Variant report

Variant	rs12589698
Chromosome Location	chr14:65920435-65920436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10138570	0.93[CEU][hapmap]
rs10483780	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158592	0.88[CEU][hapmap]
rs11158593	0.93[CEU][hapmap];0.80[MEX][hapmap]
rs11158596	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11158602	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11620749	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11621680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11622014	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11624045	0.86[EUR][1000 genomes]
rs11627084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11628196	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11851576	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12879202	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12879805	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12879971	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12882269	1.00[CHB][hapmap]
rs12883815	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886334	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12887134	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12889002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12890123	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890902	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs12890978	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12892058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12895074	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12896663	0.86[EUR][1000 genomes]
rs1953416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1958561	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2002692	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2149841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2184603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300865	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2411355	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2411357	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2411816	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2411822	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3783709	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3825640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4456409	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4581615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4899179	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902400	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902407	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67071794	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7146742	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7153297	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7154536	0.86[ASN][1000 genomes]
rs7155541	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7161123	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs743085	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8005710	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8012278	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867972	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs883081	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs883082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12589698	VTI1B	cis	parietal	SCAN
rs12589698	FUT8	cis	cerebellum	SCAN
rs12589698	HIF1A	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65892800-65929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr14:65897000-65925600	Weak transcription	Aorta	Aorta
3	chr14:65898400-65935600	Weak transcription	Gastric	stomach
4	chr14:65899600-65929000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr14:65902200-65927000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr14:65902400-65928400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr14:65903200-65922600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:65903200-65925200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:65905800-65936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:65906000-65923800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:65906000-65926800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:65906200-65922000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr14:65906600-65922800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr14:65911200-65942400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr14:65912200-65922400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr14:65913000-65924000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr14:65913200-65922400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:65913200-65927000	Weak transcription	NH-A	brain
19	chr14:65913200-65928000	Weak transcription	Osteobl	bone
20	chr14:65913800-65922800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr14:65913800-65928000	Weak transcription	HUVEC	blood vessel
22	chr14:65913800-65942400	Weak transcription	Left Ventricle	heart
23	chr14:65914200-65922400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr14:65914600-65925000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:65915600-65928200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr14:65916600-65922600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr14:65916600-65923000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr14:65917200-65936600	Weak transcription	Pancreas	Pancrea
29	chr14:65918400-65922000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:65918400-65928000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr14:65918400-65928200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr14:65918600-65921600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr14:65918600-65922800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr14:65918600-65928000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:65918600-65935600	Weak transcription	Fetal Stomach	stomach
36	chr14:65918800-65920600	Weak transcription	Dnd41	blood
37	chr14:65918800-65922400	Weak transcription	Primary T cells from cord blood	blood
38	chr14:65918800-65922600	Weak transcription	Primary B cells from cord blood	blood
39	chr14:65918800-65922600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr14:65918800-65922600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr14:65918800-65923000	Weak transcription	Brain Germinal Matrix	brain
42	chr14:65918800-65923200	Weak transcription	Fetal Intestine Small	intestine
43	chr14:65918800-65924200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:65918800-65924800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr14:65918800-65927000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:65918800-65928400	Weak transcription	Fetal Thymus	thymus
47	chr14:65919000-65921600	Enhancers	Brain Substantia Nigra	brain
48	chr14:65919200-65922800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr14:65919200-65923400	Weak transcription	Fetal Intestine Large	intestine
50	chr14:65919400-65922400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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