rs1039630

Homo sapiens
T>C
SERINC2 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0477 (14184/29704,GnomAD)
C=0496 (14447/29118,TOPMED)
T==0437 (2188/5008,1000G)
C=0427 (1647/3854,ALSPAC)
C=0431 (1597/3708,TWINSUK)
chr1:31408625 (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.31408625T>C
GRCh37.p13 chr 1 fix patch HG989_PATCHNW_003571030.1:g.8714T>C
GRCh37.p13 chr 1NC_000001.10:g.31881472T>C

Gene: SERINC2, serine incorporator 2(plus strand): 2KB Upstream Variant

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

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.451C=0.549
1000GenomesAmericanSub694T=0.490C=0.510
1000GenomesEast AsianSub1008T=0.359C=0.641
1000GenomesEuropeSub1006T=0.568C=0.432
1000GenomesGlobalStudy-wide5008T=0.437C=0.563
1000GenomesSouth AsianSub978T=0.330C=0.670
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.573C=0.427
The Genome Aggregation DatabaseAfricanSub8660T=0.439C=0.561
The Genome Aggregation DatabaseAmericanSub838T=0.500C=0.500
The Genome Aggregation DatabaseEast AsianSub1598T=0.349C=0.651
The Genome Aggregation DatabaseEuropeSub18306T=0.577C=0.422
The Genome Aggregation DatabaseGlobalStudy-wide29704T=0.522C=0.477
The Genome Aggregation DatabaseOtherSub302T=0.570C=0.430
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.503C=0.496
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.569C=0.431
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
rs10396308.72E-05alcohol dependence21703634

eQTL of rs1039630 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:31881472FABP3ENSG00000121769.3T>C1.5051e-1131775Cerebellum
Chr1:31881472FABP3ENSG00000121769.3T>C2.7794e-731775Cerebellar_Hemisphere
Chr1:31881472NKAIN1ENSG00000084628.5T>C7.6975e-16169071Amygdala

meQTL of rs1039630 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.