Table 3.

Strongest MQLS results (p < 1 × 10⁻⁵) from binary trait analyses

SNP	Chromosome	Position (bp)	MAF		HWE p	MQLS p	Nearest
			SA	Control			Genes
rs11585386	1	227085771	0.19	0.05	0.635	4.50 × 10−6	RHOU\RAB4A
rs294588	5	162931093	0.49	0.26	0.400	1.05 × 10−6	MAT2B\LOC391844
rs12518984	5	162940090	0.45	0.25	0.724	7.80 × 10−6	MAT2B\LOC391844
rs1572438	6	803970	0.49	0.27	0.502	9.22 × 10−6	HUS1B\FOXQ1
rs6942089	6	80491598	0.30	0.47	0.112	7.30 × 10−6	SH3BGRL2\ELOVL4
rs9359390	6	80493147	0.30	0.49	0.269	3.38 × 10−6	SH3BGRL2\ELOVL4
rs2038292	6	80509889	0.39	0.40	0.349	6.08 × 10−6	SH3BGRL2\ELOVL4
rs2092745	6	80511550	0.40	0.39	0.276	7.33 × 10−6	SH3BGRL2\ELOVL4
rs6925255	6	80522843	0.29	0.49	0.274	1.18 × 10−6	SH3BGRL2\ELOVL4
rs932492	6	80531291	0.37	0.46	0.086	6.49 × 10−6	SH3BGRL2\ELOVL4
rs9443716	6	80543068	0.37	0.46	0.087	6.29 × 10−6	SH3BGRL2\ELOVL4
rs1247322	6	161250642	0.24	0.10	0.771	3.56 × 10−6	PLG\MAP3K4
rs1247320	6	161253771	0.24	0.10	0.771	3.56 × 10−6	PLG\MAP3K4
rs1247319	6	161253850	0.24	0.10	0.771	3.56 × 10−6	PLG\MAP3K4
rs1247318	6	161253927	0.24	0.10	0.771	2.89 × 10−6	PLG\MAP3K4
rs1247317	6	161254404	0.24	0.10	0.771	3.56 × 10−6	PLG\MAP3K4
rs1247316	6	161255135	0.24	0.10	0.771	3.56 × 10−6	PLG\MAP3K4
rs1247363	6	161262680	0.24	0.10	0.771	7.61 × 10−6	PLG\MAP3K4
rs16892673	6	161853925	0.21	0.06	0.651	4.69 × 10−6	PARK2
rs16892698	6	161863355	0.19	0.05	0.319	6.24 × 10−6	PARK2
rs16892700	6	161864569	0.19	0.05	0.319	6.24 × 10−6	PARK2
rs9918668	7	93529680	0.19	0.43	0.403	5.84 × 10−7	BET1\COL1A2
rs643473	12	128041892	0.19	0.40	0.863	9.42 × 10−6	LOC100129252\NLRP9P

Bold indicates a deviation from HWE

bp base pair position from NCBI build 37.1, MAF minor allele frequency