rs9449291

Homo sapiens
G>A
LGSN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0466 (13917/29868,GnomAD)
A=0388 (11317/29118,TOPMED)
A=0425 (2128/5008,1000G)
G==0459 (1769/3854,ALSPAC)
G==0455 (1686/3708,TWINSUK)
chr6:63453048 (GRCh38.p7) (6q12)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.63453048G>A
GRCh37.p13 chr 6NC_000006.11:g.64162953G>A

Gene: LGSN, lengsin, lens protein with glutamine synthetase domain(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LGSN transcript variant 2NM_001143940.1:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant 1NM_016571.2:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X1XM_017010929.1:c.N/AIntron Variant
LGSN transcript variant X2XM_011535889.2:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X4XM_011535892.2:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X3XM_017010930.1:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X5XM_017010931.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.813A=0.187
1000GenomesAmericanSub694G=0.580A=0.420
1000GenomesEast AsianSub1008G=0.466A=0.534
1000GenomesEuropeSub1006G=0.433A=0.567
1000GenomesGlobalStudy-wide5008G=0.575A=0.425
1000GenomesSouth AsianSub978G=0.510A=0.490
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.459A=0.541
The Genome Aggregation DatabaseAfricanSub8704G=0.776A=0.224
The Genome Aggregation DatabaseAmericanSub834G=0.580A=0.420
The Genome Aggregation DatabaseEast AsianSub1614G=0.478A=0.522
The Genome Aggregation DatabaseEuropeSub18414G=0.425A=0.574
The Genome Aggregation DatabaseGlobalStudy-wide29868G=0.534A=0.466
The Genome Aggregation DatabaseOtherSub302G=0.370A=0.630
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.611A=0.388
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.455A=0.545
PMID Title Author Journal
22096494A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.Zuo LPLoS One

P-Value

SNP ID p-value Traits Study
rs94492917.8E-06alcohol dependence22096494

eQTL of rs9449291 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64162953LGSNENSG00000146166.12G>A1.9599e-12133071Brain_Spinal_cord_cervical

meQTL of rs9449291 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.