Table 2.

Genes significantly associated with BMI in a gene-based meta-analyses, aggregating R/LF coding SNVs

Gene	Location longest coding transcript	Testd	N variants	P-value	Conditioned P- valuea	Single variant
						Top variant	P-value
All-ancestries sex-combined
SLC6A17	chr1:110693132–110744823	SKAT	13	2.73E-07	0.13	rs41313405	4.45E-07
RAPGEF3	chr12:48128453–48152889	SKAT	19	8.91E-15	0.20	rs145878042	5.16E-14
PRKAG1	chr12:49396055–49412629	SKAT	4	2.75E-12	0.53	rs1126930	2.63E-12
RAB21	chr12:72148643–72187256	SKAT	5	4.81E-08	0.27	rs61754230	4.96E-08
KSR2	chr12:117890817–118406028	SKAT	7	7.15E-09	0.19	rs56214831	4.59E-08
MAP1A	chr15:43809806–43823818	SKAT	25	9.42E-07	0.16	rs55707100	1.01E-06
MC4R	chr18:58038564–58040001	VT	4	3.72E-09	0.01	rs13447325	2.97E-11
GIPR	chr19:46171502–46186982	VT	10	8.24E-09	1.12E-04	rs143430880	5.76E-06
All-ancestries sex-specific
ALDH3A1 (men only)	chr17:19641298–19651746	SKAT	15	3.24E-07	0.003	rs142078447	8.62E-06
ZFR2 (women only)	chr19:3804022–3869027	SKAT	19	1.81E-07	0.82	rs45465594	3.64E-07
European sex-combined
ACHE	chr7:100487615–100493592	SKAT	6	3.30E-10	0.12	rs386545548	7.22E-10
European sex-specific
ANGPTL7 (men only)	chr1:11249346–11256038	VT	3	2.50E-06	0.008	rs202182115	2.56E-05
ZNF169 (women only)	chr9:97021548–97064111	SKAT	9	1.89E-07	0.24	rs12236219	1.06E-06

Array-wide significant gene-based association is defined as P<2.5×10⁻⁶. P-values are based on the meta-analysis of Discovery Stage studies.

Gene-based analyses were performed with SKAT and VT; results shown are from the test (SKAT or VT) for which the significance exceeded P<2.5×10⁻⁶. Only results using the "broad" SNV inclusion criteria reached array-wide significance.

Transcript positions are reported according to Build 37 for the longest coding transcript supported by RefSeq (as displayed in USCS Genome Browser).

^aP-value after conditioning on the most significant (top) single variant aggregated in the gene-based test.