rs4949402

Homo sapiens
T>C
SERINC2 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0486 (58981/121304,ExAC)
C=0453 (13538/29854,GnomAD)
C=0392 (11421/29118,TOPMED)
T==0453 (5900/13006,GO-ESP)
C=0350 (1753/5008,1000G)
T==0434 (1671/3854,ALSPAC)
T==0441 (1635/3708,TWINSUK)
chr1:31425387 (GRCh38.p7) (1p35.2)
AD
GWASdb2
2   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.31425387T>C
GRCh37.p13 chr 1 fix patch HG989_PATCHNW_003571030.1:g.25476T>C
GRCh37.p13 chr 1NC_000001.10:g.31898234T>C

Gene: SERINC2, serine incorporator 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SERINC2 transcript variant 1NM_178865.4:c.450T>CI [ATT]> I [ATC]Coding Sequence Variant
serine incorporator 2 isoform 1 precursorNP_849196.2:p.Ile...NP_849196.2:p.Ile150=I [Ile]> I [Ile]Synonymous Variant
SERINC2 transcript variant 2NM_018565.3:c.462T>CI [ATT]> I [ATC]Coding Sequence Variant
serine incorporator 2 isoform 2NP_061035.2:p.Ile...NP_061035.2:p.Ile154=I [Ile]> I [Ile]Synonymous Variant
SERINC2 transcript variant 3NM_001199037.1:c....NM_001199037.1:c.462T>CI [ATT]> I [ATC]Coding Sequence Variant
serine incorporator 2 isoform 3NP_001185966.1:p....NP_001185966.1:p.Ile154=I [Ile]> I [Ile]Synonymous Variant
SERINC2 transcript variant 4NM_001199038.1:c....NM_001199038.1:c.477T>CI [ATT]> I [ATC]Coding Sequence Variant
serine incorporator 2 isoform 4NP_001185967.1:p....NP_001185967.1:p.Ile159=I [Ile]> I [Ile]Synonymous Variant
SERINC2 transcript variant 5NM_001199039.1:c....NM_001199039.1:c.285T>CI [ATT]> I [ATC]Coding Sequence Variant
serine incorporator 2 isoform 5NP_001185968.1:p....NP_001185968.1:p.Ile95=I [Ile]> I [Ile]Synonymous Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.855C=0.145
1000GenomesAmericanSub694T=0.550C=0.450
1000GenomesEast AsianSub1008T=0.641C=0.359
1000GenomesEuropeSub1006T=0.440C=0.560
1000GenomesGlobalStudy-wide5008T=0.650C=0.350
1000GenomesSouth AsianSub978T=0.670C=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.434C=0.566
The Exome Aggregation ConsortiumAmericanSub21974T=0.661C=0.338
The Exome Aggregation ConsortiumAsianSub25148T=0.643C=0.356
The Exome Aggregation ConsortiumEuropeSub73274T=0.425C=0.575
The Exome Aggregation ConsortiumGlobalStudy-wide121304T=0.513C=0.486
The Exome Aggregation ConsortiumOtherSub908T=0.500C=0.500
The Genome Aggregation DatabaseAfricanSub8684T=0.795C=0.205
The Genome Aggregation DatabaseAmericanSub838T=0.530C=0.470
The Genome Aggregation DatabaseEast AsianSub1614T=0.638C=0.362
The Genome Aggregation DatabaseEuropeSub18416T=0.423C=0.576
The Genome Aggregation DatabaseGlobalStudy-wide29854T=0.546C=0.453
The Genome Aggregation DatabaseOtherSub302T=0.440C=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.607C=0.392
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.441C=0.559
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology

P-Value

SNP ID p-value Traits Study
rs49494029.44E-05alcohol dependence21703634

eQTL of rs4949402 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:31898234FABP3ENSG00000121769.3T>C1.5051e-1148537Cerebellum
Chr1:31898234FABP3ENSG00000121769.3T>C2.7794e-748537Cerebellar_Hemisphere
Chr1:31898234NKAIN1ENSG00000084628.5T>C7.6975e-16185833Amygdala

meQTL of rs4949402 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.