rs797913

Homo sapiens
C>T
GLIS1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0143 (4291/29854,GnomAD)
T=0163 (4757/29118,TOPMED)
T=0127 (637/5008,1000G)
T=0104 (400/3854,ALSPAC)
T=0094 (347/3708,TWINSUK)
chr1:53732889 (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.53732889C>T
GRCh37.p13 chr 1NC_000001.10:g.54198562C>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=0.677T=0.323
1000GenomesAmericanSub694C=0.970T=0.030
1000GenomesEast AsianSub1008C=0.962T=0.038
1000GenomesEuropeSub1006C=0.912T=0.088
1000GenomesGlobalStudy-wide5008C=0.873T=0.127
1000GenomesSouth AsianSub978C=0.940T=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.896T=0.104
The Genome Aggregation DatabaseAfricanSub8702C=0.735T=0.265
The Genome Aggregation DatabaseAmericanSub832C=0.960T=0.040
The Genome Aggregation DatabaseEast AsianSub1620C=0.983T=0.017
The Genome Aggregation DatabaseEuropeSub18398C=0.896T=0.103
The Genome Aggregation DatabaseGlobalStudy-wide29854C=0.856T=0.143
The Genome Aggregation DatabaseOtherSub302C=0.940T=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.836T=0.163
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.906T=0.094
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
rs7979130.000928alcohol dependence21314694

eQTL of rs797913 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:54198562GLIS1ENSG00000174332.3C>T3.3415e-10-1315Cerebellum
Chr1:54198562GLIS1ENSG00000174332.3C>T1.3127e-9-1315Cerebellar_Hemisphere
Chr1:54198562GLIS1ENSG00000174332.3C>T3.0950e-3-1315Nucleus_accumbens_basal_ganglia

meQTL of rs797913 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 )
chr15420295254203047E0694390
chr15423216154232259E07433599
chr15419342554193687E081-4875
chr15419342554193687E082-4875




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr15420338754203800E0674825
chr15420382654203986E0675264
chr15420406754205413E0675505
chr15420542854205498E0676866
chr15420338754203800E0684825
chr15420382654203986E0685264
chr15420406754205413E0685505
chr15420542854205498E0686866
chr15420338754203800E0694825
chr15420382654203986E0695264
chr15420406754205413E0695505
chr15420542854205498E0696866
chr15420406754205413E0705505
chr15420338754203800E0714825
chr15420382654203986E0715264
chr15420406754205413E0715505
chr15420542854205498E0716866
chr15420326254203327E0724700
chr15420338754203800E0724825
chr15420382654203986E0725264
chr15420406754205413E0725505
chr15420542854205498E0726866
chr15420326254203327E0734700
chr15420338754203800E0734825
chr15420382654203986E0735264
chr15420406754205413E0735505
chr15420542854205498E0736866
chr15420382654203986E0745264
chr15420406754205413E0745505
chr15420542854205498E0746866
chr15420382654203986E0825264
chr15420406754205413E0825505
chr15420542854205498E0826866