Variant report

Variant	rs12108065
Chromosome Location	chr3:17074871-17074872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:17070807..17073673-chr3:17074313..17077008,2	K562	blood:
2	chr3:17061938..17064281-chr3:17072645..17075363,2	K562	blood:
3	chr3:17070050..17072867-chr3:17074097..17076055,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11128813	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11128814	0.99[ASN][1000 genomes]
rs11717433	0.90[ASN][1000 genomes]
rs11717649	0.99[ASN][1000 genomes]
rs11721224	0.83[ASN][1000 genomes]
rs11915356	0.83[ASN][1000 genomes]
rs12233492	0.81[JPT][hapmap]
rs12488103	0.83[ASN][1000 genomes]
rs12491516	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492983	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12495362	0.88[ASN][1000 genomes]
rs1372071	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17042909	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17042920	0.81[ASN][1000 genomes]
rs17272796	0.80[CHD][hapmap]
rs1806555	0.81[JPT][hapmap]
rs2014490	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs34322012	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3796299	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3906814	0.84[JPT][hapmap]
rs4131153	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4289331	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4334629	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4383507	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4402923	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4416363	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452313	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4461404	0.80[CHD][hapmap]
rs4577450	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4684305	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4684306	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4684307	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4684308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4685405	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4685409	0.82[CHD][hapmap]
rs4685411	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4685419	0.92[ASN][1000 genomes]
rs4685422	0.80[ASN][1000 genomes]
rs4685423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4685424	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4685425	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4685426	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs58679681	0.90[ASN][1000 genomes]
rs58750701	0.83[ASN][1000 genomes]
rs58765457	0.83[ASN][1000 genomes]
rs62246033	0.88[ASN][1000 genomes]
rs62247183	0.99[ASN][1000 genomes]
rs62247186	0.97[ASN][1000 genomes]
rs62247188	0.85[ASN][1000 genomes]
rs62247190	0.93[ASN][1000 genomes]
rs62247256	0.89[ASN][1000 genomes]
rs6762816	0.80[CHD][hapmap]
rs6777357	0.89[ASN][1000 genomes]
rs6780191	0.82[CHD][hapmap]
rs6796352	0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6803135	0.99[ASN][1000 genomes]
rs6806862	0.90[ASN][1000 genomes]
rs7611127	0.80[CHD][hapmap]
rs7612044	0.86[CHB][hapmap]
rs7617779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7634374	0.98[ASN][1000 genomes]
rs7639882	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7648912	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7653027	0.82[CHD][hapmap]
rs7653834	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs964576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9821630	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9824172	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs9825009	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs9844888	0.86[JPT][hapmap]
rs9853476	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9879150	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs9883633	0.86[CHB][hapmap];0.85[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12108065	CHCHD4	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17051600-17075000	Weak transcription	Fetal Brain Male	brain
2	chr3:17053600-17076200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:17053600-17080600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:17053800-17086800	Weak transcription	Fetal Stomach	stomach
5	chr3:17055000-17077000	Weak transcription	Fetal Brain Female	brain
6	chr3:17055400-17088800	Weak transcription	Thymus	Thymus
7	chr3:17055600-17079800	Weak transcription	Small Intestine	intestine
8	chr3:17055800-17087800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:17057400-17076200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:17057600-17080600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:17058600-17077000	Weak transcription	Right Ventricle	heart
12	chr3:17058600-17082400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:17060000-17082200	Weak transcription	Fetal Intestine Small	intestine
14	chr3:17060000-17088600	Weak transcription	Pancreas	Pancrea
15	chr3:17060200-17081000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:17065600-17081200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:17066600-17075600	Weak transcription	Left Ventricle	heart
18	chr3:17069400-17085600	Weak transcription	Aorta	Aorta
19	chr3:17069600-17080800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:17070000-17093600	Weak transcription	Fetal Lung	lung
21	chr3:17071400-17075000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:17071400-17079800	Weak transcription	Lung	lung
23	chr3:17071400-17080600	Weak transcription	Gastric	stomach
24	chr3:17071600-17075600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:17071800-17080600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:17072200-17079800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:17072600-17075000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:17072800-17076200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:17072800-17080200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:17072800-17080600	Weak transcription	Esophagus	oesophagus
31	chr3:17072800-17085600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:17073000-17075000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:17073000-17075200	Weak transcription	Fetal Thymus	thymus
34	chr3:17073000-17077200	Weak transcription	Ovary	ovary
35	chr3:17073000-17078400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:17073000-17080200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:17073000-17088800	Weak transcription	Right Atrium	heart
38	chr3:17073000-17093000	Weak transcription	Spleen	Spleen
39	chr3:17073200-17075200	Weak transcription	GM12878-XiMat	blood
40	chr3:17073200-17076400	Weak transcription	Psoas Muscle	Psoas
41	chr3:17073200-17077000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:17073200-17080600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:17073200-17085200	Weak transcription	Placenta	Placenta
44	chr3:17073200-17085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:17073600-17076400	Weak transcription	Primary B cells from cord blood	blood
46	chr3:17073800-17076600	Enhancers	Primary T cells from cord blood	blood
47	chr3:17074000-17077000	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr3:17074000-17077200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:17074000-17077200	Enhancers	Fetal Heart	heart
50	chr3:17074000-17077400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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