Small Variant Query

🔹 Small Variant Query

1. Input Variant

• From the Home page, choose “Single Variant”.
• Enter the variant location using the format: chromosome_position_reference allele_alternative allele \ Example: chr1_123456_A_T
• Click Run to proceed.

2. Select Reference Genome

• Choose the reference genome: GRCh37 or GRCh38.
• Click Start Analysis to begin.

  Note: Variants aligned with GRCh37 will be lifted over to GRCh38 before VEP (v114) annotation.

3. View Results

Results will appear automatically once the data is loaded. Annotations are organized into four sections:

🧬 Variant Annotation

• Contents includes:
• Transcript and protein alterations
• ClinVar information
• Global allele frequencies (gnomAD, 1000 Genomes Project)
• In silico prediction scores
• Users could customize displayed columns using the “Columns” button.

🍭 ClinVar Lollipop

• Visualizes protein alterations as a lollipop plot.
• Supports zooming and export in PNG or PDF format.

📊 GWAS & QTLs

• Displays variant-associated data in separated subpanels:
• GWAS
• eQTLs
• pQTLs
• Pharmacogenomics (PGx)

🌍 Global Allele Frequency

• Shows the maximum global minor allele frequency (MAF) on a world map, illustrating population-specific frequency distributions.

4. Export Data

• Download all results (tables and figures) as a compressed file via the “Export All” button (top-right corner).