rs2984458

Homo sapiens
T>C
LGSN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0472 (13804/29218,GnomAD)
T==0391 (11408/29118,TOPMED)
T==0430 (2151/5008,1000G)
C=0446 (1720/3854,ALSPAC)
C=0447 (1658/3708,TWINSUK)
chr6:63505258 (GRCh38.p7) (6q12)
AD
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.63505258T>C
GRCh37.p13 chr 6NC_000006.11:g.64215163T>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=0.190C=0.810
1000GenomesAmericanSub694T=0.420C=0.580
1000GenomesEast AsianSub1008T=0.548C=0.452
1000GenomesEuropeSub1006T=0.581C=0.419
1000GenomesGlobalStudy-wide5008T=0.430C=0.570
1000GenomesSouth AsianSub978T=0.480C=0.520
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.554C=0.446
The Genome Aggregation DatabaseAfricanSub8568T=0.228C=0.772
The Genome Aggregation DatabaseAmericanSub816T=0.420C=0.580
The Genome Aggregation DatabaseEast AsianSub1608T=0.552C=0.448
The Genome Aggregation DatabaseEuropeSub17926T=0.582C=0.418
The Genome Aggregation DatabaseGlobalStudy-wide29218T=0.472C=0.527
The Genome Aggregation DatabaseOtherSub300T=0.630C=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.391C=0.608
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.553C=0.447
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
rs29844581.1E-05alcohol dependence22096494

eQTL of rs2984458 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64215163LGSNENSG00000146166.12T>C1.9599e-12185281Brain_Spinal_cord_cervical

meQTL of rs2984458 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 )
chr66426311964263520E08147956
chr66426394364264222E08148780