. 2016 Jul 27;25(18):4094–4106. doi: 10.1093/hmg/ddw227

Table 2.

New variants identified as independent signals in the approximate conditional analysis

					Single SNP meta-analysis			Approximate conditional meta-analysis
Trait	Chromosome: position	rsID	Trait-raising/ other allele	%EAF	β	SE	P-value	N	β	SE	P-value	Conditioned on	Locus
HDL	4:102816487	rs116329129¹^,⁴	T/C	99.97	1.835	0.448	4.23E-05	9023	1.842	0.448	3.99E-05	rs13107325	SLC39A8
	11:117112526	rs79554110²^,³	T/G	37.94	0.038	0.009	5.69E-05	24 813	0.034	0.009	2.16E-04	rs2266788, rs35120633, rs186808413	APOA1
	11:116707044	rs138407155¹^,⁴	A/T	99.88	0.589	0.143	3.98E-05	20 910	0.505	0.143	4.09E-04	rs2266788, rs35120633, rs186808413, rs79554110	APOA1
	15:58830639	rs140029729¹^,⁴	A/G	99.92	1.019	0.273	1.88E-04	8544	0.963	0.273	4.14E-04	rs1800588, rs10468017	LIPC
	15:58837989	rs200684324¹^,⁴	A/G	0.13	0.760	0.223	6.62E-04	7941	0.721	0.223	1.23E-03	rs1800588, rs10468017, rs140029729	LIPC
	18:47113165	rs117623631¹^,⁴	T/C	0.22	0.389	0.116	8.36E-04	17 028	0.390	0.116	8.08E-04	rs77960347, rs4939883	LIPG
	19:45448465	rs5167¹^,⁴^,⁵	G/T	36.02	0.042	0.009	6.19E-06	25 337	0.046	0.009	8.70E-07	rs769449	APOE
	19:45028231	rs36053277¹^,⁴	G/A	99.62	0.304	0.079	1.14E-04	22 141	0.289	0.079	2.43E-04	rs769449, rs5167	APOE
LDL	6:161018174	rs7770628³^,⁸	C/T	45.47	0.030	0.009	1.38E-03	23 595	0.035	0.009	2.03E-04	rs3798220	LPA
	12:121660770	rs145814749¹^,⁴	G/A	99.91	0.768	0.205	1.85E-04	13 946	0.768	0.205	1.85E-04	rs34606562	HNF1A
	19:45448036	rs1132899¹^,⁴^,⁵	T/C	47.49	0.033	0.009	3.37E-04	24 201	0.037	0.009	4.71E-05	rs7412, rs769449, rs445925, rs3208856	APOE
TC	2:21229160	rs5742904¹^,⁴	T/C	0.05	1.676	0.260	2.53E-11	13 764	1.679	0.260	2.38E-11	rs541041, rs1367117, rs533617	APOB
TG	2:27550967	rs1049817¹¹	A/G	59.83	0.053	0.009	5.42E-09	26 031	−0.030^a	0.007	2.54E-05	rs1260326	GCKR
	11:116701353	rs76353203⁹^,¹⁰	C/T	99.96	1.258	0.320	8.60E-05	11 860	1.279	0.320	6.58E-05	rs2266788, rs35120633	APOA1
	15:42436237	rs139788907¹^,⁴	G/A	0.04	1.665	0.421	7.67E-05	6731	1.668	0.421	7.49E-05	rs2412710	CAPN3
	16:57015091	rs58801,4	C/G	5.09	0.085	0.021	3.85E-05	24 330	0.078	0.021	1.33E-04	rs3764261	CETP

^¹

Non-synonymous variant,

^²

common variant,

^³

intron variant,

^⁴

missense variant,

^⁵

nonsense-mediated mRNA decay transcript variant,

^⁶

non-coding exon variant,

^⁷

non-coding transcript variant,

^⁸

NHGRI catalogue,

^⁹

stop gained variant,

^¹⁰

splice region variant,

^¹¹

synonymous rs7770628 has been previously published for LPA eQTL.

^{^a}

Change in the direction of the conditional effect.