Variant report

Variant	rs4964460
Chromosome Location	chr12:106704974-106704975
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	chr12:106695771..106699164-chr12:106702286..106705903,4	MCF-7	breast:
2	chr12:106702332..106705021-chr12:106709176..106711287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166046	Chromatin interaction
ENSG00000136026	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10778462	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10778463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861573	0.96[ASN][1000 genomes]
rs11831752	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1392176	0.94[ASN][1000 genomes]
rs1532586	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243506	0.88[GIH][hapmap];0.91[MEX][hapmap]
rs2246627	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2250262	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs2250441	0.84[MKK][hapmap]
rs2252685	1.00[ASW][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap]
rs2253838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2288266	0.82[MEX][hapmap]
rs6539261	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.96[ASN][1000 genomes]
rs6539262	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539263	0.94[ASN][1000 genomes]
rs6539264	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7296927	0.93[ASN][1000 genomes]
rs7297359	0.93[ASN][1000 genomes]
rs7298576	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957421	0.94[ASN][1000 genomes]
rs7965175	0.96[ASN][1000 genomes]
rs7965616	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4964460	NUAK1	cis	cerebellum	SCAN
rs4964460	EID3	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106698000-106705600	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr12:106698000-106708400	Weak transcription	Small Intestine	intestine
3	chr12:106698000-106709000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:106698200-106706000	Weak transcription	Placenta	Placenta
5	chr12:106698200-106708000	Weak transcription	Liver	Liver
6	chr12:106698400-106708000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:106698400-106709800	Weak transcription	Fetal Lung	lung
8	chr12:106698600-106709600	Weak transcription	Brain Germinal Matrix	brain
9	chr12:106698800-106705400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:106698800-106708400	Weak transcription	Thymus	Thymus
11	chr12:106698800-106709200	Weak transcription	Fetal Thymus	thymus
12	chr12:106699000-106708200	Weak transcription	Ovary	ovary
13	chr12:106699000-106708400	Weak transcription	Fetal Brain Female	brain
14	chr12:106699400-106705400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:106699600-106705400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:106699600-106705600	Enhancers	Brain Cingulate Gyrus	brain
17	chr12:106699600-106713800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:106699800-106705000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:106699800-106708800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:106699800-106713200	Weak transcription	Esophagus	oesophagus
21	chr12:106699800-106718800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:106700600-106705200	Enhancers	Brain Anterior Caudate	brain
23	chr12:106700600-106736000	Weak transcription	Stomach Mucosa	stomach
24	chr12:106700800-106705600	Enhancers	Brain Hippocampus Middle	brain
25	chr12:106701200-106708000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:106701400-106708800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:106701400-106709400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr12:106701800-106705000	Enhancers	Fetal Muscle Leg	muscle
29	chr12:106701800-106705200	Enhancers	Psoas Muscle	Psoas
30	chr12:106702000-106705000	Enhancers	Right Atrium	heart
31	chr12:106702400-106705000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr12:106702400-106705400	Enhancers	Fetal Kidney	kidney
33	chr12:106702400-106707200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:106702600-106705000	Genic enhancers	Primary T cells from cord blood	blood
35	chr12:106702800-106705000	Enhancers	Lung	lung
36	chr12:106702800-106705000	Enhancers	Right Ventricle	heart
37	chr12:106702800-106705200	Genic enhancers	Primary B cells from cord blood	blood
38	chr12:106703000-106708000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:106703000-106708000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:106703000-106708000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:106703000-106722800	Weak transcription	Fetal Brain Male	brain
42	chr12:106703200-106705800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr12:106703200-106706400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr12:106703400-106705800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:106703600-106705200	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr12:106703600-106714400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:106703600-106715800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:106703800-106705000	Strong transcription	Aorta	Aorta
49	chr12:106703800-106705000	Enhancers	Fetal Heart	heart
50	chr12:106703800-106705200	Strong transcription	Fetal Stomach	stomach

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