Table 2. SNPs significantly (P < 5 × 10⁻⁸) associated with CSF PGRN levels.

CHR, chromosome; BP, base pair; Alt, altered allele; UTR, untranslated region; NA, not available.

CHR	SNP	LD (r2)	BP (GRCh37)	Alt	Observed MAF	Source	Closest gene	SNP location	Regulome DB score*	P values†
										P1	P2	P3	P4
17	rs708384‡	1	42437682	A	0.4074	Genotyping	FAM171A2	Intron (TF binding site)	5	5.09 × 10−12	0.0002	0.0002	…
17	rs708383‡	1	42437754	A	0.4074	Imputation	FAM171A2	Intron	5	5.09 × 10−12	0.0002	0.0002	…
17	rs34603233	NA	42455022	T	0.4201	Imputation	ITGA2B	Intron	5	6.48 × 10−12	0.0002	0.0002	0.4561
17	rs850730	0.89	42454463	C	0.4213	Imputation	ITGA2B	Intron	5	1.90 × 10−11	0.0002	0.0002	0.8554
17	rs850729	0.88	42454806	T	0.4213	Imputation	ITGA2B	Intron	NA	1.90 × 10−11	0.0002	0.0002	0.8554
17	rs850736	0.93	42446420	C	0.4225	Imputation	ITGA2B	NA	NA	2.47 × 10−11	0.0002	0.0002	0.9572
17	rs850734	0.91	42449025	G	0.4225	Imputation	ITGA2B	NA	5	2.47 × 10−11	0.0002	0.0002	0.9572
17	rs5910	0.90	42449789	A	0.4225	Genotyping	ITGA2B	Synonymous	5	2.47 × 10−11	0.0002	0.0002	0.9572
17	rs35905006	NA	42451281	C	0.4225	Imputation	ITGA2B	Intron	6	2.47 × 10−11	0.0002	0.0002	0.9572
17	rs850733	0.89	42451305	A	0.4225	Imputation	ITGA2B	Intron	NA	2.47 × 10−11	0.0002	0.0002	0.9572
17	rs5911	0.89	42453065	C	0.4225	Imputation	ITGA2B	Missense	2b	2.47 × 10−11	0.0002	0.0002	0.9572
17	rs850732	0.89	42454243	T	0.4225	Imputation	ITGA2B	Intron	NA	2.47 × 10−11	0.0002	0.0002	0.9572
17	rs708382	0.86	42442344	C	0.4340	Genotyping	FAM171A2	NA	6	2.91 × 10−11	0.0002	0.0002	0.7185
17	rs850737	0.86	42443784	C	0.4340	Imputation	FAM171A2	NA	5	2.91 × 10−11	0.0002	0.0002	0.7185
17	rs850738	0.73	42434630	G	0.4317	Imputation	FAM171A2	Intron	NA	4.89 × 10−11	0.0002	0.0004	0.2513
17	rs11389756	NA	42448210	AG	0.4699	Imputation	ITGA2B	NA	6	3.62 × 10−11	0.0002	0.0022	0.6897
17	rs850731	0.71	42454270	C	0.4699	Imputation	ITGA2B	Intron	5	3.62 × 10−11	0.0002	0.0022	0.6897
17	rs5848	0.60	42430244	T	0.3275	Imputation	GRN	3′-UTR	5	1.22 × 10−11	0.0002	0.0074	0.6925

*Lower scores indicate increasing evidence for a variant to be located in a functional region (www.regulomedb.org).

†P1 = P value for GWAS; P2 = empiric P value; P3 = permutation-based corrected empiric familywise error rate; P4 = empiric P value after controlling for rs708384

‡rs708383 is in complete LD with rs708384 (r² = 1) according to the HaploRegv4.1 online database.