Table 2.

Common CNV regions in PBMC/LCL (variant in > 50% of samples & size > 50 kb)

Index	Chr	Region start	Region end	Size (bp)	Number of genes	Ig overlap	# CNV	# CNV DGV	#CNV GS/B n=2514	#CNV GS/LCL n=1335	p-value
1	2	88,914,239	89,282,353	368,114	5	13 IgK	30	114	0	0	NA
2	3	163,995,351	164,108,689	113,338	1		18	39	0	1	0.34
3	7	142,001,624	142,203,712	202,088	58	52 TCR	20	56	16	21	0.0082
4	8	7,011,977	7,869,464	857,487	31		22	128	6	10	0.031
5	8	39,354,760	39,506,122	151,362	13		18	38	22	14	0.60
6	14	105,289,630	106,269,389	979,759	28	9 IgH	28	349	13	105	1.34e-
7	17	41,709,662	42,120,174	410,512	15		24	78	171	70	0.059

Abbreviations: Chr, chromosome; Number of genes refers to UCSC Genes track (hg18) from the UCSC Genome Browser; Ig overlap, number of immunoglobulin elements in the region based on BioMart at Ensembl (build GRCh37.p3); IgK, immunoglobulin kappa; TCR, T-cell receptor; IgH, immunoglobulin heavy chain; # CNV, number of copy number variants observed in this study; # CNV DGV, number of copy number variants present in the Database of Genomic Variants; #CNV GS/B, number of autosomal copy number variants in GENEVA SAGE samples derived from blood; #CNV GS/LCL, number of autosomal copy number variants in GENEVA SAGE samples derived from LCL; p-value, result of two-sided Fisher's Exact test on GENEVA SAGE samples (case=LCL derived samples, control=blood derived samples).