rs6942342

Homo sapiens
T>C
LGSN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0469 (14047/29920,GnomAD)
C=0392 (11423/29118,TOPMED)
C=0430 (2151/5008,1000G)
T==0447 (1724/3854,ALSPAC)
T==0447 (1658/3708,TWINSUK)
chr6:63466542 (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.63466542T>C
GRCh37.p13 chr 6NC_000006.11:g.64176447T>C

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
1000GenomesAfricanSub1322T=0.810C=0.190
1000GenomesAmericanSub694T=0.580C=0.420
1000GenomesEast AsianSub1008T=0.457C=0.543
1000GenomesEuropeSub1006T=0.419C=0.581
1000GenomesGlobalStudy-wide5008T=0.570C=0.430
1000GenomesSouth AsianSub978T=0.510C=0.490
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.447C=0.553
The Genome Aggregation DatabaseAfricanSub8712T=0.777C=0.223
The Genome Aggregation DatabaseAmericanSub838T=0.580C=0.420
The Genome Aggregation DatabaseEast AsianSub1610T=0.458C=0.542
The Genome Aggregation DatabaseEuropeSub18458T=0.421C=0.578
The Genome Aggregation DatabaseGlobalStudy-wide29920T=0.530C=0.469
The Genome Aggregation DatabaseOtherSub302T=0.370C=0.630
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.607C=0.392
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.447C=0.553
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
rs69423424.1E-06alcohol dependence22096494

eQTL of rs6942342 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64176447LGSNENSG00000146166.12T>C1.9599e-12146565Brain_Spinal_cord_cervical

meQTL of rs6942342 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.