GWAS of habitual coffee consumption reveals a sex difference in the genetic effect of the 12q24 locus in the Japanese population

Table 2 Variants associated with habitual coffee consumption

Variant	Chr	Position	Gene	EA	NEA	Population	EAF	Beta	SE (Beta)	P _association	I ²	P _{heterogeneity}
rs518341	1	78,896,492	GIPC2– PTGFR	G	A	Discovery	0.315	0.133	0.030	6.4 × 10^− 6	–	–
						Replication	0.317	0.009	0.030	0.77	–	–
						Meta-analysis	0.316	0.072	0.021	5.9 × 10⁻⁴	88.6	3.1 × 10⁻³
rs11722777	4	7,590,819	SORCS2	A	G	Discovery	0.816	−0.167	0.037	6.4 × 10⁻⁶	–	–
						Replication	0.821	−0.075	0.038	0.05	–	–
						Meta-analysis	0.819	−0.123	0.027	3.9 × 10⁻⁶	66.3	0.08
rs10941308	5	36641,007	SLC1A3	A	G	Discovery	0.115	0.189	0.043	9.3 × 10⁻⁶	–	–
						Replication	0.118	−0.026	0.044	0.55	–	–
						Meta-analysis	0.117	0.084	0.031	5.8 × 10⁻³	92.0	4.2 × 10⁻⁴
rs10648495	6	162,128,756	PRKN	CTCTTT	C	Discovery	0.463	−0.130	0.028	4.5 × 10⁻⁶	–	–
						Replication	0.459	0.040	0.029	0.16	–	–
						Meta-analysis	0.461	−0.046	0.020	0.02	94.4	2.4 × 10⁻⁵
rs10252701	7	17,280,513	AHR	C	A	Discovery	0.322	−0.194	0.031	3.2 × 10⁻¹⁰	–	–
						Replication	0.308	−0.146	0.032	4.0 × 10⁻⁶	–	–
						Meta-analysis	0.315	−0.171	0.022	1.0 × 10⁻¹⁴	15.1	0.28
rs79105258	12	111,718,231	CUX2	A	C	Discovery	0.268	0.211	0.032	4.4 × 10⁻¹¹	–	–
						Replication	0.298	0.137	0.031	1.3 × 10⁻⁵	–	–
						Meta-analysis	0.283	0.173	0.022	9.5 × 10⁻¹⁵	63.2	0.10

Chr Chromosome number, EA Effect allele, NEA Non-effect allele, EAF Effect allele frequency, SE Standard error

ISSN: 2730-6844