Variant report

Variant	rs4131153
Chromosome Location	chr3:17097254-17097255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11128813	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11128814	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717433	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11717649	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11721224	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11915356	0.84[ASN][1000 genomes]
rs12108065	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12233492	0.81[JPT][hapmap]
rs12488103	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491516	0.96[ASN][1000 genomes]
rs12492983	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs12494582	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12495362	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1372071	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17042909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17042920	0.83[ASN][1000 genomes]
rs1806555	0.81[JPT][hapmap]
rs2014490	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs34322012	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3906814	0.84[JPT][hapmap]
rs4289331	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4334629	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs4383507	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4402923	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4416363	0.90[ASN][1000 genomes]
rs4452313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4577450	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4684305	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4684306	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4684307	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4684308	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4685405	0.82[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs4685409	0.81[CHD][hapmap]
rs4685411	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4685419	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4685423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4685424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4685425	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4685426	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs58679681	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58750701	0.84[ASN][1000 genomes]
rs58765457	0.85[ASN][1000 genomes]
rs62246033	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62247183	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62247186	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62247188	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62247190	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62247256	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6777357	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6780191	0.81[CHD][hapmap]
rs6796352	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6803135	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806862	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7612044	0.87[CHB][hapmap]
rs7617779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7634374	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639882	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7648912	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7653027	0.80[CHD][hapmap]
rs7653834	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs964576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9821630	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9824172	0.80[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs9825009	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9844888	0.86[JPT][hapmap]
rs9853476	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs9879150	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs9883633	0.86[CHB][hapmap];0.85[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4131153	CHCHD4	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17081200-17111400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:17083000-17109600	Weak transcription	Fetal Intestine Large	intestine
3	chr3:17083200-17111600	Weak transcription	Stomach Mucosa	stomach
4	chr3:17085800-17112200	Weak transcription	Gastric	stomach
5	chr3:17089400-17109000	Weak transcription	Dnd41	blood
6	chr3:17089400-17135000	Weak transcription	Pancreas	Pancrea
7	chr3:17089600-17111000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:17089800-17110400	Weak transcription	Fetal Thymus	thymus
9	chr3:17089800-17112200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:17089800-17116000	Weak transcription	Thymus	Thymus
11	chr3:17090400-17110400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:17090600-17110400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:17091600-17103800	Strong transcription	Primary T cells from cord blood	blood
14	chr3:17092000-17109200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:17092200-17109000	Weak transcription	Liver	Liver
16	chr3:17094400-17098600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:17094600-17097400	Enhancers	Psoas Muscle	Psoas
18	chr3:17094800-17101400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:17094800-17112200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:17095000-17112000	Weak transcription	Right Atrium	heart
21	chr3:17095200-17098800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:17095200-17101800	Strong transcription	Primary B cells from cord blood	blood
23	chr3:17095200-17112200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:17095400-17099000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:17095400-17106800	Weak transcription	Fetal Kidney	kidney
26	chr3:17095400-17108800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:17095400-17109000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:17095400-17109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:17095400-17110200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:17095400-17114400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:17095400-17120600	Weak transcription	Aorta	Aorta
32	chr3:17095400-17120600	Weak transcription	Lung	lung
33	chr3:17095800-17099000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:17095800-17099800	Enhancers	NHDF-Ad	bronchial
35	chr3:17095800-17111600	Weak transcription	Brain Germinal Matrix	brain
36	chr3:17096000-17097600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:17096000-17097600	Enhancers	Right Ventricle	heart
38	chr3:17096000-17098800	Enhancers	NHLF	lung
39	chr3:17096000-17100200	Enhancers	Fetal Heart	heart
40	chr3:17096200-17097400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr3:17096200-17097800	Flanking Active TSS	GM12878-XiMat	blood
42	chr3:17096200-17102000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:17096400-17097600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:17096400-17097600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:17096400-17097600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:17096400-17098800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:17096400-17099200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:17096400-17099400	Enhancers	Osteobl	bone
49	chr3:17096400-17102000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:17096600-17097600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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