Variant report

Variant	rs56316091
Chromosome Location	chr12:51763758-51763759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51762201..51772634-chr12:51780037..51787148,16	MCF-7	breast:
2	chr12:51761344..51767144-chr12:51781671..51788039,11	MCF-7	breast:
3	chr12:51762991..51769009-chr12:51771008..51777485,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139629	Chromatin interaction
ENSG00000050438	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2067764	1.00[AFR][1000 genomes]
rs56302652	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57427250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57575786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57809395	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59519264	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61612083	1.00[AFR][1000 genomes]
rs73309777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73309783	1.00[AFR][1000 genomes]
rs73309787	1.00[AFR][1000 genomes]
rs73309789	0.92[AFR][1000 genomes]
rs73309790	1.00[AFR][1000 genomes]
rs74093875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74093884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv1038285	chr12:51762953-51916723	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51736400-51765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:51751200-51783400	Weak transcription	Right Atrium	heart
3	chr12:51752000-51765000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:51752800-51765000	Weak transcription	Placenta	Placenta
5	chr12:51752800-51765200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:51753200-51781400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:51754200-51764600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:51754400-51764600	Weak transcription	NHDF-Ad	bronchial
9	chr12:51755000-51765200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:51755600-51765000	Weak transcription	Esophagus	oesophagus
11	chr12:51756600-51765000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:51757200-51765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:51757800-51764200	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr12:51757800-51765200	Weak transcription	Brain Anterior Caudate	brain
15	chr12:51758000-51765400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:51758000-51765600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:51758200-51764400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:51758200-51765200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:51759600-51764400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:51759800-51765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:51761600-51764600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:51761800-51765600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:51762000-51769400	Enhancers	HUVEC	blood vessel
24	chr12:51762200-51765200	Enhancers	Fetal Thymus	thymus
25	chr12:51762400-51763800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:51762400-51763800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:51762400-51763800	Enhancers	Brain Hippocampus Middle	brain
28	chr12:51762400-51764000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:51762400-51765200	Enhancers	NH-A	brain
30	chr12:51762600-51763800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:51762600-51763800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr12:51762600-51763800	Enhancers	HSMM	muscle
33	chr12:51762600-51765600	Enhancers	Osteobl	bone
34	chr12:51762800-51766000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:51762800-51766400	Genic enhancers	NHEK	skin
36	chr12:51763000-51763800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr12:51763000-51763800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:51763000-51763800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:51763000-51764000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr12:51763000-51765000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:51763000-51765000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:51763000-51765200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:51763000-51765200	Weak transcription	Brain Substantia Nigra	brain
44	chr12:51763000-51765200	Enhancers	A549	lung
45	chr12:51763200-51764400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:51763200-51764400	Strong transcription	Fetal Intestine Small	intestine
47	chr12:51763200-51764400	Weak transcription	HSMMtube	muscle
48	chr12:51763200-51765000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:51763200-51765000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:51763200-51765200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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