rs62271282

Homo sapiens
T>C / T>G
LSAMP : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0048 (1441/29984,GnomAD)
G=0020 (602/29118,TOPMED)
G=0016 (78/5008,1000G)
G=0042 (162/3854,ALSPAC)
G=0046 (171/3708,TWINSUK)
chr3:116039221 (GRCh38.p7) (3q13.31)
AD
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.116039221T>C
GRCh38.p7 chr 3NC_000003.12:g.116039221T>G
GRCh37.p13 chr 3NC_000003.11:g.115758068T>C
GRCh37.p13 chr 3NC_000003.11:g.115758068T>G

Gene: LSAMP, limbic system-associated membrane protein(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LSAMP transcript variant 2NM_001318915.1:c.N/AIntron Variant
LSAMP transcript variant 1NM_002338.4:c.N/AIntron Variant
LSAMP transcript variant X2XM_011512840.2:c.N/AIntron Variant
LSAMP transcript variant X1XM_017006383.1:c.N/AIntron Variant
LSAMP transcript variant X3XM_017006384.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.999G=0.001
1000GenomesAmericanSub694T=0.990G=0.010
1000GenomesEast AsianSub1008T=0.999G=0.001
1000GenomesEuropeSub1006T=0.936G=0.064
1000GenomesGlobalStudy-wide5008T=0.984G=0.016
1000GenomesSouth AsianSub978T=1.000G=0.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.958G=0.042
The Genome Aggregation DatabaseAfricanSub8732T=0.992C=0.000
The Genome Aggregation DatabaseAmericanSub838T=0.980C=0.00,
The Genome Aggregation DatabaseEast AsianSub1618T=1.000C=0.000
The Genome Aggregation DatabaseEuropeSub18494T=0.927C=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29984T=0.951C=0.000
The Genome Aggregation DatabaseOtherSub302T=0.940C=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.979G=0.020
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.954G=0.046
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs622712829.16E-06alcohol dependence (age at onset)24962325

eQTL of rs62271282 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 rs62271282 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 )
chr32870922128709888E06712631
chr32870922128709888E06812631
chr32865363928653689E069-42901
chr32865385828653974E069-42616
chr32865385828653974E070-42616
chr32865753428657983E070-38607
chr32865363928653689E071-42901
chr32865385828653974E071-42616
chr32865385828653974E072-42616
chr32870922128709888E07312631
chr32865307828653179E074-43411
chr32865363928653689E074-42901
chr32865385828653974E074-42616
chr32870922128709888E07412631