Haplotype analysis was performed to confirm the observed association and to estimate the ML C1QA/C1QB (rs292001/rs913243/rs291982/rs631090) haplotype frequencies. In total, 16 haplotypes in each group of study subjects were estimated. Interestingly, haplotype comparison between patients and healthy controls revealed five haplotypes with nominally significant differences between schizophrenic patients and controls, namely, A-T-T-T (haplotype frequencies in patients vs controls: 13% vs 19%, OR = 0.57, 95%CI: 0.40-0.81, p nominal = 0.02, p corrected = 0.32), A-G-T-T (4% vs 11%, OR = 0.41, 95%CI: 0.23-0.74, p nominal = 0.002, p corrected = 0.03), A-G-G-T (8% vs 4%, OR = 2.02, 95%CI: 1.13-3.63, p nominal = 0.015, p corrected = 0.24), G-G-G-C (8% versus 2%, OR = 1.99, 95%CI: 1.03-3.84, p nominal = 0.049, p corrected = 0.78), and A-T-G-C (1% vs 0.6%, OR = 4.43, 95%CI: 1.25-15.66, p nominal = 0.009, p corrected = 0.14), only one of which (A-G-T-T) remained significant after the correction for the number of haplotypes. The difference in A-G-T-T haplotype between patients and controls suggested that the C1QB rs291982 major T allele is less frequent in patients with schizophrenia than in controls. Importantly, these data are in complete concordance with major allele frequencies in both groups. The haplotype analysis, therefore, confirmed detected association of the C1QB rs291982 variant with schizophrenia.