Table 1.

Results of integrative analysis (Sherlock) of LOAD GWAS and eQTL

Gene symbol	Gene LBF^a	Gene P-value^b	Supporting SNP	Proximity	eQTL P-value^c	GWAS P-value^d	SNP LBF^e
ZNF257	5.23	2.59 E–05	rs417628	cis	1.10 E–06	8.86 E–06	5.18
RFFL	5.22	2.59 E–05	rs4726618	trans	6.40 E–07	8.94 E–06	5.95
			rs4838429	trans	1.00 E–05	3.13 E–03	0.76
BIN1	5.18	2.59 E–05	rs744373	cis	2.40 E–07	3.00 E–10	5.89
EML2	5.17	2.59 E–05	rs2927438	cis	1.10 E–04	1.05 E–07	5.73
ZNF226	5.00	3.35 E–05	rs2927438	cis	2.90 E–06	1.05 E–07	6.36
LRRC46	4.80	5.02 E–05	rs8103315	trans	5.80 E–06	3.46 E–11	4.63
			rs7743515	trans	5.20 E–06	5.97 E–03	0.86
PVRL2	4.67	7.00 E–05	rs2927438	cis	9.00 E–04	1.05 E–07	5.89
BLOC1S3	4.61	8.06 E–05	rs10416371	cis	5.00 E–05	7.80 E–08	5.12
KLC3	4.61	8.06 E–05	rs2927438	cis	2.00 E–04	1.05 E–07	5.24
ZNF222	4.56	8.52 E–05	rs2927438	cis	3.00 E–04	1.05 E–07	4.90

rs2927438 was shown in bold since it occurred 5 times without any threshold of significance.

Key: eQTL, expression quantitative trait loci; GWAS, genome-wide association study; LBF, logarithm of Bayes factor; LOAD, late-onset Alzheimer’s disease; SNP, single-nucleotide polymorphism.

Gene LBF (Log Bayes Factors for each gene) evaluates the possibility of the combined evidence from GWAS and eQTL supporting a gene being associated with LOAD. For each gene, Sherlock computes individual LBF for each eSNP in the alignment, and the sum of these constitutes the final LBF score for the gene.

p-value for each gene based on Sherlock integrative analysis. High LBFs tend to correlate with lower p-values.

p-value for eQTL SNP from the gene expression study.

p-value for eQTL SNP from the GWAS of LOAD.

SNP LBF, Log Bayes Factors for each SNP.