rs11708620

Homo sapiens
C>T
CACNA2D3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0079 (2368/29990,GnomAD)
T=0089 (2610/29118,TOPMED)
T=0074 (370/5008,1000G)
chr3:54337764 (GRCh38.p7) (3p21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
68 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.54337764C>T
GRCh37.p13 chr 3NC_000003.11:g.54371791C>T

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

Molecule type Change Amino acid[Codon] SO Term
CACNA2D3 transcriptNM_018398.2:c.N/AIntron Variant
CACNA2D3 transcript variant X1XM_005265318.2:c.N/AIntron Variant
CACNA2D3 transcript variant X4XM_011533946.2:c.N/AIntron Variant
CACNA2D3 transcript variant X6XM_011533947.2:c.N/AIntron Variant
CACNA2D3 transcript variant X9XM_011533948.2:c.N/AIntron Variant
CACNA2D3 transcript variant X12XM_011533949.2:c.N/AIntron Variant
CACNA2D3 transcript variant X15XM_011533950.2:c.N/AIntron Variant
CACNA2D3 transcript variant X18XM_011533951.2:c.N/AIntron Variant
CACNA2D3 transcript variant X19XM_011533952.2:c.N/AIntron Variant
CACNA2D3 transcript variant X20XM_011533953.2:c.N/AIntron Variant
CACNA2D3 transcript variant X2XM_017006850.1:c.N/AIntron Variant
CACNA2D3 transcript variant X11XM_017006852.1:c.N/AIntron Variant
CACNA2D3 transcript variant X21XM_011533954.2:c.N/AGenic Upstream Transcript Variant
CACNA2D3 transcript variant X23XM_011533955.1:c.N/AGenic Upstream Transcript Variant
CACNA2D3 transcript variant X7XM_017006851.1:c.N/AGenic Upstream Transcript Variant
CACNA2D3 transcript variant X13XM_017006853.1:c.N/AGenic Upstream Transcript Variant
CACNA2D3 transcript variant X14XM_017006854.1:c.N/AGenic Upstream Transcript Variant
CACNA2D3 transcript variant X16XR_001740203.1:n.N/AIntron Variant
CACNA2D3 transcript variant X17XR_001740204.1:n.N/AIntron Variant
CACNA2D3 transcript variant X22XR_001740205.1:n.N/AIntron Variant
CACNA2D3 transcript variant X5XR_427281.2:n.N/AIntron Variant
CACNA2D3 transcript variant X3XR_940472.2:n.N/AIntron Variant
CACNA2D3 transcript variant X9XR_940473.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.926T=0.074
1000GenomesAmericanSub694C=0.920T=0.080
1000GenomesEast AsianSub1008C=0.992T=0.008
1000GenomesEuropeSub1006C=0.884T=0.116
1000GenomesGlobalStudy-wide5008C=0.926T=0.074
1000GenomesSouth AsianSub978C=0.910T=0.090
The Genome Aggregation DatabaseAfricanSub8734C=0.932T=0.068
The Genome Aggregation DatabaseAmericanSub838C=0.930T=0.070
The Genome Aggregation DatabaseEast AsianSub1620C=0.998T=0.002
The Genome Aggregation DatabaseEuropeSub18496C=0.910T=0.090
The Genome Aggregation DatabaseGlobalStudy-wide29990C=0.921T=0.079
The Genome Aggregation DatabaseOtherSub302C=0.850T=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.910T=0.089
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs117086200.000537alcohol dependence21314694

eQTL of rs11708620 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 rs11708620 in Fetal Brain

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

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr35439038254390780E06718591
chr35439086354390973E06719072
chr35439362754393727E06721836
chr35438778154387859E06815990
chr35438851654388591E06816725
chr35439002654390129E06818235
chr35439021454390341E06818423
chr35439038254390780E06818591
chr35439086354390973E06819072
chr35438877454388834E06916983
chr35438884954388931E06917058
chr35438927554389332E06917484
chr35439038254390780E06918591
chr35439086354390973E06919072
chr35433071254330773E070-41018
chr35433094254331228E070-40563
chr35433819154338280E070-33511
chr35433870554338747E070-33044
chr35433899954339142E070-32649
chr35434152954341620E070-30171
chr35434169054341855E070-29936
chr35436480654364856E070-6935
chr35436542754365708E070-6083
chr35436657754366659E070-5132
chr35439146654391560E07019675
chr35433819154338280E071-33511
chr35433870554338747E071-33044
chr35433899954339142E071-32649
chr35438927554389332E07117484
chr35433819154338280E072-33511
chr35433870554338747E072-33044
chr35433819154338280E073-33511
chr35438877454388834E07316983
chr35438884954388931E07317058
chr35438927554389332E07317484
chr35439002654390129E07318235
chr35439021454390341E07318423
chr35439038254390780E07318591
chr35439086354390973E07319072
chr35440859154408733E07336800
chr35434617654346890E081-24901
chr35435602254356339E081-15452
chr35435637754356710E081-15081
chr35436388354364327E081-7464
chr35436480654364856E081-6935
chr35436542754365708E081-6083
chr35436657754366659E081-5132
chr35438778154387859E08115990
chr35438805054388105E08116259
chr35438811554388260E08116324
chr35438851654388591E08116725
chr35438877454388834E08116983
chr35438884954388931E08117058
chr35438927554389332E08117484
chr35439002654390129E08118235
chr35439021454390341E08118423
chr35439038254390780E08118591
chr35439086354390973E08119072
chr35439146654391560E08119675
chr35440102254401160E08129231
chr35441050454410890E08138713
chr35441091154410966E08139120
chr35441108354411640E08139292
chr35441190954412019E08140118
chr35436480654364856E082-6935
chr35436657754366659E082-5132
chr35438327154383544E08211480
chr35441190954412019E08240118