Variant report

Variant	rs3809320
Chromosome Location	chr12:51421620-51421621
allele	A/T
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51385408..51389476-chr12:51420028..51421870,3	MCF-7	breast:
2	chr12:51156345..51159697-chr12:51418125..51424480,11	MCF-7	breast:
3	chr12:51417420..51423779-chr12:51473917..51478493,9	MCF-7	breast:
4	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
5	chr12:51397137..51401396-chr12:51418750..51422923,7	MCF-7	breast:
6	chr12:51418513..51423622-chr12:51474378..51479071,10	MCF-7	breast:
7	chr12:51419815..51423306-chr17:56706440..56710556,3	MCF-7	breast:
8	chr12:51419463..51422870-chr12:51476162..51478400,3	K562	blood:
9	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
10	chr12:51156017..51159008-chr12:51420473..51422056,2	MCF-7	breast:
11	chr12:51377924..51379984-chr12:51420251..51421770,2	MCF-7	breast:
12	chr12:51418785..51420716-chr12:51421022..51423680,2	K562	blood:
13	chr12:51388022..51389545-chr12:51419948..51422038,2	MCF-7	breast:
14	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
15	chr12:51419952..51421943-chr12:51475612..51477490,4	K562	blood:
16	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
17	chr12:51156114..51160622-chr12:51418657..51421869,11	K562	blood:
18	chr12:51316948..51319607-chr12:51419309..51421732,3	K562	blood:
19	chr12:51420182..51422992-chr12:51631104..51633893,3	MCF-7	breast:
20	chr12:51316948..51319607-chr12:51419309..51421732,2	K562	blood:
21	chr12:51421116..51422954-chr12:51442627..51444321,2	K562	blood:
22	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000185432	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10876122	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169625	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169629	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169634	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169640	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169643	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169651	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169653	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169658	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169662	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169674	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169681	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11169687	0.80[AMR][1000 genomes]
rs11169688	0.80[AMR][1000 genomes]
rs12227734	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1982777	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2016533	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239860	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269682	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269683	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768871	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7295893	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51420200-51422400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:51420200-51423000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:51420400-51422000	Flanking Active TSS	HepG2	liver
4	chr12:51420600-51421800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:51420600-51421800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:51420600-51421800	Weak transcription	Stomach Mucosa	stomach
7	chr12:51420600-51422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:51420600-51422000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:51420600-51422000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:51420600-51422000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:51420600-51422000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:51420600-51422000	Weak transcription	Osteobl	bone
13	chr12:51420600-51422200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:51420600-51422200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:51420600-51422200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:51420600-51422200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr12:51420600-51422200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:51420600-51422200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:51420600-51422200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:51420600-51422200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:51420600-51422200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:51420600-51422200	Weak transcription	Liver	Liver
23	chr12:51420600-51422200	Enhancers	HMEC	breast
24	chr12:51420600-51422400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:51420600-51422400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:51420600-51422400	Weak transcription	Fetal Kidney	kidney
27	chr12:51420600-51422400	Enhancers	Placenta	Placenta
28	chr12:51420600-51422600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:51420600-51422600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr12:51420600-51422600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:51420600-51422800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:51420600-51422800	Enhancers	Fetal Thymus	thymus
33	chr12:51420600-51423800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:51420600-51423800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:51420800-51421800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:51420800-51421800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:51420800-51421800	Enhancers	Duodenum Mucosa	Duodenum
38	chr12:51420800-51421800	Weak transcription	Thymus	Thymus
39	chr12:51420800-51421800	Enhancers	K562	blood
40	chr12:51420800-51422000	Weak transcription	Adipose Nuclei	Adipose
41	chr12:51420800-51422000	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:51420800-51422200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr12:51420800-51422200	Enhancers	Dnd41	blood
44	chr12:51420800-51422400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr12:51420800-51422400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:51421000-51422000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:51421000-51422200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr12:51421000-51422200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:51421000-51422400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr12:51421200-51422600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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