Table 4.

Nominally significant single-site associations (P < 0.05) of common SCARB1 variants

SNP Namea	SNP IDb	Chr12 Positionc	Location	Amino Acid Change	RegDB Scored	Major/Minor Alleles	MAF	β	SE	R2 (%)	P	FDR	Secondary Trait (Effect)	Top 3 Variants
HDL-C
p20207	rs11057853	125329313	Intron 1		5	G/A	0.4484	0.4082	0.1925	1.0650	0.0343	0.4235
p20741	rs11057851	125328779	Intron 1		5	C/T	0.3237	−0.5924	0.2067	1.3010	0.0043	0.1465	ApoA-I (↓)	Top 1
p45516	rs1902569	125304004	Intron 1		5	G/A	0.1544	0.5447	0.2629	0.6390	0.0386	0.4375
p49690	rs4765615	125299830	Intron 2		5	G/A	0.4426	−0.4646	0.1866	0.9330	0.0130	0.2526	ApoA-I (↓)
p79828	rs838895	125269692	Intron 11		5	C/G	0.3171	0.4961	0.2059	0.8220	0.0162	0.2756	ApoA-I (↑)
ApoA-I
p20741	rs11057851	125328779	Intron 1		5	C/T	0.3237	−1.2331	0.5117	0.8600	0.0162	0.3186	HDL-C (↓)
p49690	rs4765615	125299830	Intron 2		5	G/A	0.4426	−0.9139	0.4614	0.6770	0.0480	0.5022	HDL-C (↓)
p55963	rs7134858	125293557	Intron 6		6	C/T	0.1560	1.7537	0.6260	1.0710	0.0052	0.2918		Top 2
p63483	rs838912	125286037	Intron 7		7	G/A	0.0867	1.8700	0.8230	0.6880	0.0234	0.3972
p64772	rs5888	125284748	Exon 8	Ala350Ala	3a	C/T	0.0961	2.0962	0.7888	0.9460	0.0080	0.2918		Top 3
p79721	rs838896	125269799	Intron 11		5	G/C	0.3104	1.1147	0.5056	0.7270	0.0278	0.4197
p79828	rs838895	125269692	Intron 11		5	C/G	0.3171	1.2206	0.5074	0.7800	0.0164	0.3186	HDL-C (↑)
p83884	rs701106	125265636	Intron 12		5	C/T	0.2597	1.2967	0.5352	0.7770	0.0156	0.3186

ApoA-I apolipoprotein A-I, FDR false discovery rate, HDL-C high-density lipoprotein cholesterol, MAF minor allele frequency, RegDB RegulomeDB, SE standard error, SNP single nucleotide polymorphism, UTR untranslated region, R², the proportion of the phenotypic variance explained by the variant; ↓, decreased; ↑, increased

Alleles on reverse strand. HDL-C and ApoA-I variables were in mg/dL and Box-Cox transformed

Results were adjusted for covariates: sex, age, waist, current smoking (yes/no), and minutes of walking or biking to work each day (jobmin) for HDL-C; sex and age for ApoA-I

The most significant P-value for each trait is shown in bold, see the single-site association (−log₁₀ P) plot and pairwise correlations (r²) in Fig. 2

FDR that reached a threshold of <0.20 is shown in bold

^{a, c}RefSeq of SCARB1: hg19, NM_005505 (CHIP Bioinformatics)

^bdbSNP build 139: GRCh37.p10

^dDetailed RegulomeDB (version 1.0) scoring scheme is described in Additional file 17: Table S12 or at http://regulome.stanford.edu/help, see functional assignments in Additional file 18: Table S13