. Author manuscript; available in PMC: 2018 Oct 24.

Published in final edited form as: Hum Genet. 2018 Jul 17;137(6-7):553–567. doi: 10.1007/s00439-018-1910-3

Table 3.

The relation of the significant SNPs and CNVs based on published database.

Total	Significant SNPs (bp)	Whole genome (bp)

		20,726	3,095,677,412

Within the common CNVs	2,042	130,618,321

Outside the common CNVs	18,684	2,965,059,091

OR with 95% CI	2.41 (2.37-2.60)

p	<1×10⁻⁶

Within the pathogenic CNVs	20,658	3,022,313,748

Outside the pathogenic CNVs	68	73,363,664

OR with 95% CI	1.02 (1.00-1.04)

p	0.03

Within the pathogenic CNVs (<10 Mb)	20,116	2,842,153,180

Outside the pathogenic CNVs (<10 Mb)	610	253,524,232

OR with 95% CI	1.06 (1.04-1.08)

p	1.8×10⁻⁸

The distribution of SNPs in regions with or outside CNVs was compared using Pearson χ² test (two-sided). The significant SNPs collected from the National Human Genome Research Institute (NHGRI) Catalog of Published GWAS was matched with the locations of common CNVs (population frequency > 1%) acquired from the Database of Genomic Variants (DGV) and pathogenic CNVs acquired from the UCSC database.

Abbreviation: SNP, single nucleotide polymorphisms; CNV, copy number variant; OR, odds ratio; CI, confidence interval.