Variant report

Variant	rs73906055
Chromosome Location	chr20:25029362-25029363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25028498..25030240-chr4:2818576..2820268,2	MCF-7	breast:
2	chr20:25022614..25025327-chr20:25028235..25031123,4	MCF-7	breast:
3	chr20:25026036..25030944-chr20:25033529..25038477,7	MCF-7	breast:
4	chr20:25027984..25032783-chr20:25034265..25037344,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11907003	1.00[EUR][1000 genomes]
rs11908037	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12106059	1.00[EUR][1000 genomes]
rs12106164	1.00[EUR][1000 genomes]
rs12373881	1.00[EUR][1000 genomes]
rs28435893	1.00[EUR][1000 genomes]
rs35022349	1.00[EUR][1000 genomes]
rs56273742	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56976560	1.00[EUR][1000 genomes]
rs57218388	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57293656	1.00[EUR][1000 genomes]
rs58236424	1.00[EUR][1000 genomes]
rs58957358	1.00[EUR][1000 genomes]
rs60310205	1.00[EUR][1000 genomes]
rs60479943	1.00[EUR][1000 genomes]
rs6050367	1.00[EUR][1000 genomes]
rs6106987	1.00[EUR][1000 genomes]
rs6114952	1.00[EUR][1000 genomes]
rs7261401	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7270236	0.90[AMR][1000 genomes];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]
rs73337199	1.00[EUR][1000 genomes]
rs73339096	1.00[EUR][1000 genomes]
rs73339099	1.00[EUR][1000 genomes]
rs73339100	1.00[EUR][1000 genomes]
rs73341103	1.00[EUR][1000 genomes]
rs73341112	1.00[EUR][1000 genomes]
rs73341114	1.00[EUR][1000 genomes]
rs73341120	1.00[EUR][1000 genomes]
rs73348712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906063	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906065	1.00[EUR][1000 genomes]
rs73906067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906068	1.00[EUR][1000 genomes]
rs73906070	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906071	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906072	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906076	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs8114108	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8119273	1.00[EUR][1000 genomes]
rs8121557	1.00[EUR][1000 genomes]
rs8123929	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25016600-25034800	Weak transcription	A549	lung
2	chr20:25017800-25034200	Weak transcription	Fetal Kidney	kidney
3	chr20:25020600-25037400	Enhancers	Psoas Muscle	Psoas
4	chr20:25021200-25032600	Weak transcription	NHDF-Ad	bronchial
5	chr20:25022200-25033000	Weak transcription	Brain Germinal Matrix	brain
6	chr20:25024000-25032400	Weak transcription	Small Intestine	intestine
7	chr20:25024200-25031200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:25024400-25032400	Strong transcription	Fetal Intestine Small	intestine
9	chr20:25024400-25032600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr20:25024400-25032600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr20:25024400-25033000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr20:25024600-25031800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr20:25024600-25033200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr20:25025400-25029600	Strong transcription	Dnd41	blood
15	chr20:25025400-25030600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:25025600-25029400	Strong transcription	Primary T cells from cord blood	blood
17	chr20:25026000-25029400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr20:25026000-25030200	Enhancers	Liver	Liver
19	chr20:25026200-25029400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:25026200-25029600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr20:25026400-25029400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr20:25026400-25032600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr20:25026400-25033000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr20:25026400-25034600	Enhancers	Fetal Heart	heart
25	chr20:25026800-25029400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr20:25026800-25032200	Strong transcription	Thymus	Thymus
27	chr20:25027000-25029800	Genic enhancers	Gastric	stomach
28	chr20:25027000-25030000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr20:25027000-25030200	Strong transcription	Fetal Intestine Large	intestine
30	chr20:25027400-25032400	Genic enhancers	Fetal Muscle Leg	muscle
31	chr20:25027800-25037000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr20:25028000-25030200	Enhancers	Esophagus	oesophagus
33	chr20:25028200-25029400	Weak transcription	Brain Angular Gyrus	brain
34	chr20:25028400-25029600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr20:25028400-25029600	Genic enhancers	Duodenum Mucosa	Duodenum
36	chr20:25028400-25032200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr20:25028400-25034800	Enhancers	Left Ventricle	heart
38	chr20:25028600-25030400	Enhancers	Brain Anterior Caudate	brain
39	chr20:25028600-25031000	Weak transcription	GM12878-XiMat	blood
40	chr20:25028600-25031400	Enhancers	Fetal Lung	lung
41	chr20:25028600-25031800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr20:25028600-25033600	Enhancers	Right Atrium	heart
43	chr20:25028600-25037200	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr20:25028800-25029400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr20:25028800-25029800	Enhancers	Stomach Mucosa	stomach
46	chr20:25028800-25030200	Weak transcription	HepG2	liver
47	chr20:25028800-25031200	Weak transcription	Colonic Mucosa	Colon
48	chr20:25028800-25031200	Genic enhancers	Fetal Stomach	stomach
49	chr20:25028800-25031600	Enhancers	Lung	lung
50	chr20:25028800-25031800	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links