rs550864

Homo sapiens
G>T
GLYATL1 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0475 (14228/29928,GnomAD)
G==0456 (13299/29118,TOPMED)
G==0442 (2214/5008,1000G)
T=0433 (1667/3854,ALSPAC)
T=0438 (1623/3708,TWINSUK)
chr11:58926213 (GRCh38.p7) (11q12.1)
AD
GWASdb2
1   publication(s)
See rs on genome
8 Enhancers around
39 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.58926213G>T
GRCh37.p13 chr 11NC_000011.9:g.58693686G>T

Gene: GLYATL1, glycine-N-acyltransferase like 1(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
GLYATL1 transcript variant 2NM_001220494.2:c.N/AUpstream Transcript Variant
GLYATL1 transcript variant 4NM_001220496.2:c.N/AN/A
GLYATL1 transcript variant 1NM_080661.4:c.N/AN/A
GLYATL1 transcript variant X2XM_011545355.2:c.N/AUpstream Transcript Variant
GLYATL1 transcript variant X5XM_011545357.2:c.N/AUpstream Transcript Variant
GLYATL1 transcript variant X1XM_011545354.2:c.N/AN/A
GLYATL1 transcript variant X3XM_011545356.2:c.N/AN/A
GLYATL1 transcript variant X4XM_011545358.2:c.N/AN/A
GLYATL1 transcript variant X6XM_011545359.2:c.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.296T=0.704
1000GenomesAmericanSub694G=0.500T=0.500
1000GenomesEast AsianSub1008G=0.431T=0.569
1000GenomesEuropeSub1006G=0.555T=0.445
1000GenomesGlobalStudy-wide5008G=0.442T=0.558
1000GenomesSouth AsianSub978G=0.500T=0.500
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.567T=0.433
The Genome Aggregation DatabaseAfricanSub8712G=0.354T=0.646
The Genome Aggregation DatabaseAmericanSub836G=0.530T=0.470
The Genome Aggregation DatabaseEast AsianSub1606G=0.431T=0.569
The Genome Aggregation DatabaseEuropeSub18474G=0.535T=0.464
The Genome Aggregation DatabaseGlobalStudy-wide29928G=0.475T=0.524
The Genome Aggregation DatabaseOtherSub300G=0.410T=0.590
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.456T=0.543
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.562T=0.438
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs5508640.000979alcohol dependence21314694

eQTL of rs550864 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 rs550864 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 )
chr115866761558667667E070-26019
chr115866901858669092E070-24594
chr115866911158669258E070-24428
chr115866947658669562E070-24124
chr115868916258689756E070-3930
chr115867137258671453E081-22233
chr115867162958671679E081-22007
chr115869468758694776E0821001



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr115866776758667824E067-25862
chr115866784558668739E067-24947
chr115867230258673912E067-19774
chr115866776758667824E068-25862
chr115866784558668739E068-24947
chr115867230258673912E068-19774
chr115866784558668739E069-24947
chr115867230258673912E069-19774
chr115873088758731605E06937201
chr115866874458668867E070-24819
chr115867230258673912E070-19774
chr115873574258735943E07042056
chr115873597758736151E07042291
chr115866784558668739E071-24947
chr115867230258673912E071-19774
chr115873088758731605E07137201
chr115873574258735943E07142056
chr115873597758736151E07142291
chr115866776758667824E072-25862
chr115866784558668739E072-24947
chr115867230258673912E072-19774
chr115873574258735943E07242056
chr115873597758736151E07242291
chr115866784558668739E073-24947
chr115867230258673912E073-19774
chr115873574258735943E07342056
chr115873597758736151E07342291
chr115866776758667824E074-25862
chr115866784558668739E074-24947
chr115867230258673912E074-19774
chr115867230258673912E081-19774
chr115866776758667824E082-25862
chr115866784558668739E082-24947
chr115866874458668867E082-24819
chr115867230258673912E082-19774
chr115873078658730846E08237100
chr115873088758731605E08237201
chr115873574258735943E08242056
chr115873597758736151E08242291