rs4478858

Homo sapiens
T>C
SERINC2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0479 (14354/29914,GnomAD)
C=0488 (14228/29118,TOPMED)
T==0407 (2036/5008,1000G)
C=0431 (1662/3854,ALSPAC)
C=0438 (1624/3708,TWINSUK)
chr1:31411078 (GRCh38.p7) (1p35.2)
AD
GWASdb2 | GWASCatalog
3   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.31411078T>C
GRCh37.p13 chr 1 fix patch HG989_PATCHNW_003571030.1:g.11167T>C
GRCh37.p13 chr 1NC_000001.10:g.31883925T>C

Gene: SERINC2, serine incorporator 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SERINC2 transcript variant 3NM_001199037.1:c.N/AIntron Variant
SERINC2 transcript variant 4NM_001199038.1:c.N/AIntron Variant
SERINC2 transcript variant 5NM_001199039.1:c.N/AGenic Upstream Transcript Variant
SERINC2 transcript variant 2NM_018565.3:c.N/AGenic Upstream Transcript Variant
SERINC2 transcript variant 1NM_178865.4:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.470C=0.530
1000GenomesAmericanSub694T=0.480C=0.520
1000GenomesEast AsianSub1008T=0.200C=0.800
1000GenomesEuropeSub1006T=0.562C=0.438
1000GenomesGlobalStudy-wide5008T=0.407C=0.593
1000GenomesSouth AsianSub978T=0.320C=0.680
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.569C=0.431
The Genome Aggregation DatabaseAfricanSub8702T=0.459C=0.541
The Genome Aggregation DatabaseAmericanSub838T=0.490C=0.510
The Genome Aggregation DatabaseEast AsianSub1618T=0.208C=0.792
The Genome Aggregation DatabaseEuropeSub18456T=0.576C=0.423
The Genome Aggregation DatabaseGlobalStudy-wide29914T=0.520C=0.479
The Genome Aggregation DatabaseOtherSub300T=0.570C=0.430
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.511C=0.488
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.562C=0.438
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res
23455491NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent.Zuo LDrug Alcohol Depend
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology

P-Value

SNP ID p-value Traits Study
rs44788580.00000003alcohol dependence23455491
rs44788580.0000896alcohol dependence21703634

eQTL of rs4478858 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:31883925FABP3ENSG00000121769.3T>C1.5051e-1134228Cerebellum
Chr1:31883925FABP3ENSG00000121769.3T>C2.7794e-734228Cerebellar_Hemisphere

meQTL of rs4478858 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.