Table 2.

Overview of outliers found in allele frequency comparison plots

	Position	Ref/Alt	3.5KJPNv2	gnomAD EAS	Possible reason
Fig. 2a–(i)	3259463	G/T	0.6337	1.0000	Unknown
	25452223	T/C	0.3705	0.8483	Low complexity region
	35283958	T/C	0.6488	1.0000	Low complexity region
	88051052	T/C	0.5943	1.0000	Unknown
	166721424	C/T	0.4401	0.8750	Unknown
Fig. 2a–(ii)	32609253	G/A	0.5351	0.0777	HLA region (HLA-DQA1)
	(15 SNVs omitted)
	32629146	G/A	0.5370	0.0037
Fig. 2a–(iii)	32609379	C/T	0.7194	0.2405	HLA region (HLA-DQB1)
	32610825	A/G	0.7245	0.2357
	32629257	T/A	0.7793	0.2308
	32629161	A/G	0.7201	0.0683
	32629193	C/T	0.7211	0.0293
	32629247	A/C	0.7171	0.0157
	Position	Ref/Alt	3.5KJPNv2	RIKEN	Possible reason
Fig. 2b–(iv)	93743452	A/T	0.3535	0.1842	Unknown (gnomAD EAS = 0.3532)

(a) Summary of outliers in Fig. 3(a). The “Position” column shows the chromosomal position of a variant, the “Ref/Alt” column gives the reference allele and the alternative allele, the “3.5KJPNv2” column gives the allele frequency observed in 3.5KJPNv2, and the “gnomAD EAS” column gives the allele frequency observed in gnomAD EAS

(b) Summary of outliers found in Fig. 3b