Table 1. Association results for novel loci with avPC of body shape.

					1st stage up to 133,376 samples	2nd stage up to 39,904 samples	1st+2nd stage combined up to 173,278 samples			Conditioned analysis on all GIANT tophits		P value of SNPs in GIANT analysis†			P value of SNPs in GIANT analysis‡
trait	SNP (lead SNP)	Next gene	Effect/other allele	EAF*	P value	P value	beta (sebeta)	P value	N	beta (sebeta)	P value	BMI	Height	WHR	BMI	Height	WHR
avPC1	rs7640424	CD47	C/T	69%	5.40E-07	0.0015	0.05 (0.008)	3.18E-09	171,544	0.05 (0.01)	5.80E-07	0.0072	0.74	0.25	2.28E-06	0.28	0.85
avPC1	rs943466 (rs2281819)	LEMD2	G/A	76%	6.39E-07	0.016	0.049 (0.009)	3.47E-08	172,174	0.049 (0.01)	7.28E-07	2.7E-04	0.045	0.54	9.34E-06	0.75	0.25
avPC3	rs7949030	GANAB	G/A	38%	2.74E-08	0.11	0.024 (0.004)	5.58E-09	139,195	0.025 (0.004)	6.36E-09	0.082	0.80	1.4E-04	0.54	0.041	3.3E-06
avPC3	rs7492628	RPS6KA5	G/C	30%	8.75E-08	0.13	0.024 (0.004)	1.90E-08	139,874	0.024 (0.004)	7.93E-08	0.064	0.62	4.9E-05	0.0050	0.58	9.3E-08
avPC4	rs4865796 (rs1664781)	ARL15	G/A	32%	5.59E-07	0.011	0.008 (0.001)	2.25E-08	172,517	0.008 (0.002)	7.25E-07	5.1E-05	0.034	0.40	1.6E-04	0.020	0.84
avPC4	rs7855432	ANP32B	G/T	80%	1.40E-07	0.17	0.01 (0.002)	4.06E-08	140,805	0.01 (0.002)	1.78E-07	0.33	0.046	0.49	0.32	5.5E-06	0.91

The association results for the first stage, second stage and first and second stage combined analysis is given for all six loci that were genome wide significantly associated (promising P value in the first stage meta analysis (<5 × 10⁻⁶) and genome wide significant in first and second stage combined analysis e (<5 × 10⁻⁸)) with one of the avPCs and novel. Moreover, the P values of the analysis conditioned on all tophits from the recent GIANT publications on BMI, height and WHR.

^*EAF is mean of EAF of all studies in the first stage meta analysis.

^†All tophits of the GIANT analysis published before 2014 (refs ³, ⁶).

^‡All tophits of the GIANT analysis unpublished and/or published after 2014 (refs ¹, ², ⁴).