rs59539624

Homo sapiens
G>C / G>T
LINC00578 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0200 (5995/29954,GnomAD)
T=0178 (5206/29118,TOPMED)
T=0207 (1039/5008,1000G)
T=0200 (772/3854,ALSPAC)
T=0193 (716/3708,TWINSUK)
chr3:177509729 (GRCh38.p7) (3q26.32)
AD
GWASdb2
1   publication(s)
See rs on genome
1 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.177509729G>C
GRCh38.p7 chr 3NC_000003.12:g.177509729G>T
GRCh37.p13 chr 3NC_000003.11:g.177227517G>C
GRCh37.p13 chr 3NC_000003.11:g.177227517G>T

Gene: LINC00578, long intergenic non-protein coding RNA 578(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00578 transcriptNR_047568.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.859T=0.141
1000GenomesAmericanSub694G=0.700T=0.300
1000GenomesEast AsianSub1008G=0.767T=0.233
1000GenomesEuropeSub1006G=0.805T=0.195
1000GenomesGlobalStudy-wide5008G=0.793T=0.207
1000GenomesSouth AsianSub978G=0.790T=0.210
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.800T=0.200
The Genome Aggregation DatabaseAfricanSub8718G=0.849C=0.000
The Genome Aggregation DatabaseAmericanSub836G=0.660C=0.00,
The Genome Aggregation DatabaseEast AsianSub1618G=0.771C=0.000
The Genome Aggregation DatabaseEuropeSub18480G=0.783C=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29954G=0.799C=0.000
The Genome Aggregation DatabaseOtherSub302G=0.920C=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.821T=0.178
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.807T=0.193
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs595396241.42E-05alcohol consumption23743675

eQTL of rs59539624 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 rs59539624 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 )
chr372082367208471E07028172