Variant report

Variant	rs4334629
Chromosome Location	chr3:17106027-17106028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10865746	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap]
rs11128813	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs11721224	0.84[ASN][1000 genomes]
rs11926952	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12108065	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12233492	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12487288	0.96[CEU][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap]
rs12491516	0.80[ASN][1000 genomes]
rs12492983	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs12497667	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs13058764	0.96[CEU][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs13071645	0.85[CEU][hapmap]
rs13080108	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1372071	0.83[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs1441035	0.85[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs17042909	0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs17272796	0.93[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs1806555	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs1806556	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs2014490	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs34322012	0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs3796299	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3906814	0.83[CEU][hapmap]
rs3924971	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs4131153	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs4289331	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs4353792	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4383507	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs4402923	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs4452313	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap]
rs4461404	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap]
rs4472039	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4535211	0.93[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs4577450	0.85[JPT][hapmap]
rs4602367	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs4618210	0.85[CEU][hapmap]
rs4684305	0.87[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs4684306	0.87[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4684307	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs4684308	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4685404	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs4685405	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4685409	0.85[CEU][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs4685411	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4685418	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs4685420	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs4685421	0.96[CEU][hapmap]
rs4685422	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4685423	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs4685424	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4685425	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4685426	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4685427	0.84[CEU][hapmap]
rs62247256	0.89[ASN][1000 genomes]
rs6442660	0.84[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6762816	0.94[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs6775709	0.90[ASN][1000 genomes]
rs6777357	0.89[ASN][1000 genomes]
rs6780191	0.85[CEU][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs6809087	0.93[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs7610811	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7611127	0.89[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs7612044	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs7617672	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs7617779	0.81[CHB][hapmap]
rs7639882	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs7645335	0.85[CEU][hapmap]
rs7648912	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs7653027	0.85[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs7653834	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs9637429	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs964576	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9810017	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9821630	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs9824172	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs9825009	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9830460	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs9841259	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9853476	0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs9854760	0.81[CEU][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap]
rs9862613	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs9879150	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs9880307	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs9881521	0.85[JPT][hapmap]
rs9883633	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3400051	chr3:17102729-17106469	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4334629	C3orf20	cis	cerebellum	SCAN
rs4334629	CHCHD4	cis	parietal	SCAN

Chromatin state (count:66 , 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	chr3:17092000-17109200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:17092200-17109000	Weak transcription	Liver	Liver
15	chr3:17094800-17112200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:17095000-17112000	Weak transcription	Right Atrium	heart
17	chr3:17095200-17112200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:17095400-17106800	Weak transcription	Fetal Kidney	kidney
19	chr3:17095400-17108800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:17095400-17109000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:17095400-17109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:17095400-17110200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:17095400-17114400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:17095400-17120600	Weak transcription	Aorta	Aorta
25	chr3:17095400-17120600	Weak transcription	Lung	lung
26	chr3:17095800-17111600	Weak transcription	Brain Germinal Matrix	brain
27	chr3:17096600-17118000	Weak transcription	Fetal Intestine Small	intestine
28	chr3:17097000-17109000	Weak transcription	Adipose Nuclei	Adipose
29	chr3:17097200-17108200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:17097200-17109200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:17097200-17112000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:17097200-17112000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:17097200-17113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:17097400-17107000	Weak transcription	Psoas Muscle	Psoas
35	chr3:17097400-17109000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:17097600-17109000	Weak transcription	Placenta	Placenta
37	chr3:17097600-17112200	Weak transcription	Fetal Stomach	stomach
38	chr3:17097600-17120400	Weak transcription	Spleen	Spleen
39	chr3:17098000-17109000	Weak transcription	GM12878-XiMat	blood
40	chr3:17098400-17109000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:17099000-17109600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:17099000-17112200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:17099400-17109400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:17099800-17109200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:17100800-17109400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:17101600-17111600	Weak transcription	Fetal Brain Female	brain
47	chr3:17101800-17106800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:17101800-17109000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:17102000-17112200	Weak transcription	Ovary	ovary
50	chr3:17102200-17107800	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links