SNP Detail Info-rs1470598

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.46042428A>G
GRCh37.p13 chr 2	NC_000002.11:g.46269567A>G

Gene: PRKCE, protein kinase C epsilon(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PRKCE transcript	NM_005400.2:c.	N/A	Intron Variant
PRKCE transcript variant X1	XM_005264428.1:c.	N/A	Intron Variant
PRKCE transcript variant X19	XM_006712050.3:c.	N/A	Intron Variant
PRKCE transcript variant X3	XM_011532971.2:c.	N/A	Intron Variant
PRKCE transcript variant X4	XM_011532975.2:c.	N/A	Intron Variant
PRKCE transcript variant X6	XM_011532978.1:c.	N/A	Intron Variant
PRKCE transcript variant X10	XM_011532980.2:c.	N/A	Intron Variant
PRKCE transcript variant X12	XM_011532981.2:c.	N/A	Intron Variant
PRKCE transcript variant X13	XM_011532982.1:c.	N/A	Intron Variant
PRKCE transcript variant X20	XM_011532983.2:c.	N/A	Intron Variant
PRKCE transcript variant X2	XM_017004486.1:c.	N/A	Intron Variant
PRKCE transcript variant X5	XM_017004487.1:c.	N/A	Intron Variant
PRKCE transcript variant X7	XM_017004488.1:c.	N/A	Intron Variant
PRKCE transcript variant X8	XM_017004489.1:c.	N/A	Intron Variant
PRKCE transcript variant X9	XM_017004490.1:c.	N/A	Intron Variant
PRKCE transcript variant X11	XM_017004491.1:c.	N/A	Intron Variant
PRKCE transcript variant X14	XM_005264431.3:c.	N/A	Genic Downstream Transcript Variant
PRKCE transcript variant X15	XM_017004492.1:c.	N/A	Genic Downstream Transcript Variant
PRKCE transcript variant X19	XR_001738846.1:n.	N/A	Genic Downstream Transcript Variant
PRKCE transcript variant X18	XR_939695.2:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.841	G=0.159
1000Genomes	American	Sub	694	A=0.770	G=0.230
1000Genomes	East Asian	Sub	1008	A=0.879	G=0.121
1000Genomes	Europe	Sub	1006	A=0.649	G=0.351
1000Genomes	Global	Study-wide	5008	A=0.780	G=0.220
1000Genomes	South Asian	Sub	978	A=0.740	G=0.260
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.619	G=0.381
The Genome Aggregation Database	African	Sub	8716	A=0.821	G=0.179
The Genome Aggregation Database	American	Sub	838	A=0.790	G=0.210
The Genome Aggregation Database	East Asian	Sub	1616	A=0.864	G=0.136
The Genome Aggregation Database	Europe	Sub	18482	A=0.624	G=0.375
The Genome Aggregation Database	Global	Study-wide	29954	A=0.699	G=0.300
The Genome Aggregation Database	Other	Sub	302	A=0.620	G=0.380
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.733	G=0.266
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.621	G=0.379

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs1470598	0.000693	nicotine smoking	19268276

eQTL of rs1470598 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs1470598 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	46242501	46242798	E067	-26769
chr2	46242892	46243126	E067	-26441
chr2	46243316	46243427	E067	-26140
chr2	46259719	46259822	E067	-9745
chr2	46290121	46290514	E067	20554
chr2	46220384	46220528	E068	-49039
chr2	46220570	46220978	E068	-48589
chr2	46242501	46242798	E068	-26769
chr2	46242892	46243126	E068	-26441
chr2	46285274	46285324	E068	15707
chr2	46300404	46301187	E068	30837
chr2	46242145	46242464	E069	-27103
chr2	46242501	46242798	E069	-26769
chr2	46242892	46243126	E069	-26441
chr2	46246019	46246130	E069	-23437
chr2	46290121	46290514	E069	20554
chr2	46290566	46290710	E069	20999
chr2	46242501	46242798	E070	-26769
chr2	46242145	46242464	E071	-27103
chr2	46242501	46242798	E071	-26769
chr2	46242892	46243126	E071	-26441
chr2	46246019	46246130	E071	-23437
chr2	46289518	46289654	E071	19951
chr2	46289715	46289775	E071	20148
chr2	46290121	46290514	E071	20554
chr2	46290566	46290710	E071	20999
chr2	46300404	46301187	E071	30837
chr2	46242501	46242798	E072	-26769
chr2	46242892	46243126	E072	-26441
chr2	46243316	46243427	E072	-26140
chr2	46246019	46246130	E072	-23437
chr2	46285274	46285324	E072	15707
chr2	46285443	46285524	E072	15876
chr2	46220384	46220528	E073	-49039
chr2	46220570	46220978	E073	-48589
chr2	46242892	46243126	E073	-26441
chr2	46246019	46246130	E073	-23437
chr2	46246769	46246952	E073	-22615
chr2	46285274	46285324	E073	15707
chr2	46285443	46285524	E073	15876
chr2	46299647	46299942	E073	30080
chr2	46300404	46301187	E073	30837
chr2	46220384	46220528	E074	-49039
chr2	46220570	46220978	E074	-48589
chr2	46258551	46259069	E074	-10498
chr2	46285274	46285324	E074	15707
chr2	46285443	46285524	E074	15876
chr2	46290121	46290514	E074	20554
chr2	46310391	46310501	E074	40824
chr2	46220384	46220528	E081	-49039
chr2	46258551	46259069	E081	-10498
chr2	46265564	46265638	E081	-3929
chr2	46265882	46265926	E081	-3641

rs1470598

Genomic Coordinates

Gene: PRKCE, protein kinase C epsilon(plus strand)

Population Frequency

P-Value

eQTL of rs1470598 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs1470598 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)