Variant report

Variant	rs1979237
Chromosome Location	chr12:123325895-123325896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123325084..123327709-chr12:123347219..123349157,2	MCF-7	breast:
2	chr12:123311285..123313219-chr12:123325523..123328002,2	MCF-7	breast:
3	chr12:123324556..123326269-chr12:123405620..123407753,2	MCF-7	breast:
4	chr12:123255502..123257176-chr12:123324408..123327320,2	MCF-7	breast:
5	chr12:123324046..123325972-chr12:123462562..123465553,2	MCF-7	breast:
6	chr12:123324513..123326875-chr12:123435236..123437199,2	MCF-7	breast:
7	chr12:123324539..123327696-chr12:123450573..123452120,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150967	Chromatin interaction
ENSG00000182196	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10773627	0.90[ASN][1000 genomes]
rs10773657	0.90[ASN][1000 genomes]
rs10847826	0.90[ASN][1000 genomes]
rs10847869	0.90[ASN][1000 genomes]
rs11060064	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11060065	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11060208	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11060209	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12298151	0.87[ASN][1000 genomes]
rs12298664	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299742	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12303328	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12313006	0.83[ASN][1000 genomes]
rs12314494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314544	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319654	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321131	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12426809	0.90[ASN][1000 genomes]
rs1532835	0.88[ASN][1000 genomes]
rs1587856	0.80[ASN][1000 genomes]
rs1671685	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696326	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696349	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799618	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979236	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100500	1.00[ASN][1000 genomes]
rs2135014	0.88[ASN][1000 genomes]
rs2271051	0.85[ASN][1000 genomes]
rs2292131	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292132	0.88[ASN][1000 genomes]
rs2292134	0.86[ASN][1000 genomes]
rs2292135	0.84[ASN][1000 genomes]
rs2292136	0.82[ASN][1000 genomes]
rs2292138	0.80[ASN][1000 genomes]
rs2292139	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2343108	0.88[ASN][1000 genomes]
rs2343109	0.80[ASN][1000 genomes]
rs2343685	0.90[ASN][1000 genomes]
rs2649908	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649909	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880678	0.90[ASN][1000 genomes]
rs3817094	0.87[ASN][1000 genomes]
rs3852536	0.86[ASN][1000 genomes]
rs4759355	0.94[ASN][1000 genomes]
rs4759389	0.90[ASN][1000 genomes]
rs4759392	0.81[ASN][1000 genomes]
rs56272219	1.00[ASN][1000 genomes]
rs58182048	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59192320	0.85[ASN][1000 genomes]
rs59922385	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60308342	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7138398	0.80[ASN][1000 genomes]
rs7294991	0.81[ASN][1000 genomes]
rs7303024	1.00[ASN][1000 genomes]
rs7309225	0.81[ASN][1000 genomes]
rs73421642	1.00[ASN][1000 genomes]
rs735378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398546	0.84[ASN][1000 genomes]
rs754080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897385	0.80[ASN][1000 genomes]
rs897386	0.80[ASN][1000 genomes]
rs897391	0.90[ASN][1000 genomes]
rs897392	0.90[ASN][1000 genomes]
rs897393	0.90[ASN][1000 genomes]
rs921808	0.88[ASN][1000 genomes]
rs936083	0.82[ASN][1000 genomes]
rs937520	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937766	0.88[ASN][1000 genomes]
rs9788290	0.81[AMR][1000 genomes];0.86[ASN][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	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123321600-123326400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:123321600-123327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123321600-123332800	Weak transcription	Ovary	ovary
4	chr12:123321600-123333000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:123321800-123326200	Enhancers	Brain Anterior Caudate	brain
6	chr12:123321800-123336800	Weak transcription	Aorta	Aorta
7	chr12:123322000-123332400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:123322400-123329000	Weak transcription	Thymus	Thymus
9	chr12:123322600-123332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:123322800-123326200	Enhancers	HepG2	liver
11	chr12:123322800-123327200	Enhancers	Liver	Liver
12	chr12:123322800-123329600	Weak transcription	Spleen	Spleen
13	chr12:123322800-123334000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:123322800-123334400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:123322800-123339600	Weak transcription	Dnd41	blood
16	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:123323000-123326200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:123323000-123326600	Weak transcription	K562	blood
19	chr12:123323000-123330400	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr12:123323200-123326800	Genic enhancers	NHEK	skin
21	chr12:123323200-123340800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:123323400-123335200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:123323600-123326200	Strong transcription	Fetal Stomach	stomach
25	chr12:123323600-123326600	Strong transcription	Primary T cells from cord blood	blood
26	chr12:123323600-123332400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:123323600-123340800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:123323800-123326000	Genic enhancers	Pancreas	Pancrea
29	chr12:123323800-123326400	Genic enhancers	Duodenum Mucosa	Duodenum
30	chr12:123323800-123326600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:123323800-123327600	Genic enhancers	Fetal Intestine Small	intestine
32	chr12:123323800-123329200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:123323800-123331000	Enhancers	Stomach Mucosa	stomach
34	chr12:123324000-123326200	Weak transcription	Fetal Kidney	kidney
35	chr12:123324000-123327400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:123324200-123326800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:123324200-123327200	Strong transcription	Primary B cells from cord blood	blood
38	chr12:123324400-123326400	Enhancers	Right Ventricle	heart
39	chr12:123324400-123326600	Enhancers	NHLF	lung
40	chr12:123324400-123326800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr12:123324400-123328200	Enhancers	Lung	lung
42	chr12:123324400-123328400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr12:123324600-123326000	Enhancers	Hela-S3	cervix
44	chr12:123324600-123326400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:123324600-123326600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:123324600-123326600	Enhancers	Psoas Muscle	Psoas
47	chr12:123324600-123326800	Enhancers	Esophagus	oesophagus
48	chr12:123324600-123326800	Enhancers	NHDF-Ad	bronchial
49	chr12:123324600-123327400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:123324600-123327600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links