Table 2.

Functional annotation of 32 SNPs in the APOE region

ID	SNP ID	LD cluster	Function	Regulatory feature	Gene	Active	Poised	Score	M0&M1 macrophage	CD14+ monocytes	NHA	NHLF	Selected eQTL
1	rs7026		3'UTR	PFR	BCAM	6	2	5					NECTIN2
2	rs1871045		Downstream		BCAM			4					NECTIN2
3	rs11668536		Downstream		BCAM								NECTIN2
4	rs10402271	ε4	Downstream		BCAM			5					NECTIN2
5	rs4803760	ε2	Intergenic					6					BCAM
6	rs1871046		Intron	Promoter, TFBS	NECTIN2	46	20	2a					No
7	rs4803763		Intron		NECTIN2			5					NECTIN2
8	rs440277	ε4	Intron	PFR	NECTIN2	5	1	1f	Yesa	Yesa	Yes		NECTIN2, FOSB
9	rs3852856		Intron		NECTIN2								NECTIN2
10	rs377702		Intron		NECTIN2			2b					NECTIN2, FOSB, CLASRP
11	rs8105340		Intron		NECTIN2			6					NECTIN2
12	rs12610605	ε4	Intron		NECTIN2			5
13	rs4803766		Intron		NECTIN2			5					NECTIN2
14	rs17561351		Intron	PFR	NECTIN2	5	1	1b					NECTIN2a
15	rs8104483		Intron	PFR	NECTIN2	5	1	1b					NECTIN2a
16	rs4081918	ε4	Intron	PFR	NECTIN2	5	1	1f	Yesa	Yesa	Yes		NECTIN2a
17	rs519113	ε2	Intron		NECTIN2			1f					BCAM, NECTIN2a
18	rs2075642		Intron		NECTIN2			5					NECTIN2
19	rs387976	ε2	Intron	OCR	NECTIN2	1	1	5				Yes	NECTIN2
20	rs11667640	ε4	Intron		NECTIN2			4					NECTIN2
21	rs6859	ε4	3'UTR		NECTIN2			4					NECTIN2
22	rs11673139	ε4	Intron		NECTIN2			4					NECTIN2, MARK4
23	rs283813	ε2	Intron		NECTIN2			5					No
24	rs157580	ε4	Intron	Promoter	TOMM40	63	5	1f	Yesa	Yesa	Yes		APOE, APOC1, DMPK
25	rs2075650		Intron		TOMM40			1f					No
26	rs8106922	ε2, ε4	Intron		TOMM40			5					DMPKa
27	rs405509	ε2, ε4	Upstream	Promoter	APOE			1f					APOE
28	rs440446	ε2, ε4	Missense intron	Promoter	APOE	18	32	4	Yesa	Yes	Yes	Yes	APOE, APOC1
29	rs429358		Missense	Coding region, exon 4				5					No
30	rs7412		Missense	Coding region, exon 4				4					APOE
31	rs439401	ε2, ε4	Non coding transcript exon	PFR	APOE‐APOC1	13	3	1b	Yesa		Yesa	Yesa	APOE, APOC1
32	rs12721046		Intron		APOC1			6					No

Linkage disequilibrium (LD) cluster indicates SNPs in LD with rs429358 and rs7412 SNPs, whose minor alleles code the APOE ε4 and ε2 alleles, respectively.

Table includes activity levels (active/poised) for 68 cell types (epigenoms).

Column “Score” shows RegulomeDB score based on the integration of multiple high‐throughput datasets with 1a being the highest score and 6 being the lowest score. Note that because RegulomeDB focuses on noncoding SNPs, missense SNPs may not have large scores.

NHA denotes epigenetic signature in normal human astrocytes cells.

NHFL denotes human lung fibroblasts.

eQTLs denote expression quantitative trait loci selected for affected protein‐coding gene in specific cell types.

OCR, open chromatin region; PFR, promoter flanking region; TF, transcription factor; TFBS, TF binding site.

^aActive state.