rs4557499

Homo sapiens
G>T
LGSN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0471 (13975/29648,GnomAD)
T=0391 (11406/29118,TOPMED)
T=0430 (2154/5008,1000G)
chr6:63480642 (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.63480642G>T
GRCh37.p13 chr 6NC_000006.11:g.64190547G>T
EEF1B2P5 pseudogeneNG_029026.1:g.665G>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
1000GenomesAfricanSub1322G=0.812T=0.188
1000GenomesAmericanSub694G=0.580T=0.420
1000GenomesEast AsianSub1008G=0.452T=0.548
1000GenomesEuropeSub1006G=0.420T=0.580
1000GenomesGlobalStudy-wide5008G=0.570T=0.430
1000GenomesSouth AsianSub978G=0.510T=0.490
The Genome Aggregation DatabaseAfricanSub8658G=0.774T=0.226
The Genome Aggregation DatabaseAmericanSub828G=0.580T=0.420
The Genome Aggregation DatabaseEast AsianSub1606G=0.450T=0.550
The Genome Aggregation DatabaseEuropeSub18254G=0.419T=0.580
The Genome Aggregation DatabaseGlobalStudy-wide29648G=0.528T=0.471
The Genome Aggregation DatabaseOtherSub302G=0.370T=0.630
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.608T=0.391
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
rs45574991E-05alcohol dependence22096494

eQTL of rs4557499 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64190547LGSNENSG00000146166.12G>T1.9599e-12160665Brain_Spinal_cord_cervical

meQTL of rs4557499 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.