Variant report

Variant	rs12580302
Chromosome Location	chr12:51702505-51702506
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51701016..51703258-chr12:51704233..51707521,3	MCF-7	breast:
2	chr12:51696998..51699958-chr12:51701711..51703812,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11169800	0.80[ASN][1000 genomes]
rs12578771	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12580599	0.81[ASN][1000 genomes]
rs12581282	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17860277	0.84[EUR][1000 genomes]
rs17860287	0.87[EUR][1000 genomes]
rs17860296	0.89[EUR][1000 genomes]
rs17860302	0.89[EUR][1000 genomes]
rs17860346	0.85[EUR][1000 genomes]
rs17860364	0.84[EUR][1000 genomes]
rs17860365	0.85[EUR][1000 genomes]
rs17860378	0.84[EUR][1000 genomes]
rs17860380	0.85[EUR][1000 genomes]
rs17860382	0.85[EUR][1000 genomes]
rs17860387	0.85[EUR][1000 genomes]
rs1991433	0.81[EUR][1000 genomes]
rs2288367	0.85[EUR][1000 genomes]
rs3858637	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55901988	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57484374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58213562	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58673573	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60641385	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60797544	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61172662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61380773	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61570206	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61605107	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7138394	0.93[EUR][1000 genomes]
rs7308177	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7311196	0.84[EUR][1000 genomes]
rs7312857	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7316221	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316301	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7316604	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74093810	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74093814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74093823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74093827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74093853	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7975715	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51674200-51704000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:51681800-51714200	Weak transcription	Gastric	stomach
3	chr12:51686200-51702800	Weak transcription	Colonic Mucosa	Colon
4	chr12:51687000-51703800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:51687000-51707400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:51687800-51708000	Strong transcription	Thymus	Thymus
7	chr12:51696600-51712400	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr12:51698400-51712600	Weak transcription	Spleen	Spleen
9	chr12:51699200-51709400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:51699800-51710000	Strong transcription	Fetal Thymus	thymus
11	chr12:51700600-51703000	Weak transcription	Esophagus	oesophagus
12	chr12:51700600-51711000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:51700800-51703000	Weak transcription	Primary B cells from cord blood	blood
14	chr12:51701200-51704000	Enhancers	Stomach Mucosa	stomach
15	chr12:51701400-51703000	Enhancers	Fetal Intestine Small	intestine
16	chr12:51701400-51703000	Flanking Active TSS	A549	lung
17	chr12:51701400-51703000	Enhancers	Osteobl	bone
18	chr12:51701400-51704000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:51701400-51704800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr12:51701400-51706800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr12:51701400-51708600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:51701600-51702600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:51701600-51702600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:51701600-51702600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr12:51701600-51702600	Enhancers	K562	blood
26	chr12:51701600-51702600	Enhancers	NHEK	skin
27	chr12:51701600-51702800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:51701600-51703000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:51701600-51703000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:51701600-51703000	Enhancers	Fetal Intestine Large	intestine
31	chr12:51701600-51703000	Flanking Active TSS	Hela-S3	cervix
32	chr12:51701600-51703000	Enhancers	HMEC	breast
33	chr12:51701600-51703000	Enhancers	NHDF-Ad	bronchial
34	chr12:51701600-51703200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:51701600-51706400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr12:51701600-51706600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:51701600-51708400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr12:51701800-51702600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr12:51701800-51703000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:51701800-51703000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:51701800-51703200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:51702000-51703000	Weak transcription	Small Intestine	intestine
43	chr12:51702000-51705400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr12:51702200-51702600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:51702200-51702600	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr12:51702200-51702600	Enhancers	HSMMtube	muscle
47	chr12:51702200-51703000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr12:51702200-51703000	Active TSS	Rectal Smooth Muscle	rectum
49	chr12:51702200-51703400	Strong transcription	Placenta	Placenta
50	chr12:51702200-51703600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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