rs1359992

Homo sapiens
A>T
LOC100505478 : Missense Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0281 (8419/29922,GnomAD)
A==0219 (6392/29118,TOPMED)
A==0362 (3918/10810,ExAC)
A==0242 (1212/5008,1000G)
A==0393 (1516/3854,ALSPAC)
A==0379 (1407/3708,TWINSUK)
chr9:114668331 (GRCh38.p7) (9q32)
AD
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.114668331A>T
GRCh37.p13 chr 9NC_000009.11:g.117430611A>T

Gene: LOC100505478, uncharacterized LOC100505478(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TEX48 transcript variant 1NM_001199233.1:c....NM_001199233.1:c.134T>AL [CTG]> Q [CAG]Coding Sequence Variant
testis-expressed protein 48NP_001186162.1:p....NP_001186162.1:p.Leu45GlnL [Leu]> Q [Gln]Missense Variant
TEX48 transcript variant 2NR_133056.1:n.62T>AT>ANon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.033T=0.967
1000GenomesAmericanSub694A=0.160T=0.840
1000GenomesEast AsianSub1008A=0.326T=0.674
1000GenomesEuropeSub1006A=0.384T=0.616
1000GenomesGlobalStudy-wide5008A=0.242T=0.758
1000GenomesSouth AsianSub978A=0.350T=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.393T=0.607
The Exome Aggregation ConsortiumAmericanSub284A=0.200T=0.800
The Exome Aggregation ConsortiumAsianSub7642A=0.360T=0.640
The Exome Aggregation ConsortiumEuropeSub2766A=0.386T=0.614
The Exome Aggregation ConsortiumGlobalStudy-wide10810A=0.362T=0.637
The Exome Aggregation ConsortiumOtherSub118A=0.370T=0.630
The Genome Aggregation DatabaseAfricanSub8714A=0.087T=0.913
The Genome Aggregation DatabaseAmericanSub838A=0.170T=0.830
The Genome Aggregation DatabaseEast AsianSub1612A=0.328T=0.672
The Genome Aggregation DatabaseEuropeSub18456A=0.372T=0.627
The Genome Aggregation DatabaseGlobalStudy-wide29922A=0.281T=0.718
The Genome Aggregation DatabaseOtherSub302A=0.410T=0.590
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.219T=0.780
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.379T=0.621
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
rs13599920.000244alcohol dependence21314694

eQTL of rs1359992 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 rs1359992 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 )
chr9117424327117424831E067-5780
chr9117424835117425378E069-5233
chr9117415137117416365E071-14246
chr9117424327117424831E071-5780
chr9117424835117425378E071-5233
chr9117384040117384730E072-45881
chr9117415137117416365E072-14246
chr9117380742117380786E073-49825
chr9117380836117380886E073-49725
chr9117380957117381007E073-49604
chr9117415137117416365E073-14246
chr9117415137117416365E074-14246
chr9117424327117424831E074-5780
chr9117424835117425378E074-5233
chr9117427345117427463E074-3148