Variant report

Variant	rs983545
Chromosome Location	chr3:16959652-16959653
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	chr3:16958786..16960675-chr3:16962652..16964960,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1025818	0.90[ASN][1000 genomes]
rs10865746	0.85[JPT][hapmap]
rs11128810	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11128813	0.81[CHD][hapmap]
rs1156336	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11926952	0.86[JPT][hapmap]
rs11928330	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11928414	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12233492	0.90[JPT][hapmap]
rs12487288	0.85[JPT][hapmap]
rs12497667	0.86[JPT][hapmap]
rs13058764	0.84[JPT][hapmap]
rs13080108	0.85[JPT][hapmap]
rs1372071	0.83[ASW][hapmap]
rs1372072	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1441035	0.86[JPT][hapmap]
rs1441039	0.84[EUR][1000 genomes]
rs17272796	0.86[JPT][hapmap]
rs1806556	0.84[JPT][hapmap]
rs1837698	0.84[EUR][1000 genomes]
rs2014490	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2197017	0.85[ASN][1000 genomes]
rs2881771	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796299	0.81[CHD][hapmap]
rs3924971	0.86[JPT][hapmap]
rs4131153	0.81[CHD][hapmap]
rs4289331	0.81[CHD][hapmap]
rs4334629	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4353792	0.85[JPT][hapmap]
rs4383507	0.81[CHD][hapmap]
rs4402923	0.81[CHD][hapmap]
rs4461404	0.86[JPT][hapmap]
rs4472039	0.85[JPT][hapmap]
rs4535211	0.86[JPT][hapmap]
rs4602367	0.86[JPT][hapmap]
rs4618210	0.81[JPT][hapmap]
rs4684307	0.81[CHD][hapmap]
rs4685400	0.81[EUR][1000 genomes]
rs4685403	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4685404	0.86[JPT][hapmap]
rs4685405	0.82[ASW][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4685409	0.86[JPT][hapmap]
rs4685418	0.81[JPT][hapmap]
rs4685426	0.85[JPT][hapmap]
rs4685427	0.81[JPT][hapmap]
rs6442660	0.86[JPT][hapmap]
rs6762816	0.86[JPT][hapmap]
rs6780191	0.86[JPT][hapmap]
rs6783752	0.81[EUR][1000 genomes]
rs6799397	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6809087	0.86[JPT][hapmap]
rs7611127	0.86[JPT][hapmap]
rs7612044	0.85[JPT][hapmap]
rs7617672	0.86[JPT][hapmap]
rs7637568	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653027	0.86[JPT][hapmap]
rs9810017	0.86[JPT][hapmap]
rs9824172	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs9830460	0.85[JPT][hapmap]
rs9841259	0.85[JPT][hapmap]
rs9854760	0.89[JPT][hapmap]
rs9862613	0.89[JPT][hapmap]
rs9872237	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876137	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9879150	0.85[ASW][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9880307	0.86[JPT][hapmap];0.84[TSI][hapmap]
rs9881521	0.81[JPT][hapmap]
rs9882937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883633	0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs983545	CHCHD4	cis	parietal	SCAN
rs983545	C3orf20	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16940800-16962200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:16949000-16965400	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr3:16949200-16961200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:16951800-16969200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:16952800-16964600	Weak transcription	Ovary	ovary
6	chr3:16953800-16960400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:16954800-16965400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:16955000-16966000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:16955600-16961600	Enhancers	GM12878-XiMat	blood
10	chr3:16956000-16961600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:16956200-16960200	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:16956200-16961600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:16956400-16960400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr3:16956400-16962200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:16956400-16963000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:16956400-16963600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:16956800-16961400	Enhancers	Fetal Heart	heart
18	chr3:16957000-16960000	Enhancers	Liver	Liver
19	chr3:16957200-16960000	Enhancers	Primary T cells from cord blood	blood
20	chr3:16957200-16960200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:16957200-16962200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:16957400-16960200	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr3:16957400-16964600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:16957600-16959800	Enhancers	Osteobl	bone
25	chr3:16957600-16960000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:16957600-16964800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:16957800-16960400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:16958000-16981800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:16958200-16960000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:16958200-16960200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:16958200-16960400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:16958200-16961600	Enhancers	Primary B cells from cord blood	blood
33	chr3:16958400-16960000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr3:16958400-16960200	Enhancers	Stomach Mucosa	stomach
35	chr3:16958400-16960400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr3:16958400-16961600	Enhancers	Fetal Intestine Large	intestine
37	chr3:16958600-16959800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:16958800-16960200	Enhancers	A549	lung
39	chr3:16958800-16961000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:16958800-16961200	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:16958800-16963200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:16959000-16960000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:16959000-16960400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:16959200-16962800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:16959200-16964600	Weak transcription	Spleen	Spleen
46	chr3:16959400-16960000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:16959400-16960200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:16959400-16961200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:16959400-16961200	Weak transcription	Gastric	stomach
50	chr3:16959400-16961200	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links