Variant report

Variant	rs7653834
Chromosome Location	chr3:17051328-17051329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17050058..17051814-chr3:17063376..17065120,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11128813	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11128814	0.94[ASN][1000 genomes]
rs11717433	0.94[ASN][1000 genomes]
rs11717649	0.95[ASN][1000 genomes]
rs11915356	0.87[ASN][1000 genomes]
rs12108065	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]
rs12233492	0.81[JPT][hapmap]
rs12488103	0.85[ASN][1000 genomes]
rs12491516	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492983	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12494582	0.81[ASN][1000 genomes]
rs12495362	0.92[ASN][1000 genomes]
rs1372071	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17042909	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17042920	0.82[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];0.91[ASN][1000 genomes]
rs3796299	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3906814	0.84[JPT][hapmap]
rs4131153	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4289331	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4334629	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs4383507	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4402923	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4416363	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4452313	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4461404	0.80[CHD][hapmap]
rs4577450	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4684305	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4684306	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4684307	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4684308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4685405	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4685409	0.82[CHD][hapmap]
rs4685411	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4685419	0.96[ASN][1000 genomes]
rs4685423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4685424	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4685425	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4685426	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs58679681	0.94[ASN][1000 genomes]
rs58750701	0.87[ASN][1000 genomes]
rs58765457	0.82[ASN][1000 genomes]
rs62246033	0.92[ASN][1000 genomes]
rs62247183	0.95[ASN][1000 genomes]
rs62247186	0.93[ASN][1000 genomes]
rs62247188	0.81[ASN][1000 genomes]
rs62247190	0.89[ASN][1000 genomes]
rs62247256	0.85[ASN][1000 genomes]
rs6762816	0.80[CHD][hapmap]
rs6777357	0.85[ASN][1000 genomes]
rs6780191	0.82[CHD][hapmap]
rs6796352	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6803135	0.95[ASN][1000 genomes]
rs6806862	0.94[ASN][1000 genomes]
rs7611127	0.80[CHD][hapmap]
rs7612044	0.87[CHB][hapmap]
rs7617779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634374	0.94[ASN][1000 genomes]
rs7639882	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs7648912	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653027	0.82[CHD][hapmap]
rs964576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9821630	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[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];0.81[ASN][1000 genomes]
rs9844888	0.86[JPT][hapmap]
rs9853476	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[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
rs7653834	CHCHD4	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17037000-17053200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:17041200-17051400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:17045000-17053800	Weak transcription	Thymus	Thymus
4	chr3:17045200-17052200	Weak transcription	Aorta	Aorta
5	chr3:17046200-17053200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:17046600-17053000	Weak transcription	Brain Substantia Nigra	brain
7	chr3:17046800-17054200	Weak transcription	Psoas Muscle	Psoas
8	chr3:17046800-17054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:17047000-17051800	Weak transcription	Fetal Brain Female	brain
10	chr3:17047000-17054200	Weak transcription	Brain Anterior Caudate	brain
11	chr3:17048000-17051400	Weak transcription	Fetal Lung	lung
12	chr3:17048000-17051400	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:17048000-17051600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:17048000-17052600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:17048200-17051400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:17048200-17051400	Weak transcription	Adipose Nuclei	Adipose
17	chr3:17048200-17051600	Weak transcription	Fetal Kidney	kidney
18	chr3:17048200-17052000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:17048200-17052400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:17048200-17052600	Weak transcription	Spleen	Spleen
21	chr3:17048200-17053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:17048200-17053000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:17048200-17053200	Weak transcription	Liver	Liver
24	chr3:17048200-17053200	Weak transcription	Stomach Mucosa	stomach
25	chr3:17048200-17054200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:17048200-17054600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:17048200-17054600	Weak transcription	Gastric	stomach
28	chr3:17048200-17054600	Weak transcription	Right Atrium	heart
29	chr3:17048200-17054800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:17048400-17051400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:17048400-17051400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:17048400-17051400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:17048400-17051800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:17048400-17052000	Weak transcription	Ovary	ovary
35	chr3:17048400-17052200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:17048400-17052600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:17048400-17052600	Weak transcription	Right Ventricle	heart
38	chr3:17048400-17053000	Weak transcription	Pancreas	Pancrea
39	chr3:17048400-17053200	Weak transcription	Brain Angular Gyrus	brain
40	chr3:17048400-17054000	Weak transcription	Fetal Heart	heart
41	chr3:17048400-17054600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:17048400-17054800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:17048400-17054800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:17048400-17054800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:17048400-17054800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:17048400-17054800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:17048800-17052400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:17049200-17051400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:17049400-17056200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:17049600-17051400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links