Table 1.

Non-synonymous Variants on Exome Chip and Distribution in Current Study

Type of Variant	Total Polymorphic	Total Number of SNPs by MAF					Het/hom rare genotypes per sample
		< .1%	.1 – .5%	.5–1%	1–5%	> 5%	Mean (SD)	Range
All Non-Synonymous	111,592	65829	18174	5099	8435	14055	5931 (84.4)	[5615, 6465]
Stop Loss	326	168	47	8	22	81	39 (4.4)	[23, 54]
Stop Gain	2336	1670	351	78	97	140	59 (5.9)	[40, 80]
Start Loss	303	175	45	16	28	39	16 (3.1)	[6, 30]
Start Gain	8	6	1	0	1	0	0 (.2)	[0, 1]
Essential Splice	969	578	128	37	35	191	79 (6.5)	[57, 103]
Normal Splice	793	35	19	6	50	683	297 (12.1)	[253, 338]

Note: All non-synonymous SNPs includes start/stop and splice-site variants. All variants were annotated relative to GENCODE v11 transcripts from the ENCODE project. Minor allele frequency was computed without respect to founder status.