Variant report

Variant	rs296738
Chromosome Location	chr12:50383369-50383370
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	chr12:50382916..50385099-chr12:50400045..50401974,2	MCF-7	breast:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	RACGAP1	hsa-miR-16-5p	chr12:50383365-50383387

Variant related genes	Relation type
RACGAP1	miRNA target site

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11169179	1.00[EUR][1000 genomes]
rs11169181	1.00[EUR][1000 genomes]
rs11169272	1.00[AMR][1000 genomes]
rs11169273	1.00[AMR][1000 genomes]
rs11169279	1.00[AMR][1000 genomes]
rs11169280	1.00[AMR][1000 genomes]
rs12299109	1.00[AMR][1000 genomes]
rs12305438	1.00[AMR][1000 genomes]
rs12309501	1.00[AMR][1000 genomes]
rs12316969	1.00[EUR][1000 genomes]
rs12318294	1.00[EUR][1000 genomes]
rs2697111	1.00[EUR][1000 genomes]
rs296735	1.00[AMR][1000 genomes]
rs296748	1.00[EUR][1000 genomes]
rs296749	1.00[EUR][1000 genomes]
rs296753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs296755	1.00[EUR][1000 genomes]
rs296757	1.00[EUR][1000 genomes]
rs296758	1.00[EUR][1000 genomes]
rs296761	1.00[EUR][1000 genomes]
rs296764	1.00[EUR][1000 genomes]
rs296765	1.00[EUR][1000 genomes]
rs372753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs425726	1.00[EUR][1000 genomes]
rs455037	1.00[EUR][1000 genomes]
rs55800109	1.00[AMR][1000 genomes]
rs57143574	1.00[AMR][1000 genomes]
rs57596053	1.00[AMR][1000 genomes]
rs60009415	1.00[EUR][1000 genomes]
rs61221429	1.00[AMR][1000 genomes]
rs672697	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7312996	1.00[AMR][1000 genomes]
rs73310966	1.00[EUR][1000 genomes]
rs74090092	1.00[AMR][1000 genomes]
rs74090094	1.00[AMR][1000 genomes]
rs74092539	1.00[AMR][1000 genomes]
rs7963427	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
9	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50362600-50385800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:50367400-50401200	Weak transcription	Gastric	stomach
3	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
4	chr12:50372400-50404800	Weak transcription	Spleen	Spleen
5	chr12:50375200-50385400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:50376200-50383800	Weak transcription	Primary T cells from cord blood	blood
7	chr12:50376400-50385800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:50376800-50384000	Weak transcription	Primary B cells from cord blood	blood
9	chr12:50377200-50384600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:50377600-50403200	Weak transcription	Ovary	ovary
11	chr12:50377600-50405600	Strong transcription	Fetal Thymus	thymus
12	chr12:50377800-50384000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:50377800-50399800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:50377800-50400800	Strong transcription	Thymus	Thymus
15	chr12:50378000-50386400	Weak transcription	Adipose Nuclei	Adipose
16	chr12:50378000-50399000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:50378200-50383600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:50378200-50385800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:50378200-50399200	Weak transcription	Fetal Brain Male	brain
20	chr12:50378200-50400000	Weak transcription	HSMMtube	muscle
21	chr12:50378400-50385800	Weak transcription	Brain Angular Gyrus	brain
22	chr12:50378400-50385800	Weak transcription	Lung	lung
23	chr12:50378400-50386000	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:50378400-50386600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:50378600-50383600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:50378600-50383600	Weak transcription	Fetal Brain Female	brain
27	chr12:50378600-50383800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:50378600-50385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:50378600-50385800	Weak transcription	Esophagus	oesophagus
30	chr12:50378600-50385800	Weak transcription	Left Ventricle	heart
31	chr12:50378600-50391800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:50378600-50400600	Strong transcription	A549	lung
33	chr12:50378600-50412800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:50378800-50385800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:50378800-50385800	Weak transcription	Brain Anterior Caudate	brain
36	chr12:50378800-50385800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:50378800-50385800	Weak transcription	Brain Substantia Nigra	brain
38	chr12:50378800-50385800	Weak transcription	Placenta	Placenta
39	chr12:50378800-50396000	Weak transcription	Right Ventricle	heart
40	chr12:50378800-50401400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:50379000-50385400	Weak transcription	Fetal Intestine Small	intestine
42	chr12:50379000-50385800	Weak transcription	Fetal Kidney	kidney
43	chr12:50379000-50388200	Strong transcription	NHEK	skin
44	chr12:50379000-50405800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:50379200-50401400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:50379400-50384600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:50379400-50401400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:50379400-50405600	Strong transcription	Hela-S3	cervix
49	chr12:50379600-50383600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:50379600-50383800	Weak transcription	Primary T cells fromperipheralblood	blood

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