Table 2.

Single Nucleotide Polymorphisms (SNPs) with P<1x10⁻⁶ for the Transmission-Disequilibrium Test (TDT) in the Discovery Cohort with Results from TDT in Discovery, Replication, and Combined Cohorts, National Birth Defects Prevention Study, 1997-2011.

Chromosome	SNP	Position	Locus	Minor Allele (Effect Allele)	Major Allele	Cohort	N Triads	MAF†	N Allele Transmitted	N Allele Untransmitted	OR‡	P
6	rs55877192	44129213	6p21.1	G	A	Discovery	396	0.080	34	93	0.37	1.61x10−7
						Replication	257	0.095	33	65	0.51	1.60x10−3
						Combined	653	0.086	67	158	0.42	1.18x10−9
10	rs113920486	54299613	10q21.1	G	C	Discovery	374	0.023	3	31	0.10	7.66x10−7
						Replication	269	0.014	6	9	0.67	0.61
						Combined	643	0.019	9	40	0.23	9.26x10−6
19	rs2360743	10736514	19p13.2	T	C	Discovery	377	0.023	1	33	0.03	4.08x10−9
						Replication	250	0.013	0	13	0.00	2.44x10−4
						Combined	627	0.019	1	46	0.02	6.82x10−13
X	rs5913271	79731210	Xq21.1	A	T	Discovery	401	0.039	4	34	0.12	6.04x10−7
						Replication	267	0.069	11	21	0.52	0.11
						Combined	668	0.051	15	55	0.27	1.65x10−6

SNPs that replicated at a threshold of 0.05/4=0.0125 are shown in bold font.

^†MAF = minor allele frequency, calculated in parents of triads used in TDT

^‡OR = odds ratio