Table 1.

Results of the Hardy–Weinberg equilibrium test for each SNP.

LD Number	#	Tag	SNP	Position (hg19)	ObsHET	PredHET	HWpval	%Geno	FamTrio	MendErr	MAF	Rating	Results
	1		rs1048433	122748996	0.481	0.465	0.771	99	0	0	0.368		Used
LD1	2	Tag	rs1507994	122749541	0.382	0.346	0.2236	100	0	0	0.223		Used
LD1	3	Tag	rs13145213	122750079	0.527	0.493	0.4445	98.4	0	0	0.439		Used
	4		rs12499222	122774917	0.361	0.34	0.5514	100	0	0	0.217		Used
	5		rs6838198	122781263	0	0	0	0	0	0	0	BAD	-
	6		rs10518290	122805872	0	0	1	100	0	0	0	BAD	-
LD2	7	Tag	rs11726196	122806228	0.361	0.379	0.616	100	0	0	0.254		Used
LD2	8	Tag	rs2135976	122816181	0.131	0.131	1	100	0	0	0.071		Used
LD2	9	Tag	rs11732666	122824052	0.577	0.496	0.0406	99	0	0	0.458		Used
LD2	10	Tag	rs17517624	122824591	0.257	0.261	0.9592	100	0	0	0.154		Used
LD2	11	Tag	rs3762839	122825364	0.157	0.145	0.5814	100	0	0	0.079		Used
LD2	12	Tag	rs884701	122830406	0.56	0.495	0.0973	100	0	0	0.448		Used
LD2	13	Tag	rs13127488	122830800	0.56	0.495	0.0973	100	0	0	0.448		Used
LD2	14	Tag	rs906496	122833314	0.539	0.498	0.335	100	0	0	0.469		Used
	15		rs4292355	122842267	0.45	0.423	0.4946	100	0	0	0.304		Used
	16		rs12644087	122844819	0.152	0.14	0.6334	100	0	0	0.076		Used
	17		rs6841843	122857568	0.366	0.36	1	100	0	0	0.236		Used
	18		rs4833779	122861426	0	0	0	0	0	0	0	BAD	-
	19		rs950574	122864241	0.487	0.463	0.6025	100	0	0	0.364		Used
	20		rs970349	122871632	0.225	0.246	0.3395	100	0	0	0.144		Used
	21		rs4001038	122886240	0.026	0.026	1	100	0	0	0.013		Used
LD3	22	Tag	rs1358229	122896734	0.555	0.499	0.1734	100	0	0	0.482		Used
LD3	23	Tag	rs6838639	122899165	0.524	0.452	0.0449	100	0	0	0.346		Used
	24		rs13109219	122900529	0.005	0.005	1	100	0	0	0.003		Used
	25		rs9999992	122902084	0.314	0.325	0.7639	100	0	0	0.204		Used
LD4	26	Tag	rs6817255	122902923	0.455	0.489	0.399	100	0	0	0.427		Used
LD4	27	Tag	rs11098653	122903090	0.257	0.254	1	100	0	0	0.149		Used
LD4	28	Tag	rs13130390	122903206	0.173	0.166	1	100	0	0	0.092		Used
	29		rs11098654	122909415	0.33	0.282	0.0251	100	0	0	0.17		Used

# Matches the number in Figure 1. Tag SNPs are indicated with a circle. MAF, minor allele frequency (those with a value of 0 were excluded [=BAD], and finally 26 [=Used] in the results column were used); ObsHET, observed heterozygosity p value; PredHET, predicted heterozygosity p value; HWpval, Hardy–Weinberg equilibrium p value; %Geno, percentage of the non-missing genotypes for this marker; FamTrio, number of fully genotyped family trios for this marker (0 for datasets with unrelated individuals); MendErr, number of the observed Mendelian inheritance errors (0 for datasets with unrelated individuals).