Variant report

Variant	rs7166478
Chromosome Location	chr15:52906322-52906323
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	chr15:52906245..52907882-chr15:52919782..52921282,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10775148	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10775149	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070904	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11070910	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11629479	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11634879	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12102061	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12900462	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908944	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12916276	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12916405	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414162	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414164	0.81[AMR][1000 genomes]
rs2414165	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414168	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414169	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414170	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2414171	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2414174	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414176	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414177	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2899493	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35756938	0.88[EUR][1000 genomes]
rs35760898	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4386077	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4404000	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4774635	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776064	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62025584	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62025586	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6493570	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7162184	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7168045	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7169849	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7179310	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8026469	0.86[AMR][1000 genomes]
rs8032889	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8035115	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8036671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8036680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8040787	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8042646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs933858	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs933859	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9806267	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52861200-52925200	Weak transcription	Stomach Mucosa	stomach
2	chr15:52861800-52908400	Weak transcription	Gastric	stomach
3	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
4	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
5	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:52872600-52920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:52873400-52928000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:52873800-52909600	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:52874200-52917000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:52875400-52916200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:52878200-52909600	Strong transcription	Liver	Liver
14	chr15:52882200-52920000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:52882400-52926000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
17	chr15:52891400-52927600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:52891600-52908400	Weak transcription	Aorta	Aorta
19	chr15:52899000-52920400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:52899600-52917000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:52900200-52906400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:52900400-52909600	Strong transcription	Adipose Nuclei	Adipose
24	chr15:52900400-52911800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:52900600-52907800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:52900600-52909600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:52901200-52906800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:52901200-52907400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:52901400-52907000	Strong transcription	Thymus	Thymus
32	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:52902400-52908000	Weak transcription	Psoas Muscle	Psoas
34	chr15:52902400-52911000	Weak transcription	A549	lung
35	chr15:52902400-52914200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:52902400-52916400	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:52902400-52925200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:52902400-52934800	Weak transcription	NH-A	brain
39	chr15:52902600-52914000	Weak transcription	Lung	lung
40	chr15:52902600-52915800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:52902600-52916400	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:52902600-52927400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:52902600-52942000	Weak transcription	HUVEC	blood vessel
44	chr15:52902800-52916400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:52903000-52911000	Weak transcription	HSMM	muscle
46	chr15:52903400-52925400	Weak transcription	Brain Germinal Matrix	brain
47	chr15:52903400-52933800	Weak transcription	Fetal Heart	heart
48	chr15:52903400-52943800	Weak transcription	Hela-S3	cervix
49	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:52903600-52907400	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links