Variant report

Variant	rs593610
Chromosome Location	chr10:5951563-5951564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5950213..5953065-chr10:6017303..6019683,2	MCF-7	breast:
2	chr10:5951474..5953291-chr10:5960290..5963166,2	K562	blood:
3	chr10:5946370..5949809-chr10:5950035..5953033,4	K562	blood:
4	chr10:5948073..5950157-chr10:5951295..5953499,3	MCF-7	breast:
5	chr10:5855622..5857223-chr10:5951043..5953758,2	MCF-7	breast:
6	chr10:5928731..5931390-chr10:5949628..5953556,4	K562	blood:

Variant related genes	Relation type
ENSG00000057608	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000272764	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000134470	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2274029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2669122	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2669126	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4293039	0.82[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap]
rs582359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591510	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591878	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.99[ASN][1000 genomes]
rs595923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598331	0.90[ASN][1000 genomes]
rs603780	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607728	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs610093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs621628	0.98[ASN][1000 genomes]
rs622758	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs626344	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs633797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs633928	1.00[ASN][1000 genomes]
rs633930	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs635532	0.97[ASN][1000 genomes]
rs636578	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs647945	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649537	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs664603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs668498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670856	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs672126	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs680020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685852	0.99[ASN][1000 genomes]
rs686854	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688388	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792348	0.84[ASN][1000 genomes]
rs907687	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap]
rs980230	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap]

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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:5933600-5951600	Weak transcription	Stomach Mucosa	stomach
3	chr10:5935600-5962000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr10:5936600-5952600	Weak transcription	Hela-S3	cervix
5	chr10:5936800-5953200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
7	chr10:5944400-5952000	Strong transcription	K562	blood
8	chr10:5944400-5955000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr10:5944600-5952800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
11	chr10:5945000-5953800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
13	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
15	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
16	chr10:5947400-5970800	Strong transcription	Liver	Liver
17	chr10:5947400-5974400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr10:5947600-5968400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:5947600-5968600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:5947600-5968600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:5947600-5975000	Strong transcription	Primary T cells from cord blood	blood
23	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr10:5947800-5961000	Strong transcription	Fetal Brain Female	brain
29	chr10:5947800-5974000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:5947800-5974400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr10:5947800-5974600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr10:5948000-5955800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:5948000-5960200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr10:5948000-5974600	Strong transcription	Fetal Lung	lung
35	chr10:5948000-5974800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr10:5948000-5975000	Strong transcription	Primary B cells from cord blood	blood
37	chr10:5948000-5975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr10:5948200-5974000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr10:5948200-5974800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:5948400-5952000	Strong transcription	Fetal Stomach	stomach
41	chr10:5948400-5952400	Weak transcription	Right Atrium	heart
42	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr10:5948600-5952200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr10:5948600-5952400	Strong transcription	Fetal Muscle Leg	muscle
46	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr10:5948800-5974200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links