Variant report

Variant	rs2253838
Chromosome Location	chr12:106708278-106708279
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10778462	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10778463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861573	0.94[ASN][1000 genomes]
rs11831752	0.98[ASN][1000 genomes]
rs1392176	0.96[ASN][1000 genomes]
rs1532586	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243506	0.88[GIH][hapmap];0.87[MEX][hapmap]
rs2246627	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2250262	0.83[GIH][hapmap]
rs2252685	0.88[GIH][hapmap];0.91[MEX][hapmap]
rs4964460	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];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539261	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6539262	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs6539263	0.96[ASN][1000 genomes]
rs6539264	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7296927	0.91[ASN][1000 genomes]
rs7297359	0.94[ASN][1000 genomes]
rs7298576	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957421	0.93[ASN][1000 genomes]
rs7965175	0.94[ASN][1000 genomes]
rs7965616	0.94[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2253838	NUAK1	cis	cerebellum	SCAN
rs2253838	EID3	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106698000-106708400	Weak transcription	Small Intestine	intestine
2	chr12:106698000-106709000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:106698400-106709800	Weak transcription	Fetal Lung	lung
4	chr12:106698600-106709600	Weak transcription	Brain Germinal Matrix	brain
5	chr12:106698800-106708400	Weak transcription	Thymus	Thymus
6	chr12:106698800-106709200	Weak transcription	Fetal Thymus	thymus
7	chr12:106699000-106708400	Weak transcription	Fetal Brain Female	brain
8	chr12:106699600-106713800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:106699800-106708800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:106699800-106713200	Weak transcription	Esophagus	oesophagus
11	chr12:106699800-106718800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:106700600-106736000	Weak transcription	Stomach Mucosa	stomach
13	chr12:106701400-106708800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:106701400-106709400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:106703000-106722800	Weak transcription	Fetal Brain Male	brain
16	chr12:106703600-106714400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:106703600-106715800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:106703800-106718600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:106704000-106708600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:106704000-106716000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:106704200-106708400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:106704200-106711400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:106704200-106715000	Weak transcription	HepG2	liver
24	chr12:106704200-106715400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:106704200-106715400	Weak transcription	NHDF-Ad	bronchial
26	chr12:106704200-106716800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:106704200-106729400	Weak transcription	NHLF	lung
28	chr12:106704200-106729800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:106704400-106708400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:106704400-106712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:106704600-106717600	Weak transcription	HSMM	muscle
32	chr12:106704600-106724400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:106704800-106709400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:106704800-106715200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:106704800-106726800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:106704800-106738800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:106705000-106708400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:106705000-106708800	Weak transcription	Right Ventricle	heart
39	chr12:106705000-106708800	Weak transcription	Spleen	Spleen
40	chr12:106705000-106709000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:106705000-106709200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:106705000-106711200	Weak transcription	Aorta	Aorta
43	chr12:106705000-106711400	Weak transcription	Fetal Heart	heart
44	chr12:106705000-106714400	Weak transcription	HSMMtube	muscle
45	chr12:106705200-106708400	Weak transcription	Brain Anterior Caudate	brain
46	chr12:106705200-106708400	Weak transcription	Fetal Intestine Small	intestine
47	chr12:106705200-106708400	Weak transcription	Fetal Stomach	stomach
48	chr12:106705200-106708600	Weak transcription	Pancreas	Pancrea
49	chr12:106705200-106710600	Weak transcription	Psoas Muscle	Psoas
50	chr12:106705200-106711200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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