Table 3.

Association test of common variants.

SNP	Chr	Position	Gene	Gene region	Exonic function	ORIBS	P-valueIBS	ORALL	P-valueALL	P-valueEC
rs199665292	9	107361452	OR13C5	exonic	Synonymous	9.09	2.53 × 10−12	5.56	1.16 × 10−12	3.53 × 10−15
rs1047985	6	32605216	HLA-DQA1	UTR5	—	0.05	2.21 × 10−10	0.06	1.43 × 10−09	2.50 × 10−06
rs201623571	3	195508393	MUC4	exonic	Non-synonymous	0.08	3.55 × 10−10	0.10	2.48 × 10−10	—
rs529417345	3	195508416	MUC4	exonic	Synonymous	0.03	9.40 × 10−10	0.03	5.31 × 10−10	—
rs548345415	3	195508418	MUC4	exonic	Non-synonymous	0.03	9.40 × 10−10	0.03	5.31 × 10−10	—
rs4010971	20	29637822	MLLT10P1	ncRNA_exonic	—	0.19	2.92 × 10−08	0.20	1.16 × 10−09	3.77 × 10−06
rs935	6	33054579	HLA-DPB1	UTR3	—	0.14	3.51 × 10−08	0.15	5.09 × 10−09	—
rs231216	19	36259494	PROSER3	UTR3	—	5.35	4.43 × 10−08	3.72	5.70 × 10−08	9.27 × 10−10
rs798112	15	31110279	HERC2P10	ncRNA_exonic	—	0.10	7.43 × 10−07	0.13	8.15 × 10−06	4.30 × 10−04
rs72837837	6	15520916	JARID2	UTR3	—	—	7.59 × 10−07	—	9.09 × 10−08	—
rs3794628	16	88729788	SNAI3-AS1	ncRNA_exonic	—	0.14	8.52 × 10−07	0.13	6.29 × 10−09	—
rs149234067	11	33722084	C11orf91	exonic	Non-synonymous	0.23	9.81 × 10−07	0.30	1.67 × 10−05	—

The SNPs showing the lowest P-value against the IBS control group were further tested using CEU, GRB, and TSI as control groups and merging the three sample sets into a single one (“ALL” = IBS + CEU + GBR + TSI). EC refers to the exome sequencing data in the Spanish control group (n = 267) of Dopazo et al.⁴². The SNP rs199665292 has merged into rs75081605 (https://www.ncbi.nlm.nih.gov); a hyphen in column “P-value_EC” indicates that there is not genetic information available in the Spanish control groups concerning this variant.

Chr = chromosome; P-values: Fisher’s Exact Test; OR = odds ratio.