Variant report

Variant	rs11169423
Chromosome Location	chr12:50823766-50823767
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	chr12:50812613..50814185-chr12:50823081..50825818,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10467057	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10467107	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783361	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876033	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10876035	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17124559	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs17124706	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238105	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4321029	0.82[EUR][1000 genomes]
rs4343103	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424740	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768976	0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57594106	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58723865	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138887	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304630	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308184	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305121	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305168	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7489251	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959284	0.97[EUR][1000 genomes]
rs7964643	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967393	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970694	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973910	0.82[EUR][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	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
7	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50796800-50824000	Weak transcription	Fetal Brain Female	brain
2	chr12:50796800-50832600	Weak transcription	Brain Substantia Nigra	brain
3	chr12:50797200-50823800	Weak transcription	NH-A	brain
4	chr12:50797600-50826200	Weak transcription	NHDF-Ad	bronchial
5	chr12:50797600-50826800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:50797600-50829600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:50798400-50824000	Weak transcription	Fetal Kidney	kidney
8	chr12:50807200-50824000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:50808200-50824000	Weak transcription	Brain Angular Gyrus	brain
10	chr12:50809600-50872200	Weak transcription	Fetal Brain Male	brain
11	chr12:50810600-50824000	Weak transcription	Gastric	stomach
12	chr12:50810600-50824200	Weak transcription	Colonic Mucosa	Colon
13	chr12:50810600-50824400	Weak transcription	NHLF	lung
14	chr12:50810600-50856600	Weak transcription	Aorta	Aorta
15	chr12:50812000-50827600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:50813400-50825600	Weak transcription	Primary T cells from cord blood	blood
17	chr12:50815800-50834400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:50819000-50824400	Strong transcription	K562	blood
19	chr12:50819200-50827200	Strong transcription	Fetal Intestine Small	intestine
20	chr12:50819200-50830200	Strong transcription	Fetal Stomach	stomach
21	chr12:50819200-50870800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:50819600-50823800	Weak transcription	Right Ventricle	heart
23	chr12:50819600-50824000	Weak transcription	Spleen	Spleen
24	chr12:50819800-50830000	Weak transcription	Fetal Heart	heart
25	chr12:50819800-50842400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:50819800-50867400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:50820000-50823800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:50820000-50824000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:50820000-50824600	Weak transcription	GM12878-XiMat	blood
30	chr12:50820000-50831600	Weak transcription	Psoas Muscle	Psoas
31	chr12:50820000-50835400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:50820000-50835600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:50820000-50841400	Weak transcription	Esophagus	oesophagus
34	chr12:50820000-50845400	Weak transcription	Right Atrium	heart
35	chr12:50820000-50867200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:50820200-50823800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:50820200-50824000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:50820200-50824000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:50820200-50824000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:50820200-50824000	Weak transcription	HUVEC	blood vessel
41	chr12:50820200-50824200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:50820200-50835200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:50820200-50869800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:50820200-50871000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:50820400-50823800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:50820400-50830000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:50820600-50839400	Strong transcription	Fetal Thymus	thymus
48	chr12:50820600-50843400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:50820800-50839600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:50821000-50825000	Strong transcription	Liver	Liver

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