TABLE 1.

SNPs associated with BA.

SNP	Cohort	MAF	MAF	OR	p-values (trend test)	Adjusted p-value (FDR_BY)
		(BA cases) (aa/Aa/AA)	(Controls) (aa/Aa/AA)
rs6657965	Discovery	0.2614	0.1221			–
MAN1A2		(n = 44 of 51)	(n = 1,713 of 1,969)	2.543	7.18E-05
flanking_5UTR		(1/21/22)	(19/379/1,309)
	Replication	0.2778	0.1383			–
chr1:		(n = 45 of 53)	(n = 347 of 400)	2.396	9.73E-04
117694341 (hg18)		(2/21/22)	(12/72/263)
	Combined	0.2697	0.1249
		(n = 89 of 104)	(n = 2,060 of 2,369)	2.587	1.72E-08	2.83E-03
		(3/42/44)	(31/451/1,572) ***
rs12131109	Discovery	0.2558	0.1241	2.427	2.14E-04	–
MAN1A2		(n = 44 of 51)	(n = 1713 of 1969)
Intronic		(1/20/22) *	(19/387/1307)
	Replication	0.2778	0.1383	2.396	9.73E-04	–
chr1:		(n = 45 of 53)	(n = 347 of 400)
117744385(hg18)		(2/21/22)	(12/72/263)
	Combined	0.2697	0.1265	2.517	4.59E-08	6.50E-03
		(n = 89 of 104)	(n = 2,060 of 2,369)
		(3/41/44) *	(31/459/1,570)
	(n = 89) and	0.2603	0.1265	2.497	6.97E-10	3.11E-04
	Taqman	(n = 121)	(n = 2060)
	(n = 32)	(4/54/62) *	(31/459/1,570)
rs7531715	Discovery	0.2558	0.1232	2.447	1.89E-04	–
MAN1A2		(n = 44 of 51)	(n = 1,713 of 1,969)
intronic		(1/20/22) *	(19/383/1,307)
	Replication	0.2778	0.1383	2.396	9.73E-04	–
chr1:		(n = 45 of 53)	(n = 347 of 400)
117850460(hg18)		(2/21/22)	(12/72/263)
	Combined	0.267	0.1257	2.533	4.59E-08	6.98E-03
		(n = 89 of 104)	(n = 2,060 of 2,369)
		(3/41/44) *	(31/455/1,570) **
	(n = 89) and	0.2603	0.1258	2.497	6.97E-10	3.11E-04
	Taqman	(n = 121)	(n = 2,060)
	(n = 32)	(4/54/62) *	(31/455/1,570) **

Minor allele frequencies for two intronic SNPs in the MAN1A2 gene in cases and controls selected with multidimensional scaling (MDS) plots in the discovery and replication cohorts, and in the overall population of 121 BA cases. These 121 cases include all 89 selected BA cases genotyped with SNP arrays which were used for discovery and replication, and 32 BA cases genotyped with Taqman genotyping assays. Also shown are distribution of genotypes aa, Aa, and AA in each cohort and adjusted p-values for False Discovery Rate using Benjamini Y method (FDR_BY). MAF, minor allele frequency, OR, odds ratio; BA, biliary atresia; a, minor allele; A, major allele; *, one genotype missing in BA cases; **, four genotypes missing in controls; ***, six genotypes missing in controls.