Variant report

Variant	rs1080731
Chromosome Location	chr15:52920658-52920659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52911171..52913383-chr15:52919987..52922783,2	MCF-7	breast:
2	chr15:52919730..52922195-chr15:52969757..52972620,2	MCF-7	breast:
3	chr15:52906245..52907882-chr15:52919782..52921282,2	MCF-7	breast:
4	chr15:52920111..52923064-chr15:52929395..52931419,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10851520	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10851521	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11070906	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11070907	1.00[CHB][hapmap]
rs11070909	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs11853917	1.00[CHB][hapmap]
rs11855616	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11857150	1.00[CHB][hapmap]
rs12594964	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898644	1.00[CHB][hapmap]
rs12902679	1.00[CHB][hapmap]
rs12914502	1.00[CHB][hapmap]
rs12915981	1.00[CHB][hapmap]
rs13329393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17614559	1.00[CHB][hapmap]
rs1863512	0.89[CHB][hapmap]
rs2288271	1.00[CHB][hapmap]
rs2414160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2414161	1.00[CHB][hapmap]
rs2414163	1.00[CHB][hapmap]
rs2414166	1.00[CHB][hapmap]
rs2414167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28368342	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899492	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751614	1.00[CHB][hapmap]
rs4390542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4548810	0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs4636853	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4774634	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4776058	1.00[CHB][hapmap]
rs4776063	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776065	1.00[CHB][hapmap]
rs4776066	1.00[CHB][hapmap]
rs7167494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73396785	0.82[EUR][1000 genomes]
rs8026800	1.00[CHB][hapmap]
rs8030141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8030871	1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs8036979	1.00[TSI][hapmap]
rs933860	1.00[CHB][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	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	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
4	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
5	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:103 , 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	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
3	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
4	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:52872600-52920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:52873400-52928000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:52882400-52926000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
11	chr15:52891400-52927600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:52902400-52925200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:52902400-52934800	Weak transcription	NH-A	brain
18	chr15:52902600-52927400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:52902600-52942000	Weak transcription	HUVEC	blood vessel
20	chr15:52903400-52925400	Weak transcription	Brain Germinal Matrix	brain
21	chr15:52903400-52933800	Weak transcription	Fetal Heart	heart
22	chr15:52903400-52943800	Weak transcription	Hela-S3	cervix
23	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:52903600-52942400	Weak transcription	Dnd41	blood
25	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
26	chr15:52904000-52922800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:52904000-52934400	Weak transcription	Fetal Brain Male	brain
28	chr15:52904000-52943400	Weak transcription	Fetal Kidney	kidney
29	chr15:52904000-52945400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
31	chr15:52904800-52928400	Weak transcription	Osteobl	bone
32	chr15:52906200-52934200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:52906200-52944000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:52908600-52956200	Weak transcription	Gastric	stomach
35	chr15:52909000-52925400	Weak transcription	Brain Angular Gyrus	brain
36	chr15:52909000-52942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:52909600-52922400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:52909600-52922800	Weak transcription	NHDF-Ad	bronchial
39	chr15:52909600-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
41	chr15:52910400-52928600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:52912200-52924200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr15:52912200-52933200	Weak transcription	HSMM	muscle
44	chr15:52913400-52928800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:52914400-52925600	Weak transcription	Fetal Intestine Small	intestine
46	chr15:52914400-52927600	Weak transcription	Lung	lung
47	chr15:52914600-52920800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr15:52915000-52921400	Weak transcription	Left Ventricle	heart
49	chr15:52915000-52926200	Weak transcription	Fetal Stomach	stomach
50	chr15:52915000-52927600	Weak transcription	Aorta	Aorta

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