Table 3.

Genome-wide significant loci from analyses of CSF Aβ₄₂ and ptau, associations with AD risk, progression of cognitive decline, and age at disease onset from independent cohorts

SNP [effect allele]	Gene	MAF	CSF levels n = 3146		AD risk [48] n = 74,026		Progression n = 1530		AAO n = 39,855
			β	P	OR	P	β	P	β	P
CSF Aβ42 associated loci
rs185031519[G]a	GLIS1	0.042	−0.059	2.08 × 10−8	1.105	3.43 × 10−2b	0.277	1.92 × 10−2	0.032	6.15 × 10−1
rs316341[G]a	SERPINB1	0.301	−0.025	1.76 × 10−8	1.025	1.52 × 10−1c	0.048	2.77 × 10−1	0.043	4.62 × 10−3
rs769449[A]	APOE	0.184	−0.101	4.78 × 10−94	3.522	9.86 × 10−523	0.078	8.42 × 10−2	0.720	6.81 × 10−106
CSF ptau181 associated loci
rs35055419[C]	GMNC	0.357	0.035	7.62 × 10−10	1.044	9.08 × 10−3	0.027	5.25 × 10−1	0.037	3.14 × 10−3d
rs514716[C]	GLIS3	0.125	−0.049	2.94 × 10−8	0.954	5.05 × 10−2	−0.029	6.66 × 10−1	−0.045	1.45 × 10−2
rs9527039[C]a	PCDH8	0.069	−0.061	5.95 × 10−9	0.993	8.22 × 10−1	−0.069	4.25 × 10−1	−0.020	4.03 × 10−1
rs12961169[T]a	CTDP1	0.155	0.050	5.12 × 10−10	1.033	1.93 × 10−1	0.119	9.34 × 10−2	0.042	2.49 × 10−1
rs769449[A]	APOE	0.184	0.079	5.30 × 10−33	3.522	9.86 × 10−523	0.078	8.42 × 10−2	0.720	6.81 × 10−106

SNP based on Build 37 of reference genome followed by effect allele, Gene nearest gene, MAF minor allele frequency in our dataset, Progression association with cognitive decline measured by sum of boxes, AAO age at onset (personal communication: Huang & Goate)

P values below significance threshold are in bold text

^aNovel associated loci for CSF Aβ₄₂ or ptau₁₈₁

^bAD risk reported for rs114122417 which is in LD with rs185031519 (r² = 0.909, D′ = 1)

^cAD risk reported for rs316339 which is in LD with rs316341 (r² = 0.993, D′ = 1)

^dAge at onset reported for rs883841 which is in LD with rs35055419 (r² = 0.996, D′ = 0.999)