Genetic study of quantitative biomarkers in Alzheimer’s disease (AD) is a promising method to identify novel genetic factors of AD and their associated endophenotypes, which provides valuable information to help deconvolute mechanistic complexity and better understand disease subtypes. Using the data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), we performed a genome-wide association study (GWAS) between 565,373 single nucleotide polymorphisms (SNPs) and 16 key AD biomarkers from 1,324 subjects at four visits. We identified a novel locus rs5011804 at 12p12.1 significantly associated with several AD biomarkers, including Clinical Dementia Rating - Sum of Boxes (CDRSB), Functional Activities Questionnaire (FAQ), and the Alzheimer’s Disease Assessment Scale 13-item Cognitive Subscale (ADAS13) score, and the fusiform volume. Our GWAS not only affirms key AD genes but also suggests the promising role of the SNP rs5011804 due to its associations with several AD cognitive and imaging  outcomes. The SNP rs5011804 has a reported association with adult asthma and slightly affects intracranial volume but has not been associated with AD before. Post-hoc mediation, stratified, and interaction analyses additionally highlight the significance of this SNP.