rs1353899

Homo sapiens
T>A / T>G
LINC00578 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0188 (5648/29920,GnomAD)
G=0164 (4798/29118,TOPMED)
G=0199 (996/5008,1000G)
G=0200 (770/3854,ALSPAC)
G=0194 (719/3708,TWINSUK)
chr3:177511191 (GRCh38.p7) (3q26.32)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.177511191T>A
GRCh38.p7 chr 3NC_000003.12:g.177511191T>G
GRCh37.p13 chr 3NC_000003.11:g.177228979T>A
GRCh37.p13 chr 3NC_000003.11:g.177228979T>G

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
1000GenomesAfricanSub1322T=0.889G=0.111
1000GenomesAmericanSub694T=0.700G=0.300
1000GenomesEast AsianSub1008T=0.766G=0.234
1000GenomesEuropeSub1006T=0.807G=0.193
1000GenomesGlobalStudy-wide5008T=0.801G=0.199
1000GenomesSouth AsianSub978T=0.790G=0.210
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.800G=0.200
The Genome Aggregation DatabaseAfricanSub8712T=0.885G=0.115
The Genome Aggregation DatabaseAmericanSub834T=0.660G=0.34,
The Genome Aggregation DatabaseEast AsianSub1620T=0.770G=0.230
The Genome Aggregation DatabaseEuropeSub18452T=0.785G=0.215
The Genome Aggregation DatabaseGlobalStudy-wide29920T=0.811G=0.188
The Genome Aggregation DatabaseOtherSub302T=0.920G=0.08,
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.835G=0.164
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.806G=0.194
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
rs13538994E-06alcohol consumption23743675

eQTL of rs1353899 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 rs1353899 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 )
chr38852774588527892E081-34500
chr38858477488585025E08122382
chr38858477488585025E08222382