Table 1.

Significantly associated PAX3 and T known variants in non-Hispanic white cases with spina bifida, 2006–2010

rs number	Allelesa, b	Locationc/ Position	Conservation Scoresd	Cases (N=104)		1,000 Genomese Phase 1 (N=381)		HapMapf (N=113)		Exome Sequencing Projectg (N=8,600)
				Allele 1	Allele 2	ORh	95% CIi	ORh	95% CIi	ORh	95% CIi
PAX3
rs13022712	c.1173 +26G>A	Intron 8; 223084833	0.98, 0.96, 2.81	169	23	1.61	0.97–2.69	3.36	1.41–8.05	1.59	1.00–2.44
rs13014735	c.*211+195C>T	Intron 9; 223066237	1, 2.65, 5.77	187	25	1.56	0.94–2.60			1.67	1.03–2.60
T
rs3099267	c.1034+17A>G	Intron 7; 166574308	0, −0.40, −1.78	186	14	0.53	0.30–0.95			0.55	0.30–0.91
rs3816304j	c.*339A>G	Exon 8; 166571464	0, −0.11, 0.53	193	15	0.56	0.32–0.99
rs35606910j	c.*273C>T	Exon 8; 166571530	0, −1.60, −6.33	193	15	0.56	0.32–0.99

^aGenomic Build 37.2; Group term GRCh37.2

^bPositions and alleles are listed in reverse orientation (i.e., increasing position number from 3’ to 5’ on the coding strand)

^cPAX3 exon/intron numbering based on 11 total exons present in 8 alternative transcripts; T exon/intron numbering based on 8 total coding exons in 2 alternative transcripts

^dVertebrate evolutionary conservation score from phastCons (range: 0–1) phyloP (range: −12–6), and GERP++ (range: −12–6), respectively, from the conservation track of the UCSC Genome Browser

^e1000 Genomes phase 1 release version 3.20101123

^fHapMap Genome Browser release 28 (phase 1, 2 and 3 merge)

^gExome Variant Server release ESP6500SI

^hOdds ratio for allelic association test; only reported for variants with significant associations

ⁱExact 95% confidence interval

^jrs3816304 and rs35606910 are 66 base pairs apart in the 3’ non-coding region of exon 8 and are in tight linkage disequilibrium (r²=1.0).