Table 2.

Nomenclature used to describe combinations of analytic strategies and subsets of regions analyzed.

Description	Nomenclature
SKAT tests without any weighting based on PolyPhen-2 scores, all rare variants with MAF <0.01	N
SKAT tests with weighting based on PolyPhen-2 scores, all rare variants with MAF <0.01	P
SKAT tests only on rare variants (MAF <0.01) with benign, possibly damaging, or probably damaging PolyPhen-2 scores	S
All windows	All
Windows that contained only variants with either missing or benign PolyPhen2 scores	Stratum 1 or St1
Windows that contained at least one variant with a possibly or probably damaging PolyPhen-2 score	Stratum 2 or St2
A stratified analysis that combines results from Stratum 1 and Stratum 2	Strat or Str
Windows containing at least one causal variant	H1
Windows containing at least one variant correlated with a causal SNP at r ≥ 0.9	H1-Corr0.90
Windows containing at least one variant correlated with a causal SNP at r ≥ 0.75	H1-Corr0.75
Standard error associated with random error or noise	σ