Variant report

Variant	rs56976560
Chromosome Location	chr20:24938766-24938767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24932720..24935500-chr20:24938353..24940512,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11087478	1.00[EUR][1000 genomes]
rs11907003	1.00[EUR][1000 genomes]
rs11908037	1.00[EUR][1000 genomes]
rs35022349	1.00[EUR][1000 genomes]
rs56273742	1.00[EUR][1000 genomes]
rs56776926	1.00[EUR][1000 genomes]
rs56871329	1.00[EUR][1000 genomes]
rs57218388	1.00[EUR][1000 genomes]
rs58236424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60310205	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050009	1.00[EUR][1000 genomes]
rs6106954	1.00[EUR][1000 genomes]
rs6106955	1.00[EUR][1000 genomes]
rs6106956	1.00[EUR][1000 genomes]
rs6106987	1.00[EUR][1000 genomes]
rs6114879	1.00[EUR][1000 genomes]
rs6114883	1.00[EUR][1000 genomes]
rs6114885	1.00[EUR][1000 genomes]
rs6114889	1.00[EUR][1000 genomes]
rs6114952	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61169433	1.00[EUR][1000 genomes]
rs7270236	1.00[EUR][1000 genomes]
rs73333142	1.00[EUR][1000 genomes]
rs73333167	1.00[EUR][1000 genomes]
rs73333174	1.00[EUR][1000 genomes]
rs73333187	1.00[EUR][1000 genomes]
rs73337236	1.00[EUR][1000 genomes]
rs73337245	1.00[EUR][1000 genomes]
rs73337248	1.00[EUR][1000 genomes]
rs73337258	1.00[EUR][1000 genomes]
rs73337265	1.00[EUR][1000 genomes]
rs73337267	1.00[EUR][1000 genomes]
rs73337270	1.00[EUR][1000 genomes]
rs73337284	1.00[EUR][1000 genomes]
rs73348712	1.00[EUR][1000 genomes]
rs73906055	1.00[EUR][1000 genomes]
rs73906057	1.00[EUR][1000 genomes]
rs73906063	1.00[EUR][1000 genomes]
rs73906065	1.00[EUR][1000 genomes]
rs73906067	1.00[EUR][1000 genomes]
rs73906068	1.00[EUR][1000 genomes]
rs73906070	1.00[EUR][1000 genomes]
rs73906071	1.00[EUR][1000 genomes]
rs73906072	1.00[EUR][1000 genomes]
rs8114108	1.00[EUR][1000 genomes]
rs8119958	1.00[EUR][1000 genomes]
rs8123929	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24928600-24940400	Weak transcription	Right Atrium	heart
2	chr20:24930200-24939400	Weak transcription	Right Ventricle	heart
3	chr20:24930400-24939000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:24930600-24943000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:24931400-24939600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr20:24932000-24943000	Weak transcription	HSMM	muscle
7	chr20:24932000-24943400	Weak transcription	HSMMtube	muscle
8	chr20:24932200-24941000	Weak transcription	A549	lung
9	chr20:24932600-24939200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr20:24933200-24940400	Weak transcription	Colon Smooth Muscle	Colon
11	chr20:24933600-24939000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr20:24933800-24941600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:24933800-24943800	Weak transcription	NHEK	skin
14	chr20:24934600-24943200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr20:24935000-24939000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
16	chr20:24935000-24943000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr20:24935000-24943800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr20:24935000-24953600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr20:24935200-24943200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr20:24935200-24957600	Strong transcription	Liver	Liver
21	chr20:24935200-24971800	Weak transcription	K562	blood
22	chr20:24935400-24940200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr20:24935400-24943000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr20:24935600-24940200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr20:24935800-24939400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr20:24935800-24941200	Weak transcription	Small Intestine	intestine
27	chr20:24935800-24942600	Weak transcription	Osteobl	bone
28	chr20:24935800-24945200	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr20:24936000-24939800	Weak transcription	Primary B cells from cord blood	blood
30	chr20:24936000-24941000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr20:24936000-24942000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr20:24936000-24955600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr20:24936200-24939000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr20:24936200-24939800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr20:24936200-24940600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr20:24936200-24941400	Strong transcription	Brain Angular Gyrus	brain
37	chr20:24936200-24947400	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr20:24936200-24954400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr20:24936400-24940000	Strong transcription	Brain Cingulate Gyrus	brain
40	chr20:24936400-24941600	Strong transcription	Esophagus	oesophagus
41	chr20:24936400-24943000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr20:24936400-24947000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr20:24936400-24954400	Strong transcription	Fetal Intestine Small	intestine
44	chr20:24936400-24954400	Strong transcription	Fetal Stomach	stomach
45	chr20:24936400-24954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr20:24936400-24954600	Strong transcription	Brain Germinal Matrix	brain
47	chr20:24936400-24954600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr20:24936400-24954800	Strong transcription	Spleen	Spleen
49	chr20:24936400-24956000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr20:24936600-24939200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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