Variant report

Variant	rs10005764
Chromosome Location	chr4:152113901-152113902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152108334..152110110-chr4:152112946..152114914,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10016856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10028324	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11099784	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027541	1.00[EUR][1000 genomes]
rs17027575	1.00[EUR][1000 genomes]
rs28399915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28401367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28432996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28493533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28566074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594255	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28644282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28658039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28791569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28836884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56681758	1.00[EUR][1000 genomes]
rs58001315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58602547	1.00[EUR][1000 genomes]
rs60001201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60661732	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6812606	1.00[AMR][1000 genomes]
rs6820298	1.00[EUR][1000 genomes]
rs6855493	1.00[EUR][1000 genomes]
rs6856037	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72967593	1.00[EUR][1000 genomes]
rs73859998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73860000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73861187	1.00[EUR][1000 genomes]
rs73861286	1.00[EUR][1000 genomes]
rs7658238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7659047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9918061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991362	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997354	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152088200-152114600	Weak transcription	Psoas Muscle	Psoas
2	chr4:152096600-152118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:152096800-152120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:152097200-152123600	Weak transcription	Pancreas	Pancrea
5	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
6	chr4:152097400-152123600	Weak transcription	Aorta	Aorta
7	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:152097800-152117200	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:152097800-152120000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:152098200-152117000	Weak transcription	Brain Anterior Caudate	brain
11	chr4:152098200-152118400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:152098400-152116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:152098400-152118400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:152100200-152116600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:152100600-152118000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:152106600-152115600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:152106600-152116600	Weak transcription	NHEK	skin
19	chr4:152106600-152117200	Weak transcription	Left Ventricle	heart
20	chr4:152106800-152116600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:152107200-152116000	Weak transcription	Ovary	ovary
22	chr4:152107200-152120000	Weak transcription	HepG2	liver
23	chr4:152107600-152116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:152111800-152116600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:152112000-152117200	Weak transcription	Lung	lung
26	chr4:152112200-152116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:152112200-152117200	Weak transcription	Right Atrium	heart
28	chr4:152112200-152120000	Weak transcription	Right Ventricle	heart
29	chr4:152112400-152117200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:152112400-152117200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:152112400-152120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:152112600-152116000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:152112600-152117200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:152112600-152117400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:152112800-152120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:152113400-152115000	Enhancers	Fetal Heart	heart
37	chr4:152113400-152124400	Weak transcription	Fetal Intestine Small	intestine
38	chr4:152113600-152114800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:152113600-152117200	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:152113800-152114800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:152113800-152114800	Enhancers	Adipose Nuclei	Adipose
42	chr4:152113800-152115800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links