Table 2.

Associations and functional prioritization of SNPs in NEFL and its surrounding region (+/−20Kb)

		SNP Association in GWAS dataset								SNP functional prioritization
SNP	Role	A1	F_A	F_U	A2	P	OR	L95	U95	Proxy SNP ID	Proxy SNP function	* r2	RegPotential Score	Conservation Score
rs118727	intergenic	C	0.14	0.12	T	0.0026	1.18	1.06	1.32	rs3761	NEFL/3′-UTR	1	0.21	0.132
rs196830	intergenic	C	0.15	0.12	A	0.0012	1.19	1.07	1.33	rs3761	NEFL/3′-UTR	1	0.21	0.132
rs169061	intergenic	C	0.40	0.43	T	0.0008	0.88	0.81	0.95	^ no-LD	-	-	-	-
rs11994014	Downstream	A	0.20	0.22	G	0.0368	0.91	0.83	0.99	° rs2979704 and rs1059111	NEFL/3′-UTR	0.63	0.07 and 0.36	0.96 and 1.00
rs2979685	Promoter	T	0.36	0.36	G	0.8723	1.01	0.93	1.09	-	-	-	-	-
rs17830286	Promoter	T	0.16	0.15	C	0.0085	1.15	1.04	1.27	rs3761	NEFL/3′-UTR	0.64	0.21	0.132
rs13254844	Promoter	T	0.05	0.05	C	0.5270	0.95	0.80	1.12	-	-	-	-	-
rs17830392	Promoter	G	0.08	0.07	A	0.2101	1.09	0.95	1.26	-	-	-	-	-

A1: minor allele; A2: major allele; F_A: minor allele frequency in cases; F_U: minor allele frequency in controls

OR: odds ratio; L95: lower bound of 95% confidence interval for odds ratio; U95: upper bound of 95% confidence interval for odds ratio

^*Cut-off = 0.60

^°rs2979704 and rs1059111 are in strong LD (r²=1)

^{^}No SNP was found in LD with r²>0.60

RegPotential: regulatory potential score (ESPERR regulatory potential based on 7 species) downloaded from UCSC genome bioinformatics web site

Conservation: vertebrate Multiz Alignment and Conservation score (17 Species) downloaded from UCSC genome website