Variant report

Variant	rs17042909
Chromosome Location	chr3:16979755-16979756
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:16971569..16973509-chr3:16977702..16980574,2	K562	blood:
2	chr3:16967326..16970983-chr3:16976551..16980496,4	K562	blood:
3	chr3:16967326..16970983-chr3:16976849..16980496,3	K562	blood:
4	chr3:16975880..16977553-chr3:16979453..16981431,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1025818	0.81[ASN][1000 genomes]
rs11128813	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11128814	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717433	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11717649	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11915356	0.89[ASN][1000 genomes]
rs12108065	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12233492	0.81[JPT][hapmap]
rs12488103	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12491516	0.86[ASN][1000 genomes]
rs12492983	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12494582	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12495362	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1372071	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17042920	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1806555	0.81[JPT][hapmap]
rs2014490	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs34322012	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796299	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs3906814	0.84[JPT][hapmap]
rs4131153	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]
rs4289331	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[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4334629	0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4383507	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4402923	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4416363	0.92[ASN][1000 genomes]
rs4452313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4577450	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4684305	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4684306	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4684307	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4684308	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4685405	0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4685411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4685419	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4685423	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4685424	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs4685425	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4685426	0.82[JPT][hapmap]
rs58679681	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58750701	0.87[ASN][1000 genomes]
rs58765457	0.86[ASN][1000 genomes]
rs62246033	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62247183	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62247186	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62247190	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6796352	0.83[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6803135	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6806862	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7612044	0.83[CHB][hapmap]
rs7617779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7634374	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639882	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7648912	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7653834	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs964576	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9821630	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9824172	0.80[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs9825009	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9844888	0.86[JPT][hapmap]
rs9853476	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9879150	0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[ASN][1000 genomes]
rs9883633	0.81[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17042909	CHCHD4	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16958000-16981800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:16959400-16986600	Weak transcription	Aorta	Aorta
3	chr3:16967000-16985000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:16971600-16982400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:16972400-16983600	Weak transcription	Brain Angular Gyrus	brain
6	chr3:16973400-16980400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:16973800-16985000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:16974200-16982600	Enhancers	Fetal Heart	heart
9	chr3:16974800-16984800	Weak transcription	Stomach Mucosa	stomach
10	chr3:16975600-16985000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:16975600-16985800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:16975800-16985000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:16976000-16983800	Weak transcription	Pancreas	Pancrea
14	chr3:16976200-16981400	Weak transcription	Right Atrium	heart
15	chr3:16976400-16982400	Weak transcription	Right Ventricle	heart
16	chr3:16976400-16982400	Weak transcription	Spleen	Spleen
17	chr3:16976400-16983800	Weak transcription	Gastric	stomach
18	chr3:16977200-16980200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:16977400-16980400	Enhancers	Psoas Muscle	Psoas
20	chr3:16977600-16979800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:16977800-16987400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:16978000-16979800	Weak transcription	Small Intestine	intestine
23	chr3:16978000-16980000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:16978000-16985800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:16978000-16991200	Weak transcription	Adipose Nuclei	Adipose
26	chr3:16978200-16981400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:16978200-16983000	Weak transcription	Liver	Liver
28	chr3:16978400-16980600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:16978400-16981800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:16978600-16981600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:16978800-16980800	Enhancers	Primary T cells from cord blood	blood
32	chr3:16978800-16981600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:16979000-16990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:16979200-16979800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:16979200-16980600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:16979200-16981400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:16979200-16981400	Weak transcription	Left Ventricle	heart
38	chr3:16979200-16981400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:16979200-16981600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:16979200-16982400	Weak transcription	Ovary	ovary
41	chr3:16979200-16984200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:16979400-16979800	Enhancers	GM12878-XiMat	blood
43	chr3:16979400-16980000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:16979400-16982400	Weak transcription	Fetal Lung	lung
45	chr3:16979400-16983600	Weak transcription	Primary B cells from cord blood	blood
46	chr3:16979400-16985000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:16979400-16989800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:16979600-16979800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links