Table 2. Genome-wide significant... | Rockefeller University Press

Table 2.

Genome-wide significant variants associated with KD susceptibility

Chr:position	SNP	Gene	Effect	Odds ratio	Risk allele frequency in 1000 Genomes, European/East Asian populations	References
1:161479745	rs1801274	FCGR2A	Missense (H131R)	1.32^a	0.49/0.72	Khor et al., 2011
4:185568113	rs2720378	CASP3	Intron	1.20	0.73/0.30	Johnson et al., 2020
6:27869631	rs1873212	TRX-CAT1-7	Downstream	1.2	0.07/0.17	Johnson et al., 2020
6:28248594	rs1778477	PGBD1	Upstream	1.30	0.83/0.86	Johnson et al., 2020
6:30411903	rs1264516	LOC105375012	Downstream	1.24	0.44/0.67	Johnson et al., 2020
6:31533378	rs2857602	LTA	Intron	1.28	0.40/0.34	Johnson et al., 2020
6:32300809	rs3129960	C6orf10	Intron	1.37	0.15/0.15	Johnson et al., 2020
6:32658079	rs7775228	HLA-DQB1	Upstream	1.26	0.16/0.23	Johnson et al., 2020
6:32763514	rs2857151	HLA-DQB2–H-DOB	Intergenic	1.47^b	0.67/0.69	Onouchi et al., 2012
6:32782605	rs2071473	HLA-DOB	Intron	1.26	0.39/0.43	Johnson et al., 2020
8:11343973	rs2736340^c	BLK	Upstream	1.55	0.24/0.72	Johnson et al., 2020
14:107152027	rs4774175	IGHV1-69	Downstream	1.20	0.40/0.48	Johnson et al., 2020
19:41224204	rs28493229^d	ITPKC	Intron	1.52^a/1.41	0.12/0.065	Khor et al., 2011; Johnson et al., 2020
20:44746982	rs1883832^e	CD40	5′ UTR	1.28	0.74/0.57	Johnson et al., 2020

Chr:position	SNP	Gene	Effect	Odds ratio	Risk allele frequency in 1000 Genomes, European/East Asian populations	References
1:161479745	rs1801274	FCGR2A	Missense (H131R)	1.32^a	0.49/0.72	Khor et al., 2011
4:185568113	rs2720378	CASP3	Intron	1.20	0.73/0.30	Johnson et al., 2020
6:27869631	rs1873212	TRX-CAT1-7	Downstream	1.2	0.07/0.17	Johnson et al., 2020
6:28248594	rs1778477	PGBD1	Upstream	1.30	0.83/0.86	Johnson et al., 2020
6:30411903	rs1264516	LOC105375012	Downstream	1.24	0.44/0.67	Johnson et al., 2020
6:31533378	rs2857602	LTA	Intron	1.28	0.40/0.34	Johnson et al., 2020
6:32300809	rs3129960	C6orf10	Intron	1.37	0.15/0.15	Johnson et al., 2020
6:32658079	rs7775228	HLA-DQB1	Upstream	1.26	0.16/0.23	Johnson et al., 2020
6:32763514	rs2857151	HLA-DQB2–H-DOB	Intergenic	1.47^b	0.67/0.69	Onouchi et al., 2012
6:32782605	rs2071473	HLA-DOB	Intron	1.26	0.39/0.43	Johnson et al., 2020
8:11343973	rs2736340^c	BLK	Upstream	1.55	0.24/0.72	Johnson et al., 2020
14:107152027	rs4774175	IGHV1-69	Downstream	1.20	0.40/0.48	Johnson et al., 2020
19:41224204	rs28493229^d	ITPKC	Intron	1.52^a/1.41	0.12/0.065	Khor et al., 2011; Johnson et al., 2020
20:44746982	rs1883832^e	CD40	5′ UTR	1.28	0.74/0.57	Johnson et al., 2020

This table lists variants reaching genome-wide significance (P < 5 × 10⁻⁸) in the primary GWAS in which they were identified (Khor et al., 2011; Kim et al., 2017; Lee et al., 2012; Onouchi et al., 2012) or in a follow up meta-analysis (Johnson et al., 2020) of the three Asian GWASs (Kim et al., 2017; Lee et al., 2012; Onouchi et al., 2012). Chr, chromosome; SNP, single nucleotide polymorphism; UTR, untranslated region.

Odds ratio in the combined discovery GWAS and replication cohorts from the primary publication.

Odds ratio in the discovery GWAS from the primary publication.

In linkage disequilibrium (r² > 0.5) in the 1000 Genomes Chinese and Japanese populations with rs2254546 (Onouchi et al., 2012), rs2618476 (Lee et al., 2012), and rs6993775 (Kim et al., 2017).

In linkage disequilibrium (r² > 0.5) in the 1000 Genomes Chinese and Japanese populations with rs2233152 (Khor et al., 2011).

In linkage disequilibrium (r² > 0.5) in the 1000 Genomes Chinese and Japanese populations with rs1569723 (Lee et al., 2012) and rs4813003 (Onouchi et al., 2012).

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