TABLE 1.

Regulatory SNP effects on transcription factor binding affinity

	Enhancer
	SNP	Chr	Location	Effect allele	Non effect allele	Beta	Beta SE	P value	TF	Binding loss or gain	MotifbreakR p value
1	rs111378762	6	32,577,504	A	G	−0.0744	0.0595	0.2108	POU3F1	–	1.59E‐02
2	rs10795875	10	11,716,429	A	G	0.0055	0.0153	0.7176	SPI1	–	1.56E‐04
3	rs11257243	10	11,724,372	A	G	−0.0194	0.0187	0.2976	IRF5	–	2.74E‐03
4	rs10792832	11	85,867,875	A	G	−0.1195	0.0148	7.56E‐16	SPI1	–	1.60E‐02
5	rs11234564	11	85,869,944	C	G	0.0494	0.0179	0.005818	SP1	–	1.66E‐02
6	rs11234565	11	85,870,006						FOXO1	–	1.10E‐02
7	rs76292249	11	59,951,740						SPI1	–	2.45E‐04
8	rs116371174	11	47,421,694	A	G	−0.4308	0.4317	0.3182	RUNX3	+	5.83E‐02
9	rs10131374	14	92,927,531	A	G	−0.0403	0.0211	0.05672	E2F1	+	1.28E‐02
10	rs1065853	19	45,413,233						NR2F2, POLR2A, TEAD4, TAL1	+	9.99E‐04
11	rs10414043	19	45,415,713	A	G	1.1368	0.0201	0	ARNT2	–	2.13E‐02
12	rs1065853	19	45,413,233						NR2F2, POLR2A, TEAD4, TAL1	+	9.99E‐04
13	rs10414043	19	45,415,713	A	G	1.1368	0.0201	0	ARNT2	–	2.13E‐02

	GWAS									Linkage disequilibrium
	SNP	Location	Gene	Major/minor allele	Effect allele	Non effect allele	Beta	Beta SE	P value	Distance GWAS SNP to enhancer SNP	R2 GWAS SNP and enhancer SNP	Correlated alleles enhancer‐GWAS
1	rs9271058	32,575,406	HLA ‐DRB1	T/A	A	T	0.094	0.0172	5.14E‐08	2098	0.0334
2	rs7920721	11,720,308	ECHDC3	A/G	A	G	−0.0782	0.015	1.94E‐07	3879	0.28	G‐G, A‐A
3	rs7920721	11,720,308	ECHDC3	A/G	A	G	−0.0782	0.015	1.94E‐07	4064	0.055
4	rs3851179	85,868,640	PICALM	C/T	T	C	−0.1198	0.0148	5.81E‐16	765	0.987	A‐T, G‐C
5	rs3851179	85,868,640	PICALM	C/T	T	C	−0.1198	0.0148	5.81E‐16	1304	0.132	G‐T, C‐C
6	rs3851179	85,868,640	PICALM	C/T	T	C	−0.1198	0.0148	5.81E‐16	1366	0.197	T‐T, G‐C
7	rs7933202	59,936,926	MS4A6A	A/C	A	C	0.1165	0.0147	2.15E‐15	14814	0.001
8	rs3740688	47,380,340	SPI1	T/G	T	G	0.0935	0.0144	9.7E‐11	41354	0.001
9	rs12881735	92,932,828	SLC24A4	T/C	T	C	0.088	0.0175	4.88E‐07	5297	0.048
10	rs429358	45,411,941	APOE	T/C	T	C	−1.2017	0.0189	0	1292	0.012
11	rs429358	45,411,941	APOE	T/C	T	C	−1.2017	0.0189	0	3772	0.759	G‐T, A‐C
12	rs7412	45,412,079	APOE	C/T	T	C	−0.4673	0.0305	6.4E‐53	1154	1	G‐C, T‐T
13	rs7412	45,412,079	APOE	C/T	T	C	−0.4673	0.0305	6.4E‐53	3634	0.009

Notes: Effect allele, non‐effect allele, beta, standard error for beta, and P value for all SNPs are from the LOAD GWAS reported in Kunkle et al. ⁷ For binding loss or gain, +/‐ indicates gain or loss of binding function for the effect allele of the enhancer SNP on the specified transcription factor motif. MotifbreakR P value estimates the statistical significance of the effect allele to disrupt (gain or loss of binding function) specific motifs in the transcription factor. Correlated alleles column indicates the specific alleles of the enhancer and GWAS SNPs that are in linkage disequilibrium. All genomic data and coordinates are based on the February 2009 version of the genome: hg19, GRCh37.

Abbreviations: Chr, chromosome; eQTL, expression quantitative trait loci; GWAS, genome‐wide association study; LOAD, late‐onset Alzheimer's disease; SE, standard error; SNP, single nucleotide polymorphism; TF, transcription factor