CHI3L1 and Alzheimer disease: CHI3L1 encodes the YKL-40 protein and two independent SNPs in or near this gene showed genome-wide significant associations with the non-AD inflammation PC: the strongest effect was observed for intronic variant rs7551263 (T allele: β =  − 0.39SD, SE = 0.05, p = 5.7 × 10−17, MAF = 0.16; Fig. 4).