We identified four loci shared between the six autoimmune and allergic diseases (rs10803431 at PRDM2, OR=1.07, p=2.3×10−8, rs2053062 at G3BP1, OR=0.90, p=2.9×10−8, rs2210366 at HBS1L, OR=1.07, p=2.5×10−8 in Japanese and rs4529910 at POU2AF1, OR=0.96, p=1.9×10−10 across ancestries). Here, PRDM2 is linked to allergic disease.