Variant report

Variant	rs3782470
Chromosome Location	chr12:51755790-51755791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:51754815-51755865	A549	lung:	n/a	n/a
2	RAD21	chr12:51755456-51755822	A549	lung:	n/a	n/a
3	RAD21	chr12:51755377-51755898	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51754890..51757082-chr12:51783252..51784847,2	K562	blood:
2	chr12:51751580..51754546-chr12:51755369..51757595,3	MCF-7	breast:
3	chr12:51754295..51757629-chr12:51759740..51762921,4	K562	blood:

Variant related genes	Relation type
GALNT6	TF binding region
ENSG00000139629	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11341	0.93[CEU][hapmap]
rs17860277	0.89[EUR][1000 genomes]
rs17860287	0.85[EUR][1000 genomes]
rs17860296	0.84[EUR][1000 genomes]
rs17860299	0.86[CEU][hapmap]
rs17860302	0.84[EUR][1000 genomes]
rs17860317	0.85[CEU][hapmap]
rs17860346	0.83[EUR][1000 genomes]
rs17860364	0.82[EUR][1000 genomes]
rs17860365	0.80[EUR][1000 genomes]
rs17860378	0.82[EUR][1000 genomes]
rs17860380	0.83[EUR][1000 genomes]
rs17860382	0.83[EUR][1000 genomes]
rs17860387	0.83[EUR][1000 genomes]
rs2067763	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2288367	0.86[CEU][hapmap]
rs3858637	0.93[CEU][hapmap]
rs4761870	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4761881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4761898	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7311196	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7312857	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51735400-51756000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:51735600-51761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:51736400-51765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:51744200-51761400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:51745800-51763000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:51746000-51756400	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr12:51746200-51757400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:51746200-51761400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:51746200-51762400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:51746200-51762600	Weak transcription	Colonic Mucosa	Colon
11	chr12:51746200-51762800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:51746800-51759000	Strong transcription	Primary T cells from cord blood	blood
13	chr12:51746800-51759600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:51746800-51762600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:51747400-51758200	Strong transcription	Thymus	Thymus
16	chr12:51747400-51759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:51747400-51759600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr12:51747400-51759800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:51747400-51760000	Strong transcription	Fetal Thymus	thymus
20	chr12:51747400-51761200	Strong transcription	Dnd41	blood
21	chr12:51747400-51762800	Strong transcription	NHEK	skin
22	chr12:51747800-51756400	Strong transcription	NHLF	lung
23	chr12:51747800-51758200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:51748000-51757600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr12:51749000-51762000	Weak transcription	HUVEC	blood vessel
26	chr12:51749200-51761200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:51749600-51759400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:51750200-51759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:51751200-51783400	Weak transcription	Right Atrium	heart
30	chr12:51751600-51757800	Weak transcription	Spleen	Spleen
31	chr12:51751600-51762400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:51752000-51757400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:51752000-51758800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:51752000-51762800	Weak transcription	Lung	lung
35	chr12:51752000-51765000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:51752600-51759600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:51752800-51762600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:51752800-51765000	Weak transcription	Placenta	Placenta
39	chr12:51752800-51765200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:51753200-51756800	Strong transcription	Stomach Mucosa	stomach
41	chr12:51753200-51762000	Weak transcription	GM12878-XiMat	blood
42	chr12:51753200-51781400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr12:51753400-51757000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:51753400-51757800	Weak transcription	Fetal Stomach	stomach
45	chr12:51753800-51755800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:51753800-51755800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr12:51753800-51756000	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr12:51753800-51758400	Enhancers	Brain Substantia Nigra	brain
49	chr12:51754000-51756000	Enhancers	HepG2	liver
50	chr12:51754000-51757600	Enhancers	Brain Angular Gyrus	brain

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