Population differentiation in allele frequencies of obesity-associated SNPs

Mao, Linyong; Fang, Yayin; Campbell, Michael; Southerland, William M.

doi:10.1186/s12864-017-4262-9

BMC Genomics

Table 2 Effect allele frequencies (EAF) of 39 obesity risk SNPs in continental groups

From: Population differentiation in allele frequencies of obesity-associated SNPs

SNP ID	chr	Position^a	function^b	Nearby / containing gene^b	Effect allele^c	Other allele^c	African EAF	American EAF	East Asian EAF	European EAF	South Asian EAF	Global EAF	GWAS p-value
rs1011731	1	172,346,548	intron	DNM3	G	A	0.90	0.36	0.13	0.42	0.43	0.48	1.0E-17
rs10146997	14	79,945,162	intron	NRXN3	G	A	0.41	0.20	0.00	0.21	0.11	0.20	5.0E-08
rs10150332	14	79,936,964	intron	NRXN3	C	T	0.44	0.20	0.00	0.21	0.11	0.21	3.0E-11
rs10182181	2	25,150,296	intergene	ADCY3 - DNAJC27	G	A	0.91	0.38	0.44	0.47	0.48	0.57	1.0E-17
rs10195252	2	165,513,091	intron	LOC101929615	T	C	0.20	0.74	0.90	0.56	0.79	0.60	2.0E-24
rs10261878	7	25,950,545	intergene	UBA52P1 - MIR148A	C	A	0.34	0.89	0.96	0.94	0.96	0.78	1.0E-10
rs1055144	7	25,871,109	ncRNA	LOC100506236	T	C	0.04	0.16	0.43	0.21	0.46	0.25	1.0E-24
rs10767664	11	27,725,986	intron	BDNF	A	T	0.95	0.83	0.51	0.77	0.70	0.76	5.0E-26
rs10838738	11	47,663,049	intron	MTCH2	G	A	0.05	0.40	0.28	0.35	0.33	0.26	5.0E-09
rs11030104	11	27,684,517	intron;intron	BDNF, BDNF-AS	A	G	0.98	0.83	0.51	0.78	0.74	0.78	2.0E-20
rs11847697	14	30,515,112	intergene	PRKD1 - RPS6P24	T	C	0.41	0.05	0.00	0.05	0.11	0.15	6.0E-11
rs12229654	12	111,414,461	intergene	MYL2 - CUX2	T	G	1.00	1.00	0.84	1.00	1.00	0.97	5.0E-09
rs1294421	6	6,743,149	intergene	LY86 - BTF3P7	G	T	0.77	0.50	0.26	0.61	0.40	0.53	2.0E-17
rs13034723	2	190,985,680	intron	C2orf88	A	G	0.06	0.45	0.69	0.46	0.70	0.45	2.0E-08
rs13389219	2	165,528,876	intergene	EIF3EP3 - COBLL1	C	T	0.20	0.74	0.90	0.56	0.78	0.60	3.0E-08
rs1443512	12	54,342,684	intergene	HOXC13 - HOXC12	A	C	0.64	0.21	0.17	0.22	0.32	0.34	6.0E-17
rs1555543	1	96,944,797	intergene	EEF1A1P11 - NDUFS5P2	C	A	0.39	0.57	0.88	0.58	0.51	0.58	4.0E-10
rs1957894	14	61,908,111	intron	PRKCH	T	G	0.77	0.13	0.41	0.08	0.11	0.34	3.0E-10
rs2030323	11	27,728,539	intron	BDNF	C	A	0.95	0.83	0.51	0.77	0.70	0.76	3.0E-22
rs2075064	9	126,783,847	intron	LHX2	C	T	0.93	0.54	0.58	0.56	0.65	0.68	2.0E-08
rs2307111	5	75,003,678	missense	POC5	T	C	0.08	0.52	0.47	0.60	0.40	0.38	3.0E-12
rs2568958	1	72,765,116	intergene	GDI2P2 - RPL31P12	A	G	0.53	0.70	0.93	0.64	0.62	0.68	4.0E-16
rs2815752	1	72,812,440	intergene	RPL31P12 - KRT8P21	A	G	0.53	0.70	0.93	0.64	0.62	0.68	2.0E-22
rs2890652	2	142,959,931	intergene	RPS16P3 - KYNU	C	T	0.38	0.09	0.00	0.17	0.06	0.16	1.0E-10
rs29941	19	34,309,532	intergene	KCTD15 - RPS4XP20	G	A	0.85	0.61	0.24	0.67	0.62	0.61	7.0E-12
rs3101336	1	72,751,185	intergene	GDI2P2 - RPL31P12	C	T	0.53	0.70	0.93	0.64	0.62	0.68	1.0E-13
rs3810291	19	47,569,003	3′-UTR	ZC3H4	A	G	0.09	0.51	0.27	0.66	0.40	0.36	2.0E-12
rs591166	18	57,841,589	intergene	RPS3AP49 - MC4R	A	T	0.82	0.38	0.22	0.43	0.49	0.50	7.0E-14
rs6265	11	27,679,916	missense;ncRNA	BDNF, BDNF-AS	C	T	0.99	0.85	0.51	0.80	0.80	0.80	5.0E-10
rs6545814	2	25,131,316	intron	ADCY3	G	A	0.85	0.35	0.42	0.43	0.46	0.54	1.0E-13
rs671	12	112,241,766	missense	ALDH2	G	A	1.00	1.00	0.83	1.00	1.00	0.96	3.0E-11
rs713586	2	25,158,008	intergene	ADCY3 - DNAJC27	C	T	0.92	0.38	0.48	0.47	0.48	0.58	6.0E-22
rs718314	12	26,453,283	intergene	SSPN - ITPR2	G	A	0.19	0.49	0.70	0.24	0.24	0.35	1.0E-17
rs7184597	16	28,921,809	intron	RABEP2	T	C	0.01	0.45	0.12	0.28	0.16	0.18	7.0E-09
rs7359397	16	28,885,659	downstream of SH2B1	SH2B1	T	C	0.01	0.47	0.12	0.33	0.19	0.19	2.0E-20
rs7531118	1	72,837,239	intergene	RPL31P12 - KRT8P21	C	T	0.05	0.38	0.26	0.55	0.29	0.29	2.0E-17
rs7586879	2	25,116,977	intron	ADCY3	T	C	0.86	0.29	0.37	0.35	0.43	0.50	4.0E-08
rs7708584	5	153,543,466	intergene	MFAP3 - GALNT10	A	G	0.26	0.63	0.96	0.44	0.47	0.53	5.0E-14
rs9356744	6	20,685,486	intron	CDKAL1	T	C	0.30	0.67	0.61	0.68	0.71	0.57	5.0E-13

^aThe variant coordinates were based on the human genome assembly GRCh37
^bAnnotations were obtained from the NHGRI-EBI GWAS Catalog
^cAll alleles were reported on the forward strand

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