Variant report

Variant	rs2564943
Chromosome Location	chr3:53139058-53139059
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	chr3:53137358..53139996-chr3:53159100..53161040,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12486028	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1991567	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2564925	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2564927	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2564946	1.00[EUR][1000 genomes]
rs2581814	1.00[EUR][1000 genomes]
rs2710315	1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs4234640	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4687685	1.00[EUR][1000 genomes]
rs4687690	1.00[EUR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs58561805	0.93[AFR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs72967404	1.00[EUR][1000 genomes]
rs72967414	0.93[AFR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9833487	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9869545	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53107800-53151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:53117800-53147200	Weak transcription	Psoas Muscle	Psoas
3	chr3:53119000-53154200	Weak transcription	Stomach Mucosa	stomach
4	chr3:53120800-53144400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:53121400-53142600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr3:53122400-53143200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:53122800-53152200	Weak transcription	Small Intestine	intestine
8	chr3:53123200-53148600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:53124200-53151600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:53124800-53139400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:53127000-53154200	Weak transcription	Right Atrium	heart
12	chr3:53127400-53144000	Weak transcription	Fetal Heart	heart
13	chr3:53130800-53146400	Strong transcription	Fetal Intestine Large	intestine
14	chr3:53131200-53139200	Strong transcription	Dnd41	blood
15	chr3:53131600-53139600	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr3:53131600-53140800	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:53131600-53144000	Strong transcription	Liver	Liver
18	chr3:53131800-53139400	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr3:53131800-53140800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:53132000-53139600	Strong transcription	Aorta	Aorta
21	chr3:53132000-53139600	Strong transcription	Thymus	Thymus
22	chr3:53132000-53141800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:53132000-53148000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:53132200-53140200	Strong transcription	Right Ventricle	heart
25	chr3:53132400-53139400	Strong transcription	Ovary	ovary
26	chr3:53132400-53139800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:53132800-53139200	Strong transcription	Brain Angular Gyrus	brain
28	chr3:53133000-53139600	Strong transcription	Left Ventricle	heart
29	chr3:53133600-53152600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:53133800-53139200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:53133800-53144000	Weak transcription	Fetal Kidney	kidney
32	chr3:53134000-53139200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:53134800-53143600	Strong transcription	Placenta	Placenta
34	chr3:53135000-53139400	Strong transcription	Esophagus	oesophagus
35	chr3:53135000-53139800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:53135000-53140600	Strong transcription	Brain Germinal Matrix	brain
37	chr3:53135000-53140600	Strong transcription	Fetal Brain Female	brain
38	chr3:53135000-53140800	Strong transcription	Brain Hippocampus Middle	brain
39	chr3:53135000-53144600	Strong transcription	Lung	lung
40	chr3:53135200-53139200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:53135200-53139200	Genic enhancers	Fetal Thymus	thymus
42	chr3:53135200-53139800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:53135200-53139800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr3:53135200-53140600	Strong transcription	Brain Anterior Caudate	brain
45	chr3:53135200-53141400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:53135200-53143000	Strong transcription	Fetal Stomach	stomach
47	chr3:53135200-53146000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:53135400-53139200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr3:53135400-53139200	Strong transcription	Brain Substantia Nigra	brain
50	chr3:53135400-53139200	Strong transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links