5:179205600-179209600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:179206000-179208600	Weak transcription	HMEC	breast
43	chr5:179206000-179210200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:179206000-179210400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:179206000-179211600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:179206000-179220200	Weak transcription	Ovary	ovary
47	chr5:179206200-179208800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:179206200-179209600	Weak transcription	Fetal Kidney	kidney
49	chr5:179206400-179214600	Weak transcription	HepG2	liver
50	chr5:179206400-179219200	Weak transcription	Gastric	stomach

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