Table 2.

Associations of Obesity-Related Genetic Loci With Body Mass Index and Body Weight in Chinese Women, 1996–2007

Trait and SNP	Chromosomea	Base Positiona	Nearest Gene	Effective Allele and Frequency (Proportion)b	Community Controls (n = 2,076)		Breast Cancer Cases (n = 2,069)		Type 2 Diabetes Cases (n = 885)		All Women (n = 5,030)
					Per-Allele Effectc	P Valued	Per-Allele Effect	P Value	Per-Allele Effect	P Value	Per-Allele Effect	P Value
BMIe
rs2815752f	1	72585028	NEGR1	A (0.92)	0.03	0.87	0.07	0.74	0.01	0.99	0.05	0.71
rs10913469	1	176180142	SEC16Bg	C (0.21)	0.35	4.0 × 10−3	0.26	0.03	0.23	0.26	0.28	4.1 × 10−4
rs6548238f	2	624905	TMEM18	C (0.90)	0.16	0.34	0.01	0.93	0.30	0.32	0.12	0.29
rs7647305	3	187316984	ETV5	C (0.95)	−0.64	4.6 × 10−3	0.57	0.01	0.74	0.07	0.10	0.49
rs10938397	4	44877284	GNPDA2	G (0.29)	−0.10	0.35	0.08	0.49	0.31	0.10	0.05	0.52
rs6235	5	95754654	PCSK1g	C (0.34)	0.09	0.37	−0.01	0.96	0.25	0.18	0.07	0.29
rs4712652	6	22186594	PRL	G (0.12)	0.06	0.70	−0.22	0.17	−0.34	0.21	−0.13	0.20
rs2844479	6	31680935	BAT2	T (0.56)	0.29	3.4 × 10−3	0.05	0.62	0.13	0.46	0.16	0.01
rs4074134	11	27603861	BDNF	G (0.54)	0.13	0.19	0.18	0.08	−0.16	0.36	0.10	0.15
rs10838738	11	47619625	MTCH2g	G (0.33)	0.21	0.05	0.07	0.53	−0.04	0.83	0.10	0.13
rs7138803f	12	48533735	FAIM2	A (0.28)	−0.06	0.57	0.07	0.53	0.21	0.28	0.04	0.60
rs7498665	16	28790742	SH2B1g	G (0.11)	0.16	0.31	0.42	6.6 × 10−3	0.70	7.6 × 10−3	0.38	1.8 × 10−4
rs9939609f	16	52378028	FTOg	A (0.12)	0.27	0.07	0.22	0.16	0.62	0.01	0.32	4.0 × 10−3
rs1424233	16	78240252	MAF	A (0.67)	0.01	0.92	0.05	0.66	−0.18	0.31	−0.02	0.82
rs1805081	18	19394430	NPC1g	G (0.23)	−0.18	0.13	−0.19	0.12	0.18	0.39	−0.12	0.13
rs17782313f	18	56002077	MC4R	C (0.20)	0.41	1.1 × 10−4	0.19	0.12	0.68	1.0 × 10−3	0.37	4.6 × 10−6
rs29941	19	39001372	KCTD15	C (0.23)	0.12	0.29	−0.04	0.75	−0.11	0.60	0.02	0.77
Body weight
rs2815752f	1	72585028	NEGR1	A (0.92)	0.08	0.86	0.23	0.64	0.00	1.00	0.15	0.64
rs10913469	1	176180142	SEC16Bg	C (0.21)	0.91	2.6 × 10−3	0.64	0.04	0.60	0.24	0.71	3.5 × 10−4
rs6548238f	2	624905	TMEM18	C (0.90)	0.44	0.28	0.00	1.00	0.75	0.32	0.29	0.29
rs7647305	3	187316984	ETV5	C (0.95)	−1.49	8.0 × 10−3	1.50	8.6 × 10−3	1.81	0.07	0.31	0.41
rs10938397	4	44877284	GNPDA2	G (0.29)	−0.25	0.36	0.17	0.52	0.77	0.09	0.11	0.53
rs6235	5	95754654	PCSK1g	C (0.34)	0.21	0.41	0.03	0.91	0.65	0.16	0.20	0.24
rs4712652	6	22186594	PRL	G (0.12)	0.15	0.70	−0.54	0.17	−0.78	0.24	−0.31	0.22
rs2844479	6	31680935	BAT2	T (0.56)	0.73	3.2 × 10−3	0.10	0.69	0.35	0.42	0.40	0.01
rs4074134	11	27603861	BDNF	G (0.54)	0.31	0.22	0.40	0.12	−0.36	0.39	0.22	0.18
rs10838738	11	47619625	MTCH2g	G (0.33)	0.51	0.05	0.15	0.56	−0.05	0.92	0.26	0.13
rs7138803f	12	48533735	FAIM2	A (0.28)	−0.17	0.54	0.16	0.57	0.52	0.27	0.08	0.65
rs7498665	16	28790742	SH2B1g	G (0.11)	0.41	0.29	1.05	7.0 × 10−3	1.75	6.7 × 10−3	0.95	1.7 × 10−4
rs9939609f	16	52378028	FTOg	A (0.12)	0.67	0.07	0.49	0.21	1.63	8.1 × 10−3	0.79	1.4 × 10−3
rs1424233	16	78240252	MAF	A (0.67)	0.03	0.91	0.11	0.68	−0.46	0.30	−0.05	0.79
rs1805081	18	19394430	NPC1g	G (0.23)	−0.49	0.09	−0.50	0.09	0.53	0.31	−0.31	0.11
rs17782313f	18	56002077	MC4R	C (0.20)	1.05	5.9 × 10−4	0.51	0.09	1.67	1.1 × 10−3	0.94	2.6 × 10−6
rs29941	19	39001372	KCTD15	C (0.23)	0.33	0.26	−0.12	0.69	−0.21	0.68	0.07	0.71

Abbreviations: BAT2, HLA-B-associated transcript 2; BDNF, brain-derived neurotrophic factor; BMI, body mass index; ETV5, ets variant 5; FAIM2, Fas apoptotic inhibitory molecule 2; FTO, fat mass- and obesity-associated; GNPDA2, glucosamine-6-phosphate deaminase 2; HLA-B, human leukocyte antigen B; KCTD15, potassium channel tetramerization domain containing 15; MAF, v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian); MC4R, melanocortin 4 receptor; MTCH2, mitochondrial carrier homolog 2 (Caenorhabditis elegans); NEGR1, neuronal growth regulator 1; NPC1, Niemann-Pick disease, type C1; PCSK1, proprotein convertase subtilisin/kexin type 1; PRL, prolactin; SEC16B, SEC16 homolog B (Saccharomyces cerevisiae); SH2B1, SH2B adaptor protein 1; SNP, single nucleotide polymorphism; TMEM18, transmembrane protein 18.

^aChromosome and base position were based on the March 2006 genome assembly (human genome version 18 (University of California, Santa Cruz), Build 36.1 (National Center for Biotechnology Information)).

^bFrequency of the BMI- or weight-increasing allele (increasing effect defined by initially reported genome-wide association studies in populations of European ancestry; effective allele defined by nucleotide on forward strand in this study) in the Chinese community controls.

^cChange in BMI or body weight (kg) for each copy of the effective allele.

^dP values were not corrected for multiple tests.

^eWeight (kg)/height (m)².

^fThis SNP was one of the 5 SNPs directly typed using Affymetrix SNP Array 6.0 (Affymetrix, Inc., Santa Clara, California). All other SNPs were imputed using MACH 1.0 (http://www.sph.umich.edu/csg/abecasis/MACH/).

^gThe tested SNPs are located on the corresponding genes: SEC16B rs10913469 (intron), PCSK1 rs6235 (missense ^Ser690^Thr in exon 14), MTCH2 rs10838738 (intron), SH2B1 rs7498665 (missense ^Ala484^Thr in exon 5), FTO rs9939609 (intron), and NPC1 rs1805081 (missense ^His215^Arg in exon 5).