Table 2.

Association results of BMIz with EUR tag SNPs compared to population-specific tag SNPs selected from the 1 MB interval of these known obesity loci in SLS. CHR – chromosome; SNP – single nucleotide polymorphism; EA – effect allele; OA – other allele; EAF - effect allele frequency; β – beta coefficient; SE – standard error, P – P-value; R2 – linkage disequilibrium (LD) for SNPs; D’ – D prime; Chile – LD between SNPs within SLS cohort; CEU – LD between SNPs in European descent population

Nearest Gene	CHR	EUR Tag SNPs			R2		D’	Population-Specific Tag SNPs							Conditional Analyses#
		SNP/Proxy	Included in GRS	Distance	SLS	CEU	CEU	SNP	Included in GRS	EA/OA	EAF	β	SE	P	β	SE	P
TNNI3K	1	rs12041852	EUR, ALL	−174105	0.008	0.042	1	rs61790698	SLS, ALL	G/A	0.047	0.239	0.109	0.029	0.237	0.110	0.032
GPR61	1	rs7550711	EUR, ALL	−348505	0.001	0.001	1	rs11102023	SLS, ALL	A/C	0.989	0.635	0.248	0.010	0.640	0.248	0.010
SEC16B	1	rs543874	EUR	−58402	0.122	-	-	rs200787218	SLS, ALL	A/C	0.328	0.198	0.051	1.1E-04	0.155	0.054	0.004
ADCY3	2	rs11676272	EUR	467182	0.037	-	-	rs138716876	SLS, ALL	T/G	0.817	0.178	0.059	0.003	0.157	0.061	0.010
GNPDA2	4	rs13130484	EUR, ALL	384441	0.004	0.029	1	rs75426894	SLS, ALL	T/C	0.976	0.388	0.153	0.012	0.374	0.153	0.015
TFAP2B	6	rs987237	EUR, ALL	−398207	0.051	0.001	0.079	rs2709670	SLS, ALL	T/G	0.223	0.218	0.055	9.4E-05	0.245	0.056	1.5E-05
FAIM2	12	rs7132908	EUR, ALL	−27580	0.004	0.022	0.298	rs297935	SLS, ALL	G/A	0.789	0.174	0.056	0.002	0.172	0.056	0.002
OLFM4	13	rs12429545	EUR, ALL	28422	0.160	0.131	1	rs1072900	SLS, ALL	C/A	0.498	0.180	0.046	1.1E-04	0.169	0.051	9.8E-04
FTO	16	rs1421085	EUR, ALL	3771	0.002	0.052	1	rs62048379	SLS, ALL	A/C	0.060	0.314	0.095	9.9E-04	0.306	0.095	1.3E-03
MC4R	18	rs6567160	EUR, ALL	339892	0.003	0.042	0.278	rs62092638	SLS, ALL	C/T	0.173	0.184	0.062	0.003	0.186	0.062	0.003
TMEM18	2	rs4854349/	EUR, ALL	−203384	0.007	0.001	0.072	rs11682609	SLS, ALL	A/C	0.959	0.323	0.128	0.012	0.314	0.128	0.014
		rs4854348*
ELP3	8	rs13253111/	EUR, ALL	175550	0.014	0.049	0.268	rs10097488	SLS, ALL	C/T	0.741	0.154	0.054	0.005	0.150	0.055	0.006
		rs7821358*
LMX1B	9	rs3829849/	EUR, ALL	−72782	0.009	0.024	0.329	rs10987410	SLS, ALL	C/T	0.068	0.267	0.095	0.005	0.258	0.095	0.007
		rs62578126*
RAB27B	18	rs8092503/	EUR, ALL	−276712	0.001	0.005	0.115	rs12961347	SLS, ALL	T/C	0.535	0.159	0.046	4.9E-04	0.160	0.046	4.9E-04
		rs8085272*
ADAM23	2	rs13387838/		217117	-	-	-	rs77068085	SLS, ALL	T/C	0.957	0.331	0.115	0.004	-	-	-
		No Proxy

^*- LD (R2) between Tag and Proxy SNPs ranged from 0.94 to 1.0.

^#Conditional analyses results from PLINK, the beta coefficients for the Population-Specific Tag SNPs still remained significant after entering the model with covariates pc1 to pc5 and corresponding EUR Tag SNP for each locus. These results suggest that Population-Specific Tag SNPs indeed have an effect independent of EUR Tag SNP and other covariates