Table 2.

a. Enrichment of gene sets based on trait-association p-values of functional single nucleotide polymorphisms.
Gene set name	Gene set p-value	Gene set FDR	Significant gene number	Selected gene number	All gene number
NUCLEAR_REPLICATION_FORK	< 0.001	0.032	3	5	10
NUCLEAR_CHROMOSOME_PART	< 0.001	0.049	7	15	34

b. Enrichment of gene sets based on trait-association p-values of single nucleotide polymorphisms within a range of 500kb upstream and downstream of genes.
Gene set name	Gene set p-value	Gene set FDR	Significant gene number	Selected gene number	All gene number
NUCLEAR_CHROMOSOME_PART	< 0.001	0	19	29	34
POSITIVE_REGULATION_OF_T_CELL_ACTIVATION	< 0.001	0.006	15	20	21
HSA04140_REGULATION_OF_AUTOPHAGY	< 0.001	0.007667	14	26	30
CXCR4PATHWAY	< 0.001	0.0086	17	23	24
REGULATION_OF_T_CELL_ACTIVATION	< 0.001	0.01025	18	27	28
REGULATION_OF_LYMPHOCYTE_ACTIVATION	< 0.001	0.010286	20	33	35
POSITIVE_REGULATION_OF_LYMPHOCYTE_ACTIVATION	< 0.001	0.011667	16	23	24
NUCLEAR_CHROMOSOME	< 0.001	0.01175	26	44	54
CCR3PATHWAY	< 0.001	0.012	16	20	23
POSITIVE_REGULATION_OF_T_CELL_PROLIFERATION	< 0.001	0.0143	9	12	13
T_CELL_PROLIFERATION	< 0.001	0.019455	12	17	19
ANATOMICAL_STRUCTURE_MORPHOGENESIS	< 0.001	0.02525	198	347	379
SPRYPATHWAY	< 0.001	0.028077	12	17	18
ACETYLCHOLINE_SYNTHESIS	< 0.001	0.0365	6	6	8
IGF1RPATHWAY	0.001	0.036533	9	15	15
CELLULAR_MONOVALENT_INORGANIC_CATION_HOMEOSTASIS	0.001	0.039625	7	11	11
REGULATION_OF_T_CELL_PROLIFERATION	< 0.001	0.040706	10	15	16
SODDPATHWAY	0.003	0.041056	6	8	10
MAINTENANCE_OF_LOCALIZATION	0.002	0.046579	11	19	22
LATE_ENDOSOME	0.002	0.047591	6	8	12
RIBONUCLEOPROTEIN_COMPLEX	0.002	0.04815	42	118	143
CORTICAL_ACTIN_CYTOSKELETON	< 0.001	0.048333	9	12	13

Only those gene sets with an FDR < 0.05 are shown here. See Table a, Supplemental Digital Content 2, for detailed results.

Only those gene sets with an FDR < 0.05 are shown here. See Table b, Supplemental Digital Content 2, for detailed results.