Applied to WTCCC type 1 diabetes and rheumatoid arthritis cohorts, ASTWAS not only rediscovers known susceptibility genes but also suggests novel candidates (e.g. GABBR1, RGL2) that form coherent interaction modules and enrich immune-related pathways, underscoring the biological significance of our algorithm in complex trait genetics. Here, GABBR1 is linked to type 1 diabetes mellitus.