rs1347992

Homo sapiens
T>C
SCN3A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0213 (6393/29932,GnomAD)
C=0214 (6246/29118,TOPMED)
C=0243 (1217/5008,1000G)
C=0202 (778/3854,ALSPAC)
C=0218 (809/3708,TWINSUK)
chr2:165105355 (GRCh38.p7) (2q24.3)
AD
GWASdb2
2   publication(s)
See rs on genome
42 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.165105355T>C
GRCh37.p13 chr 2NC_000002.11:g.165961865T>C
SCN3A RefSeqGeneNG_042289.1:g.103734A>G

Gene: SCN3A, sodium voltage-gated channel alpha subunit 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SCN3A transcript variant 2NM_001081676.1:c.N/AIntron Variant
SCN3A transcript variant 3NM_001081677.1:c.N/AIntron Variant
SCN3A transcript variant 1NM_006922.3:c.N/AIntron Variant
SCN3A transcript variant X1XM_011511610.2:c.N/AIntron Variant
SCN3A transcript variant X5XM_011511613.2:c.N/AIntron Variant
SCN3A transcript variant X2XM_017004660.1:c.N/AIntron Variant
SCN3A transcript variant X3XM_017004661.1:c.N/AIntron Variant
SCN3A transcript variant X4XM_017004662.1:c.N/AIntron Variant
SCN3A transcript variant X6XM_017004663.1:c.N/AIntron Variant
SCN3A transcript variant X7XM_017004664.1:c.N/AGenic Downstream Transcript Variant
SCN3A transcript variant X8XM_017004665.1:c.N/AGenic Downstream Transcript Variant
SCN3A transcript variant X9XM_017004666.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.771C=0.229
1000GenomesAmericanSub694T=0.800C=0.200
1000GenomesEast AsianSub1008T=0.738C=0.262
1000GenomesEuropeSub1006T=0.777C=0.223
1000GenomesGlobalStudy-wide5008T=0.757C=0.243
1000GenomesSouth AsianSub978T=0.710C=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.798C=0.202
The Genome Aggregation DatabaseAfricanSub8710T=0.805C=0.195
The Genome Aggregation DatabaseAmericanSub836T=0.780C=0.220
The Genome Aggregation DatabaseEast AsianSub1618T=0.750C=0.250
The Genome Aggregation DatabaseEuropeSub18466T=0.782C=0.217
The Genome Aggregation DatabaseGlobalStudy-wide29932T=0.786C=0.213
The Genome Aggregation DatabaseOtherSub302T=0.720C=0.280
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.785C=0.214
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.782C=0.218
PMID Title Author Journal
24386469Use of systems biology approaches to analysis of genome-wide association studies of myocardial infarction and blood cholesterol in the nurses' health study and health professionals' follow-up study.Reilly DPLoS One
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs13479920.000485alcohol dependence24277619

eQTL of rs1347992 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 rs1347992 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 )
chr2165925233165925321E067-36544
chr2165970211165970432E0678346
chr2165970731165970859E0678866
chr2165970908165971087E0679043
chr2165971117165971281E0679252
chr2165925233165925321E068-36544
chr2165925425165925964E068-35901
chr2165925233165925321E069-36544
chr2165925425165925964E069-35901
chr2165923770165923827E070-38038
chr2165925233165925321E070-36544
chr2165925425165925964E070-35901
chr2165926259165926309E070-35556
chr2165926600165926860E070-35005
chr2165970731165970859E0708866
chr2165970908165971087E0709043
chr2165971117165971281E0709252
chr2165925425165925964E071-35901
chr2165911969165912102E081-49763
chr2165912123165912204E081-49661
chr2165921386165921493E081-40372
chr2165922252165922462E081-39403
chr2165922734165923038E081-38827
chr2165923770165923827E081-38038
chr2165925233165925321E081-36544
chr2165925425165925964E081-35901
chr2165926259165926309E081-35556
chr2165926600165926860E081-35005
chr2165926935165926985E081-34880
chr2165927092165927329E081-34536
chr2165998289165998360E08136424
chr2165998503165998835E08136638
chr2165999833165999927E08137968
chr2166000953166001082E08139088
chr2165911969165912102E082-49763
chr2165925233165925321E082-36544
chr2165925425165925964E082-35901
chr2165926600165926860E082-35005
chr2165926935165926985E082-34880
chr2165927698165927748E082-34117
chr2165998503165998835E08236638
chr2165999833165999927E08237968







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2165924281165925143E067-36722
chr2165924281165925143E068-36722
chr2165924281165925143E069-36722
chr2165924281165925143E070-36722
chr2165924281165925143E071-36722
chr2165924281165925143E072-36722
chr2165924281165925143E074-36722
chr2165924281165925143E082-36722