Variant report

Variant	rs2190667
Chromosome Location	chr7:38900848-38900849
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	chr7:38900320..38904154-chr7:38910727..38914259,3	K562	blood:
2	chr7:38900726..38902861-chr7:38904557..38906481,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10085487	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012976	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10224856	1.00[CHB][hapmap]
rs10225415	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10225550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10232614	1.00[ASN][1000 genomes]
rs10239757	1.00[ASN][1000 genomes]
rs10239904	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254354	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10254873	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264217	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266279	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270483	0.88[EUR][1000 genomes]
rs10275873	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10951574	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs11983387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12701653	1.00[CHB][hapmap]
rs12701656	1.00[AFR][1000 genomes]
rs12701657	1.00[AFR][1000 genomes]
rs12701661	1.00[CHB][hapmap]
rs12701671	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13224619	1.00[CHB][hapmap]
rs13230196	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13231372	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235997	1.00[CHB][hapmap]
rs13236092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1558111	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.81[EUR][1000 genomes]
rs2040878	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2058073	0.88[AMR][1000 genomes]
rs2079546	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs2190668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214667	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2214668	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2215032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2245773	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2286089	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2286093	1.00[CHB][hapmap]
rs2286101	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2392599	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2392608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs34349310	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34358406	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34621392	1.00[AFR][1000 genomes]
rs34886315	1.00[AFR][1000 genomes]
rs35220172	0.81[EUR][1000 genomes]
rs35667896	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36114334	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36121032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275134	0.86[EUR][1000 genomes]
rs4720300	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4723780	1.00[CHB][hapmap]
rs4723781	1.00[CHB][hapmap]
rs4723784	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4723787	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4723802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4723804	0.92[EUR][1000 genomes]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462873	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6462874	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949958	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6951429	1.00[CHB][hapmap]
rs6960945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6963090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6964985	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967384	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6971632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974764	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	1.00[CHB][hapmap]
rs6976302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6976579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6976580	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6978805	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71548633	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs758088	0.92[EUR][1000 genomes]
rs7782140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs7782277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs7783723	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784065	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7788663	0.87[EUR][1000 genomes]
rs7789864	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793250	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803488	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976352	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9886108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2190667	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
4	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
5	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
9	chr7:38876400-38906200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:38877200-38901200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
12	chr7:38880800-38905600	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:38881200-38907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
15	chr7:38883400-38907600	Weak transcription	Esophagus	oesophagus
16	chr7:38884600-38905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:38886200-38901400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:38886400-38907400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:38886400-38907400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:38886400-38907600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:38886600-38901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:38886600-38907200	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:38887200-38906600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:38887200-38907400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:38887600-38902800	Weak transcription	Liver	Liver
27	chr7:38889200-38903000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:38889200-38907200	Weak transcription	Ovary	ovary
29	chr7:38889400-38906800	Weak transcription	Fetal Stomach	stomach
30	chr7:38889400-38907200	Weak transcription	Lung	lung
31	chr7:38889400-38907400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:38889400-38909600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:38889400-38948200	Weak transcription	Gastric	stomach
34	chr7:38889600-38902400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:38889600-38902400	Weak transcription	Fetal Intestine Small	intestine
36	chr7:38889600-38932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:38890800-38901000	Weak transcription	Placenta	Placenta
38	chr7:38891200-38903200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr7:38893800-38925600	Weak transcription	Thymus	Thymus
40	chr7:38894000-38903600	Weak transcription	Small Intestine	intestine
41	chr7:38895200-38907200	Weak transcription	Brain Anterior Caudate	brain
42	chr7:38896000-38907600	Weak transcription	Spleen	Spleen
43	chr7:38896600-38906200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:38897000-38903400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr7:38897200-38901000	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr7:38897400-38902800	Weak transcription	HepG2	liver
47	chr7:38897600-38907400	Weak transcription	Brain Angular Gyrus	brain
48	chr7:38897600-38909000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr7:38898000-38902800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:38898000-38907600	Weak transcription	HSMM	muscle

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