Table 2.

Genome-wide significant loci for EduYears in cross-ancestry meta-analysis combining EAS and EUR populations

Chr	Start	End	Credible set ID	Credible set size	Total PIP	N of significant variantsa,*	SNP with maximum PIP	Maximum PIP	A1	Effect size (EAS)	A1 Freq (EAS)	Marginal P value (EAS)	Effect size (EUR)	A1 Freq (EUR)	Marginal P value (EUR)	Gene	Annotation
2	161,721,597	162,351,261	1	2	0.99	2	rs11678980	0.93	A	−0.020	0.39	4.19 × 10−9	−0.017	0.43	3.69 × 10−24	NA	NA
4	180,613,679	181,136,169	1	4	0.99	4	rs4861427	0.38	C	0.020	0.47	6.81 × 10−9	0.005	0.48	3.66 × 10−3	NA	NA
5	93,838,858	94,392,030	1	15	0.95	14	rs255338	0.18	C	0.022	0.73	1.11 × 10−8	0.007	0.90	6.08 × 10−3	MCTP1	Intron
5	106,947,725	107,455,182	1	2	0.95	2	rs7708343	0.51	A	−0.021	0.32	4.46 × 10−9	−0.012	0.11	2.28 × 10−6	FBXL17	Intron
5	106,947,725	107,455,182	2	15	0.96	2	rs6868799	0.17	A	0.009	0.36	9.40 × 10−3	0.009	0.35	3.13 × 10−8	FBXL17	Intron
6	27,515,505	29,611,229	1	3	0.96	3	rs9461540	0.39	G	−0.027	0.17	6.19 × 10−10	NA	NA	NA	GABBR1	Upstream gene
6	27,515,505	29,611,229	2	35	0.96	25	rs112644424	0.13	T	−0.022	0.28	2.33 × 10−9	−0.014	0.08	2.45 × 10−6	NA	NA
10	103,385,878	104,057,295	1	26	0.96	26	rs3758551	0.07	G	−0.013	0.77	1.06 × 10−3	−0.012	0.60	6.24 × 10−14	GBF1, PITX3	Upstream gene
10	103,385,878	104,057,295	2	4	0.98	4	rs11191193	0.70	G	−0.021	0.23	6.89 × 10−8	−0.017	0.34	5.89 × 10−23	C10orf76	Intron
10	103,385,878	104,057,295	3	3	0.98	0	rs11598489	0.54	T	NA	NA	NA	0.023	0.04	2.65 × 10−7	NA	NA
17	42,899,988	43,438,117	1	2	0.97	1	rs2867316	0.90	T	0.004	0.62	2.84 × 10−1	−0.010	0.32	2.32 × 10−8	MAP3K14	Intron
17	42,899,988	43,438,117	2	7	0.97	6	rs12948326	0.71	G	−0.020	0.53	4.90 × 10−9	−0.004	0.39	1.04 × 10−2	NMT1, PLCD3	Downstream gene
17	42,899,988	43,438,117	3	3	1.00	3	rs11871429	0.51	G	−0.005	0.33	1.45 × 10−1	−0.014	0.21	1.73 × 10−12	HIGD1B	Upstream gene

Abbreviations: A1 Freq, frequency of A1; A1, effect allele; Chr, chromosome; N, number; NA, not available. Gene symbols are italicized.

^aNumber of genome-wide significant variants with P value of a two-sided test <5 × 10⁻⁸. *at least in one population.

Base pair position is based on the human genome assembly GRCh37 (hg19).

‘Credible set ID’: the ID of credible sets used to identify different credible sets in the same region.

‘Gene’: the genes affected by the variant using the Variant Effect Predictor tool.

‘Annotation’: the consequence of variants on the protein sequence using the Variant Effect Predictor tool.