Table 1. Variants identified in the two independent cohorts.

	Discovery (case=525, control=619)						Replication (case=456, control=336)
Variant typea	Novel	dbSNP	MAF⩽1%b	Case only	Control only	Case and control	Novel	dbSNP	MAF⩽1%b	Case only	Control only	Case and control
Downstream	72	57	92	27	39	63	69	56	80	32	27	66
Intergenic	64	49	89	39	30	44	54	29	63	30	17	36
Intronic	4001	3143	4967	1706	2066	3372	2953	2846	3512	1540	1130	3129
ncRNA	303	258	350	129	129	303	236	228	264	111	75	278
Nonsynonymous	812	241	918	323	412	318	596	193	642	304	203	281
Splicing	31	11	33	12	18	12	18	8	17	10	4	12
Stop codon	16	3	15	9	5	5	11	3	10	7	1	6
Synonymous	600	305	733	246	320	339	381	247	452	215	131	282
Upstream	67	46	77	25	35	53	74	51	82	36	32	57
UTR3	925	425	1067	370	415	565	649	360	719	320	228	461
UTR5	181	59	203	47	97	96	130	56	145	67	37	82

Abbreviations: dbSNP, single-nucleotide polymorphism database; MAF, minor allele frequency.

^aTranscripts from ENSEMBL V63 were used to annotate these variants.

^bMAF less than or equal to 1% in each of the cohorts.