Table 1.

Multitrait colocalization evidence for loci with causal-variant sharing between birthweight, placental DNAm, and gene expression.

GWAS lead SNP	SNP position (hg19)	eGene	DNAm site (nearest gene)	DNAm site position (hg19)	DNAm site relation to gene	Distance from GWAS SNP to eGene|to DNAm site	N SNPs	PPA for G, EM	PPA for GM, E	PPA for GE, M	PPA for GEM
rs71486610	Chr10:124134803	PLEKHA1	cg02556345 (PLEKHA1)	124181965	Body	Intronic | 47.1 kb	726	4.1 × 10−2	3.7 × 10−2	2.4 × 10−2	0.88
			cg06474225 (HTRA1)	124228770	Body	Intronic | 93.9 kb	686	4.1 × 10−2	2.0 × 10−2	3.2 × 10−2	0.85
			cg14366292 (DMBT1)	124328787	Body	Intronic | 194.0 kb	684	9.3 × 10−5	7.8 × 10−11	0.92	1.0 × 10−8
			cg17033087 (DMBT1)	124329533	Body	Intronic | 194.7 kb	682	1.2 × 10−4	1.1 × 10−5	0.90	1.3 × 10−3
			cg11976790 (DMBT1)	124320064	TSS	Intronic | 185.3 kb	686	1.7 × 10−4	1.7 × 10−12	0.88	2.7 × 10−14
			cg27015047 (DMBT1)	124320805	Body	Intronic | 186.0 kb	687	2.1 × 10−4	1.4 × 10−7	0.88	1.3 × 10−5
rs4932373	Chr15:91429287	FES	cg25647583 (FES)	91427184	TSS	Intronic | 2.1 kb	507	4.6 × 10−3	2.2 × 10−2	4.9 × 10−3	0.91
			cg20992439* (FES)	91429916	Body	Intronic | 0.6 kb	510	2.4 × 10−2	9.6 × 10−3	1.7 × 10−2	0.91
			cg06330618 (FES)	91428456	Exon	Intronic | 0.8 kb	509	1.9 × 10−2	1.9 × 10−2	1.0 × 10−2	0.90
			cg09397246 (FES)	91427361	TSS	Intronic | 1.9 kb	507	6.2 × 10−3	2.3 × 10−2	1.7 × 10−2	0.88
			cg07718650 (FES)	91434288	Body	Intronic | 5.0 kb	527	2.1 × 10−2	2.1 × 10−2	1.6 × 10−2	0.88
			cg26405020 (FES)	91427363	TSS	Intronic | 1.9 kb	507	6.6 × 10−3	2.3 × 10−2	2.9 × 10−2	0.86
			cg08724371 (FES)	91442212	–	Intronic | 12.9 kb	544	8.4 × 10−3	2.2 × 10−2	3.4 × 10−2	0.85
			cg26899598* (FES)	91429088	Body	Intronic | 0.2 kb	509	1.1 × 10−2	3.4 × 10−2	2.9 × 10−2	0.82
			cg18661868* (FES)	91427965	5’UTR	Intronic | 1.3 kb	508	1.6 × 10−2	2.6 × 10−2	3.1 × 10−2	0.80
rs1868158	Chr16:68398924	PRMT7	cg02226672 (SMPD3)	68398533	Body	6.4 kb | 0.4 kb	373	3.6 × 10−2	3.0 × 10−2	2.5 × 10−2	0.80
rs222857	Chr17:7164563	CTDNEP1**	cg17265693 (CLDN7)	7166490	TSS	9.3 kb | 1.9 kb	434	4.5 × 10−3	2.1 × 10−2	2.6 × 10−3	0.78
			cg01697794 (DLG4)	7117125	Body	9.3 kb | 47.4 kb	473	5.4 × 10−3	2.0 × 10−2	4.0 × 10−3	0.77
			cg19466160* (DLG4)	7117160	Body	9.3 kb | 47.4 kb	473	5.1 × 10−3	1.9 × 10−2	4.6 × 10−3	0.77
		EIF5A	cg17265693 (CLDN7)	7217367	Body	45.8 kb | 52.8 kb	434	3.7 × 10−7	0.92	2.8 × 10−7	3.6 × 10−5
			cg01697794 (DLG4)	7222668	Body	45.8 kb | 58.1 kb	473	6.1 × 10−5	0.88	3.4 × 10−7	3.2 × 10−5
			cg19466160 (DLG4)	124181965	Body	45.8 kb | 47.4 kb	473	3.7 × 10−6	0.88	3.9 × 10−7	3.2 × 10−5
			cg17579446 (GPS2)	124228770	Body	45.8 kb | 52.8 kb	396	0.97	4.8 × 10−13	1.1 × 10−7	1.9 × 10−17
			cg04514024 (NEURL4)	124328787	Body	45.8 kb | 58.1 kb	403	0.88	1.9  × 10−19	4.7 × 10−7	3.3 × 10−20

Chr chromosome.

Evidence of colocalization for a given scenario was based on the posterior probability of association (PPA) ≥ 0.8. For each locus indexed by the GWAS lead SNP, N SNPs denotes the number of SNPs within 1 Mb from the index SNP. This table presents loci associated with all three traits and have evidence of colocalization in ≥2 of the traits birthweight, placental gene expression and placental DNA methylation (i.e, PPA ≥ 0.80 for any of the following four scenarios out of 15 Hypotheses tested by moloc): (1) PPA for G, EM corresponding H10: association for GWAS trait (G), eQTL trait (E) and mQTL trait (M), but different causal variants for {G} and {E,M}. (2) PPA for GM, E corresponding H12: association for traits G, E and M, but different causal variants for {G,M} and {E}. (3) PPA for GE, M corresponding H11: association for traits G, E and M, but different causal variants for {G,E} and {M}. (4) PPA for GEM corresponding H14: SNP is associated with all 3 traits {G,E,M}. *CpG site has the promoter-associated regulatory feature. TSS denotes transcription start site. **PPA is very close to 0.8. In bold is PPA close to or ≥0.8.