rs1378559

This is a intergenic variant variant in the LOC105373146 gene.

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GWAS Catalog Trait Associations (4)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

schizophrenia

Trubetskoy V et al. “Mapping genomic loci implicates genes and synaptic biology in schizophrenia.” Nature 604(7906):502-508 (2022)

Allele T

OR 1.08

p 2.0e-18

N 175,799

Large GWAS

multi-ancestry

“Biological insights from 108 schizophrenia-associated genetic loci.” Nature 511(7510):421-7 (2014)

Allele T

OR 1.09

p 2.0e-12

N 83,550

Large GWAS

multi-ancestry

insomnia

Watanabe K et al. “Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways.” Nature Genetics 54(8):1125-1132 (2022)

Allele T

OR 0.01

p 2.0e-10

N 1,409,137

Meta-analysisLarge GWAS

European

attention deficit hyperactivity disorder, bipolar disorder, autism spectrum disorder, schizophrenia, major depressive disorder

Yao X et al. “Integrative analysis of genome-wide association studies identifies novel loci associated with neuropsychiatric disorders.” Translational Psychiatry 11(1):69 (2021)

Allele T

OR 5.87

p 4.0e-9

N 728,648

Large GWAS

European

post-traumatic stress disorder

Nievergelt CM et al. “Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder.” Nature Genetics 56(5):792-808 (2024)

Allele T

OR 5.54

p 3.0e-8

N 1,280,933

Large GWAS

multi-ancestry

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Research that mentions this SNP (1)

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Common variants in QPCT gene confer risk of schizophrenia in the Han Chinese population

MethodsRaja Amjad Waheed Khan et al.(2016)· American Journal of Medical Genetics Part B: Neuropsychiatric Genetics

This paper presents CalPen, a web-based tool for calculating penetrance (disease likelihood given a mutation) in complex genetic disorders. The authors validated CalPen against published penetrance calculations for schizophrenia-associated copy number variants (CNVs) and single nucleotide polymorphisms (SNPs). They analyzed 15 CNVs in 39,059 schizophrenia patients and 55,084 controls (average penetrance 7%, ranging from ~1.4% for 15q11.2 deletions to ~20% for 22q11.21 CNVs) and 145 SNPs in 45,405 patients and 122,761 controls (average penetrance 0.7%, with rs1801028 showing the highest at 1.6%).

Traits studied:Schizophrenia

PubMed DOI Metascience Observatory

This variant is in our database but has no known associations or PRS memberships yet.

rs1378559

GWAS Catalog Trait Associations (4)

schizophrenia

insomnia

attention deficit hyperactivity disorder, bipolar disorder, autism spectrum disorder, schizophrenia, major depressive disorder

post-traumatic stress disorder

Research that mentions this SNP (1)

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