rs2758259

Homo sapiens
C>T
LGSN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0469 (14042/29888,GnomAD)
C==0391 (11403/29118,TOPMED)
C==0430 (2153/5008,1000G)
T=0447 (1723/3854,ALSPAC)
T=0448 (1663/3708,TWINSUK)
chr6:63483202 (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.63483202C>T
GRCh37.p13 chr 6NC_000006.11:g.64193107C>T

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
1000GenomesAfricanSub1322C=0.188T=0.812
1000GenomesAmericanSub694C=0.420T=0.580
1000GenomesEast AsianSub1008C=0.549T=0.451
1000GenomesEuropeSub1006C=0.580T=0.420
1000GenomesGlobalStudy-wide5008C=0.430T=0.570
1000GenomesSouth AsianSub978C=0.490T=0.510
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.553T=0.447
The Genome Aggregation DatabaseAfricanSub8700C=0.224T=0.776
The Genome Aggregation DatabaseAmericanSub838C=0.420T=0.580
The Genome Aggregation DatabaseEast AsianSub1616C=0.546T=0.454
The Genome Aggregation DatabaseEuropeSub18432C=0.578T=0.421
The Genome Aggregation DatabaseGlobalStudy-wide29888C=0.469T=0.530
The Genome Aggregation DatabaseOtherSub302C=0.630T=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.391T=0.608
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.552T=0.448
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
rs27582591.1E-05alcohol dependence22096494

eQTL of rs2758259 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64193107LGSNENSG00000146166.12C>T1.9599e-12163225Brain_Spinal_cord_cervical

meQTL of rs2758259 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.