Table 2 Genome-wide variants significantly associated with serum lipids using a 2df joint test of main effect and interaction in Meta-Analysis of Stages 1 & 2 and were independent of known lipids loci^a.

rsid Index Variant Nearest Gene^b	Chr:BP (GRCh37)	Tested Allele: Freq	Main Effect	SE	Interaction Effect	SE	P_1df^c	P_2df^c	Population, Sample Size	Lipid^d	Psychosocial Factor
rs6730082 RNU4-73P	2:9877621	C:0.26	−0.0038	0.0040	−0.045	0.0096	3.1E-06	2.5E-08	AFR, n = 16,886	HDLC	DEPR
rs142378953 AC090043.1	3:1695235	G:0.01	0.039	0.032	0.24	0.060	6.0E-05	4.9E-08	CPMA, n = 18,911	TG	DEPR
rs34636484 CD96	3:111356092	G:0.03	-4.5	0.80	1.8	1.6	0.27	3.1E-08	CPMA, n = 42,162	LDLC	SOCS
rs11949029 CTC-207P7.1	5:163470425	A:0.02	6.6	2.2	−19.0	3.5	4.1E-08	2.4E-08	CPMA, n = 16,927	LDLC	SOCS
rs4562311 NKAIN3	8:63589187	G:0.22	0.013	0.014	−0.13	0.032	3.5E-05	8.5E-09	CPMA, n = 6,667	TG	ANXT
rs59808825 GRAMD1B	11:123152496	C:0.03	5.0	2.1	−22.9	4.2	4.3E-08	8.8E-09	CPMA, n = 5,973	LDLC	ANXT
rs73597733 MACROD2	20:15941137	A:0.04	-0.015	0.010	0.14	0.025	8.4E-09	1.0E-08	AFR, n = 11,234	HDLC	DEPR
rs11702544 RRP1B	21:45091861	C:0.39	0.0049	0.0010	0.0043	0.0027	0.1	2.3E-08	CPMA^e/EUR, n = 100,182	HDLC	DEPR

^aListed variants were more than 500 KB from 95% Credible Sets reported in Graham et al. (https://doi.org/10.1038/s41586-021-04064-3).
^bIndex variant is for the most statistically significant association in the region and Nearest Gene is determined based on ANNOVAR annotations implemented in FUMA. While the “Nearest Gene” is listed for simplicity, we acknowledge that the nearest gene may not be of functional relevance for the given variant.
^cBolded values indicate P < 5 × 10⁻⁸.
^dAnalyses were conducted on natural log-transformed HDLC and TG values, while LDLC was untransformed (all original values in mg/dL).
^eThe most statistically significant analysis (indicated) is displayed in table. Full results for all genome-wide significant associations given in Supplementary Table S4.

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