rs2459572

Homo sapiens
C>T
LGSN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0358 (10706/29848,GnomAD)
C==0425 (12400/29118,TOPMED)
C==0374 (1875/5008,1000G)
C==0343 (1320/3854,ALSPAC)
C==0358 (1328/3708,TWINSUK)
chr6:63283470 (GRCh38.p7) (6q12)
OD
GWASdb2
1   publication(s)
See rs on genome
6 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.63283470C>T
GRCh37.p13 chr 6NC_000006.11:g.63993375C>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/AIntron Variant
LGSN transcript variant 1NM_016571.2:c.N/AIntron Variant
LGSN transcript variant X2XM_011535889.2:c.N/AIntron Variant
LGSN transcript variant X4XM_011535892.2:c.N/AIntron Variant
LGSN transcript variant X1XM_017010929.1:c.N/AIntron Variant
LGSN transcript variant X3XM_017010930.1:c.N/AIntron Variant
LGSN transcript variant X5XM_017010931.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.545T=0.455
1000GenomesAmericanSub694C=0.280T=0.720
1000GenomesEast AsianSub1008C=0.324T=0.676
1000GenomesEuropeSub1006C=0.342T=0.658
1000GenomesGlobalStudy-wide5008C=0.374T=0.626
1000GenomesSouth AsianSub978C=0.300T=0.700
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.343T=0.657
The Genome Aggregation DatabaseAfricanSub8678C=0.493T=0.507
The Genome Aggregation DatabaseAmericanSub836C=0.230T=0.770
The Genome Aggregation DatabaseEast AsianSub1604C=0.319T=0.681
The Genome Aggregation DatabaseEuropeSub18428C=0.305T=0.694
The Genome Aggregation DatabaseGlobalStudy-wide29848C=0.358T=0.641
The Genome Aggregation DatabaseOtherSub302C=0.300T=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.425T=0.574
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.358T=0.642
PMID Title Author Journal
23183491Genome-wide association study identifies a potent locus associated with human opioid sensitivity.Nishizawa DMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs24595720.000247Opioid sensitivity23183491

eQTL of rs2459572 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs2459572 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 )
chr66395717763957231E081-36144
chr66395728263957481E081-35894
chr66402993964030128E08136564
chr66403041164030526E08137036
chr66403096364031016E08137588
chr66403271364033358E08139338