SNP Detail Info-rs56247223

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.54608201G>A
GRCh37.p13 chr 3	NC_000003.11:g.54642228G>A

Gene: CACNA2D3, calcium voltage-gated channel auxiliary subunit alpha2delta 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA2D3 transcript	NM_018398.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X1	XM_005265318.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X4	XM_011533946.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X6	XM_011533947.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X9	XM_011533948.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X12	XM_011533949.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X15	XM_011533950.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X18	XM_011533951.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X19	XM_011533952.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X20	XM_011533953.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X2	XM_017006850.1:c.	N/A	Intron Variant
CACNA2D3 transcript variant X7	XM_017006851.1:c.	N/A	Intron Variant
CACNA2D3 transcript variant X11	XM_017006852.1:c.	N/A	Intron Variant
CACNA2D3 transcript variant X21	XM_011533954.2:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X23	XM_011533955.1:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X13	XM_017006853.1:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X14	XM_017006854.1:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X16	XR_001740203.1:n.	N/A	Intron Variant
CACNA2D3 transcript variant X17	XR_001740204.1:n.	N/A	Intron Variant
CACNA2D3 transcript variant X22	XR_001740205.1:n.	N/A	Intron Variant
CACNA2D3 transcript variant X5	XR_427281.2:n.	N/A	Intron Variant
CACNA2D3 transcript variant X3	XR_940472.2:n.	N/A	Intron Variant
CACNA2D3 transcript variant X9	XR_940473.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.695	A=0.305
1000Genomes	American	Sub	694	G=0.870	A=0.130
1000Genomes	East Asian	Sub	1008	G=0.992	A=0.008
1000Genomes	Europe	Sub	1006	G=0.758	A=0.242
1000Genomes	Global	Study-wide	5008	G=0.818	A=0.182
1000Genomes	South Asian	Sub	978	G=0.830	A=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.760	A=0.240
The Genome Aggregation Database	African	Sub	8706	G=0.696	A=0.304
The Genome Aggregation Database	American	Sub	838	G=0.890	A=0.110
The Genome Aggregation Database	East Asian	Sub	1622	G=0.993	A=0.007
The Genome Aggregation Database	Europe	Sub	18478	G=0.741	A=0.258
The Genome Aggregation Database	Global	Study-wide	29946	G=0.746	A=0.253
The Genome Aggregation Database	Other	Sub	302	G=0.800	A=0.200
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.739	A=0.260
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.759	A=0.241

PMID	Title	Author	Journal
28440896	Genome-wide meta-analysis identifies a novel susceptibility signal at CACNA2D3 for nicotine dependence.	Yin X	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs56247223	4E-08	nicotine dependence	28440896

eQTL of rs56247223 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 rs56247223 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 )
chr3	54635004	54635077	E067	-7151
chr3	54634437	54634829	E068	-7399
chr3	54635004	54635077	E068	-7151
chr3	54666425	54666590	E068	24197
chr3	54634437	54634829	E069	-7399
chr3	54635004	54635077	E069	-7151
chr3	54597533	54597783	E070	-44445
chr3	54608029	54608117	E070	-34111
chr3	54609689	54609754	E070	-32474
chr3	54633796	54634297	E070	-7931
chr3	54634437	54634829	E070	-7399
chr3	54655046	54655216	E070	12818
chr3	54655284	54655537	E070	13056
chr3	54655706	54655754	E070	13478
chr3	54656069	54656183	E070	13841
chr3	54665541	54666258	E070	23313
chr3	54666425	54666590	E070	24197
chr3	54666625	54666712	E070	24397
chr3	54667031	54667120	E070	24803
chr3	54667203	54667253	E070	24975
chr3	54667393	54667453	E070	25165
chr3	54667675	54667740	E070	25447
chr3	54667880	54667981	E070	25652
chr3	54633796	54634297	E071	-7931
chr3	54634437	54634829	E071	-7399
chr3	54635004	54635077	E071	-7151
chr3	54633796	54634297	E072	-7931
chr3	54634437	54634829	E072	-7399
chr3	54635004	54635077	E072	-7151
chr3	54635004	54635077	E073	-7151
chr3	54609689	54609754	E074	-32474
chr3	54633796	54634297	E074	-7931
chr3	54634437	54634829	E074	-7399
chr3	54635004	54635077	E074	-7151
chr3	54608029	54608117	E081	-34111
chr3	54633796	54634297	E081	-7931
chr3	54634437	54634829	E081	-7399
chr3	54635004	54635077	E081	-7151
chr3	54665541	54666258	E081	23313
chr3	54667031	54667120	E081	24803
chr3	54597533	54597783	E082	-44445
chr3	54598364	54598759	E082	-43469
chr3	54598877	54599072	E082	-43156
chr3	54633796	54634297	E082	-7931
chr3	54634437	54634829	E082	-7399
chr3	54655284	54655537	E082	13056
chr3	54655706	54655754	E082	13478
chr3	54665541	54666258	E082	23313
chr3	54666425	54666590	E082	24197

rs56247223

Genomic Coordinates

Gene: CACNA2D3, calcium voltage-gated channel auxiliary subunit alpha2delta 3(plus strand)

Population Frequency

P-Value

eQTL of rs56247223 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs56247223 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)