rs12075528

Homo sapiens
C>T
GLIS1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0086 (2593/29968,GnomAD)
T=0074 (2164/29118,TOPMED)
T=0051 (255/5008,1000G)
T=0103 (398/3854,ALSPAC)
T=0093 (345/3708,TWINSUK)
chr1:53733811 (GRCh38.p7) (1p32.3)
AD
GWASdb2
1   publication(s)
See rs on genome
4 Enhancers around
33 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.53733811C>T
GRCh37.p13 chr 1NC_000001.10:g.54199484C>T

Gene: GLIS1, GLIS family zinc finger 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GLIS1 transcriptNM_147193.2:c.N/AIntron Variant
GLIS1 transcript variant X1XM_017000408.1:c.N/AIntron Variant
GLIS1 transcript variant X2XM_017000409.1:c.N/AIntron Variant
GLIS1 transcript variant X3XM_017000410.1:c.N/AIntron Variant
GLIS1 transcript variant X4XM_017000411.1:c.N/AIntron Variant
GLIS1 transcript variant X5XM_017000412.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.918T=0.082
1000GenomesAmericanSub694C=0.980T=0.020
1000GenomesEast AsianSub1008C=1.000T=0.000
1000GenomesEuropeSub1006C=0.913T=0.087
1000GenomesGlobalStudy-wide5008C=0.949T=0.051
1000GenomesSouth AsianSub978C=0.950T=0.050
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.897T=0.103
The Genome Aggregation DatabaseAfricanSub8724C=0.925T=0.075
The Genome Aggregation DatabaseAmericanSub838C=0.970T=0.030
The Genome Aggregation DatabaseEast AsianSub1618C=1.000T=0.000
The Genome Aggregation DatabaseEuropeSub18486C=0.897T=0.103
The Genome Aggregation DatabaseGlobalStudy-wide29968C=0.913T=0.086
The Genome Aggregation DatabaseOtherSub302C=0.950T=0.050
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.925T=0.074
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.907T=0.093
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
rs120755280.000488alcohol dependence21314694

eQTL of rs12075528 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:54199484GLIS1ENSG00000174332.3C>T3.3415e-10-393Cerebellum
Chr1:54199484GLIS1ENSG00000174332.3C>T1.3127e-9-393Cerebellar_Hemisphere
Chr1:54199484GLIS1ENSG00000174332.3C>T3.0950e-3-393Nucleus_accumbens_basal_ganglia

meQTL of rs12075528 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 )
chr15420295254203047E0693468
chr15423216154232259E07432677
chr15419342554193687E081-5797
chr15419342554193687E082-5797




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr15420338754203800E0673903
chr15420382654203986E0674342
chr15420406754205413E0674583
chr15420542854205498E0675944
chr15420338754203800E0683903
chr15420382654203986E0684342
chr15420406754205413E0684583
chr15420542854205498E0685944
chr15420338754203800E0693903
chr15420382654203986E0694342
chr15420406754205413E0694583
chr15420542854205498E0695944
chr15420406754205413E0704583
chr15420338754203800E0713903
chr15420382654203986E0714342
chr15420406754205413E0714583
chr15420542854205498E0715944
chr15420326254203327E0723778
chr15420338754203800E0723903
chr15420382654203986E0724342
chr15420406754205413E0724583
chr15420542854205498E0725944
chr15420326254203327E0733778
chr15420338754203800E0733903
chr15420382654203986E0734342
chr15420406754205413E0734583
chr15420542854205498E0735944
chr15420382654203986E0744342
chr15420406754205413E0744583
chr15420542854205498E0745944
chr15420382654203986E0824342
chr15420406754205413E0824583
chr15420542854205498E0825944