Variant report

Variant	rs7571562
Chromosome Location	chr2:55234312-55234313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55233909..55236096-chr2:55275198..55277851,2	K562	blood:
2	chr2:55221144..55223516-chr2:55232255..55235111,2	K562	blood:
3	chr2:55232527..55234772-chr2:55240251..55243156,4	K562	blood:
4	chr2:55219389..55222736-chr2:55233484..55237490,3	MCF-7	breast:
5	chr2:55233328..55235365-chr2:55235431..55237589,2	K562	blood:
6	chr2:55228082..55231303-chr2:55231498..55236378,7	K562	blood:
7	chr2:55224682..55227904-chr2:55233478..55236485,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs15029	0.81[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046509	1.00[EUR][1000 genomes]
rs17046510	1.00[EUR][1000 genomes]
rs1992615	0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2972097	0.82[YRI][hapmap]
rs4254542	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57207110	1.00[EUR][1000 genomes]
rs6718315	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6729675	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6747990	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72910826	1.00[EUR][1000 genomes]
rs72910837	1.00[EUR][1000 genomes]
rs72910854	1.00[EUR][1000 genomes]
rs7559999	0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7576504	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7584654	1.00[EUR][1000 genomes]
rs7585495	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7607946	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
3	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:55220400-55236800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:55223000-55237200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55224800-55236800	Enhancers	A549	lung
8	chr2:55225200-55234600	Enhancers	Liver	Liver
9	chr2:55226600-55237200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:55226800-55235200	Enhancers	Colon Smooth Muscle	Colon
11	chr2:55226800-55236600	Weak transcription	Right Atrium	heart
12	chr2:55226800-55237000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:55227000-55236600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:55227200-55236800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55227400-55236800	Weak transcription	Fetal Brain Male	brain
16	chr2:55227400-55237000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:55227600-55236400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:55227600-55236800	Weak transcription	HSMMtube	muscle
19	chr2:55227600-55239000	Weak transcription	Hela-S3	cervix
20	chr2:55227800-55234400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:55227800-55234400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:55227800-55235600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:55227800-55236800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:55227800-55236800	Weak transcription	NH-A	brain
25	chr2:55228000-55234400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:55228000-55236400	Weak transcription	GM12878-XiMat	blood
27	chr2:55228000-55236600	Weak transcription	Primary B cells from cord blood	blood
28	chr2:55228400-55235800	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:55228400-55236000	Enhancers	Brain Hippocampus Middle	brain
30	chr2:55228400-55236200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:55228600-55235000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:55229000-55235800	Weak transcription	Fetal Kidney	kidney
33	chr2:55229000-55236800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:55229600-55237200	Weak transcription	Pancreas	Pancrea
35	chr2:55230000-55236600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:55230600-55235200	Enhancers	Fetal Intestine Small	intestine
37	chr2:55230800-55237000	Weak transcription	HUVEC	blood vessel
38	chr2:55231000-55234600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:55231000-55235000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:55231000-55237400	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr2:55231000-55238200	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr2:55231200-55234600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:55231200-55234600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:55231600-55236600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:55231600-55236800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:55232000-55236600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr2:55232000-55236800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr2:55232200-55234400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:55232200-55234800	Enhancers	Fetal Lung	lung
50	chr2:55232200-55236600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links