Table S1. List of obesity genetic loci included in the analysis

Locus / Chromosome / Index SNP / Discovery Population / Alleles / Hit/proxya / GWAS HIT / R2Discoveryb / R2Mexicansc / Reference
FTO / 16 / rs1121980 / EUR / A/G / Hit / NA / NA / Hinney et al. PLoS ONE 2007.
MC4R / 18 / rs2168708 / EUR / T/G / Proxy / rs12970134 / 0.995 / 1.000 / Thorleifsson et al. Nat. Genet. 2009.
MC4R / 18 / rs17066842 / EUR / G/A / Hit / NA / NA / Locke et al. Nature 2015.
TMEM18 / 2 / rs7561317 / EUR / G/A / Hit / NA / NA / Thorleifssonet al. Nat. Genet. 2009.
GNPDA2 / 4 / rs10938397 / EUR / G/A / Hit / NA / NA / Felix et al. Hum. Mol. Gen. 2016.
SH2B1 / 16 / rs12443881 / EUR / T/C / Proxy / rs7498665 / 0.996 / 1.000 / Thorleifssonet al. Nat. Genet. 2009.
KCTD15 / 19 / rs29937 / EUR / T/G / Proxy / rs29941 / 0.952 / 0.905 / Locke et al. Nature 2015.
MTCH2 / 11 / rs59360790 / EUR / C/T / Proxy / rs3817334 / 0.972 / 1.000 / Locke et al. Nature 2015.
NEGR1 / 1 / rs61765651 / EUR / C/T / Proxy / rs1993709 / 0.960 / 1.000 / Wheeler et al. Nat. Genet. 2013.
SEC16B / 1 / rs591120 / EUR / C/G / Hit / NA / NA / Graff et al. Hum. Mol. Gen. 2013.
ETV5 / 3 / rs73052046 / EUR / C/T / Proxy / rs9816226 / 0.993 / 1.000 / Berndt et al. Nat. Genet. 2013.
BDNF / 11 / rs7103411 / EUR / T/C / Proxy / rs6265 / 0.779 / 1.000 / Thorleifssonet al. Nat. Genet. 2009.
FAIM2 / 12 / rs7138803 / EUR / A/G / Hit / NA / NA / Locke et al. Nature 2015.
TFAP2B / 6 / rs2206277 / EUR / T/C / Proxy / rs987237 / 0.993 / 1.000 / Felix et al. Hum. Mol. Gen. 2016.
NRXN3 / 14 / rs10146997 / EUR / G/A / Proxy / rs10150332 / 0.994 / 0.946 / Spelioteset al. Nat. Genet. 2010.
GPRC5B / 16 / rs12444979 / EUR / C/T / Hit / NA / NA / Spelioteset al. Nat. Genet. 2010.
ADCY3 / 2 / rs13410999 / EAS / C/T / Proxy / rs6545814 / 0.936 / 0.818 / Wen et al. Hum. Mol. Gen. 2014.
MAP2K5 / 15 / rs35395156 / EUR / G/A / Proxy / rs997295 / 1.000 / 1.000 / Guoet al. Hum. Mol. Gen. 2013.
GIPR / 19 / rs34783010 / EUR / G/T / Proxy / rs1800437 / 1.000 / 1.000 / Berndt et al. Nat. Genet. 2013.
FANCL / 2 / rs4671328 / EUR / T/G / Hit / NA / NA / Locke et al. Nature 2015.
FANCL / 2 / rs887912 / EUR / T/C / Hit / NA / NA / Berndt et al. Nat. Genet. 2013.
TNNI3K / 1 / rs1514175 / EUR / A/G / Hit / NA / NA / Graff et al. Hum. Mol. Gen. 2013.
LRRN6C / 9 / rs10968576 / EUR / G/A / Hit / NA / NA / Locke et al. Nature 2015.
FLJ35779 / 5 / rs16872768 / EUR / T/C / Proxy / rs2112347 / 0.958 / 0.931 / Locke et al. Nature 2015.
SLC39A8 / 4 / rs13107325 / EUR / T/C / Hit / NA / NA / Felix et al. Hum. Mol. Gen. 2016.
TMEM160 / 19 / rs28590228 / EUR / T/C / Proxy / rs3810291 / 0.947 / 0.969 / Locke et al. Nature 2015.
CADM2 / 3 / rs11926524 / EUR / A/G / Proxy / rs13078807 / 0.994 / 0.909 / Berndt et al. Nat. Genet. 2013.
LRP1B / 2 / rs2890652 / EUR / C/T / Hit / NA / NA / Spelioteset al. Nat. Genet. 2010.
PRKD1 / 14 / rs11847697 / EUR / T/C / Hit / NA / NA / Locke et al. Nature 2015.
MTIF3 / 13 / rs4771122 / EUR / G/A / Hit / NA / NA / Spelioteset al. Nat. Genet. 2010.
PTBP2 / 1 / rs1973993 / EUR / C/T / Proxy / rs1555543 / 0.980 / 1.000 / Spelioteset al. Nat. Genet. 2010.
TUB / 11 / rs10769922 / EUR / A/G / Proxy / rs4929949 / 0.927 / 1.000 / Spelioteset al. Nat. Genet. 2010.
HMGA1 / 6 / rs206936 / EUR / G/A / Hit / NA / NA / Spelioteset al. Nat. Genet. 2010.
CDKAL1 / 6 / rs9368222 / EAS / C/A / Proxy / rs9356744 / 1.000 / 0.687 / Wen et al. Hum. Mol. Gen. 2014.
PCSK1 / 5 / rs1837269 / EAS / C/T / Proxy / rs261967 / 0.953 / 0.908 / Wen et al. Hum. Mol. Gen. 2014.
PCSK1 / 5 / rs6232 / EAS / C/T / Hit / NA / NA / Wen et al. Hum. Mol. Gen. 2014.
PCSK1 / 5 / rs59139497 / EUR / A/G / Proxy / rs6235 / 0.904 / 1.000 / Benzinouet al. Nat. Genet. 2008.
GP2 / 16 / rs8045740 / EUR / G/T / Proxy / rs11074446 / 1.000 / 1.000 / Locke et al. Nature 2015.
KLF9 / 9 / rs10780928 / EAS / A/G / Proxy / rs11142387 / 0.929 / 0.909 / Wen et al. Hum. Mol. Gen. 2014.
TOMM40 / 19 / rs2075650 / EUR / A/G / Hit / NA / NA / Locke et al. Nature 2015.
NTRK2 / 9 / rs1147199 / EUR / G/A / Proxy / rs1211166 / 0.967 / 0.899 / Guoet al. Hum. Mol. Gen. 2013.
GALNT10 / 5 / rs2099044 / AFR / T/C / Proxy / rs7708584 / 0.988 / 1.000 / Mondaet al. Nat. Genet. 2013.
KCNQ1 / 11 / rs2283228 / EAS / C/A / Proxy / rs2237892 / 0.835 / 0.960 / Wen et al. Hum. Mol. Gen. 2014.
ITIH4 / 3 / rs12487379 / EAS / A/G / Proxy / rs2535633 / 0.849 / 0.965 / Wen et al. Hum. Mol. Gen. 2014.
KCNK9 / 8 / rs2468680 / EUR / G/A / Proxy / rs2471083 / 0.995 / 0.803 / Hoggartet al. PLoS Genet. 2014.
SLC2A10 / 20 / rs3092206 / EUR / A/G / Proxy / rs3091869 / 1.000 / 1.000 / Hoggartet al. PLoS Genet. 2014.
AGBL4 / 1 / rs1925424 / EUR / T/C / Proxy / rs657452 / 0.835 / 0.939 / Locke et al. Nature 2015.
C9orf93 / 9 / rs10738405 / EUR / T/C / Proxy / rs4740619 / 0.965 / 1.000 / Locke et al. Nature 2015.
CALCR / 7 / rs1548457 / EUR / C/T / Proxy / rs9641123 / 0.940 / 0.958 / Locke et al. Nature 2015.
CBLN1 / 16 / rs1558760 / EUR / T/C / Proxy / rs2080454 / 0.906 / 0.346 / Locke et al. Nature 2015.
EPB41L4B / 9 / rs6477694 / EUR / C/T / Hit / NA / NA / Locke et al. Nature 2015.
ETS2 / 21 / rs2836755 / EUR / T/C / Proxy / rs2836754 / 1.000 / 1.000 / Locke et al. Nature 2015.
FHIT / 3 / rs815710 / EUR / A/G / Proxy / rs2365389 / 0.931 / 0.965 / Locke et al. Nature 2015.
FIGN / 2 / rs10192119 / EUR / G/T / Proxy / rs1460676 / 0.986 / 0.644 / Locke et al. Nature 2015.
FOXO3 / 6 / rs9398171 / EUR / T/C / Proxy / rs9400239 / 0.929 / 1.000 / Locke et al. Nature 2015.
GBE1 / 3 / rs3755713 / EUR / G/A / Proxy / rs3849570 / 0.921 / 0.718 / Locke et al. Nature 2015.
PGPEP1 / 19 / rs12459368 / EUR / A/G / Proxy / rs17724992 / 0.995 / 0.910 / Locke et al. Nature 2015.
GRID1 / 10 / rs73341071 / EUR / A/C / Proxy / rs7899106 / 1.000 / 1.000 / Locke et al. Nature 2015.
GRP / 18 / rs1517035 / EUR / A/G / Proxy / rs7243357 / 0.802 / 0.913 / Locke et al. Nature 2015.
HHIP / 4 / rs11727676 / EUR / Hit / NA / NA / Locke et al. Nature 2015.
HIP1 / 7 / rs17207196 / EUR / C/T / Proxy / rs1167827 / 0.915 / 0.812 / Locke et al. Nature 2015.
HSD17B12 / 11 / rs2176598 / EUR / T/C / Hit / NA / NA / Locke et al. Nature 2015.
IFNGR1 / 6 / rs72981422 / EUR / T/G / Proxy / rs13201877 / 0.904 / 0.925 / Locke et al. Nature 2015.
KAT8 / 16 / rs1549293 / EUR / C/T / Proxy / rs9925964 / 1.000 / 1.000 / Locke et al. Nature 2015.
LMX1B / 9 / rs3829849 / EUR / T/C / Hit / NA / NA / Felix et al. Hum. Mol. Gen. 2016.
LOC285762 / 6 / rs17636630 / EUR / A/G / Proxy / rs9374842 / 0.990 / 0.944 / Locke et al. Nature 2015.
INO80E / 16 / rs4238959 / EUR / G/A / Proxy / rs4787491 / 0.753 / 0.908 / Locke et al. Nature 2015.
MIR548X2 / 13 / rs9540493 / EUR / A/G / Hit / NA / NA / Locke et al. Nature 2015.
NAV1 / 1 / rs2820292 / EUR / C/A / Hit / NA / NA / Locke et al. Nature 2015.
NT5C2 / 10 / rs11191531 / EUR / C/G / Proxy / rs11191560 / 0.988 / 1.000 / Locke et al. Nature 2015.
PARK2 / 6 / rs68144677 / EUR / T/C / Proxy / rs13191362 / 0.947 / 1.000 / Locke et al. Nature 2015.
USP37 / 2 / rs600057 / EUR / A/G / Proxy / rs492400 / 0.988 / 0.968 / Locke et al. Nature 2015.
PMS2L11 / 7 / rs4307272 / EUR / C/T / Proxy / rs2245368 / 0.988 / 0.969 / Locke et al. Nature 2015.
RABEP1 / 17 / rs3026101 / EUR / C/T / Proxy / rs1000940 / 0.987 / 1.000 / Locke et al. Nature 2015.
RALYL / 8 / rs7815593 / EUR / T/A / Proxy / rs2033732 / 0.897 / 0.939 / Locke et al. Nature 2015.
RASA2 / 3 / rs77586571 / EUR / T/C / Proxy / rs16851483 / 0.984 / 0.782 / Locke et al. Nature 2015.
TAL1 / 1 / rs1015890 / EUR / G/A / Proxy / rs977747 / 0.959 / 0.908 / Locke et al. Nature 2015.
TCF7L2 / 10 / rs7903146 / EUR / C/T / Hit / NA / NA / Locke et al. Nature 2015.
UBE2E3 / 2 / rs2887185 / EUR / A/C / Proxy / rs1528435 / 0.992 / 1.000 / Locke et al. Nature 2015.
AKAP6 / 14 / rs12896446 / EUR / G/T / Proxy / rs12885467 / 0.942 / 1.000 / Horikoshiet al. PLoS Genet. 2015.
CBLN4 / 20 / rs73281101 / EUR / A/G / Proxy / rs11908421 / 0.927 / 0.842 / Winkler et al. PLoS Genet. 2015.
DDC / 7 / rs4947644 / EUR / T/C / Hit / NA / NA / Winkler et al. PLoS Genet. 2015.
OLFM4 / 13 / rs1927861 / EUR / T/C / Proxy / rs12429545 / 0.980 / 1.000 / Felix et al. Hum. Mol. Gen. 2016.
ELP3 / 8 / rs7821358 / EUR / A/G / Proxy / rs13253111 / 0.996 / 1.000 / Felix et al. Hum. Mol. Gen. 2016.
RAB27B / 18 / rs12970682 / EUR / A/G / Proxy / rs8092503 / 0.994 / 1.000 / Felix et al. Hum. Mol. Gen. 2016.
MAF / 16 / rs1424233 / EUR / T/C / Hit / NA / NA / Meyreet al. Nat. Genet. 2009.
SDCCAG8 / 1 / rs61833916 / EUR / C/T / Proxy / rs12145833 / 0.973 / 1.000 / Scheraget al. PLoS Genet. 2010.
KCNMA1 / 10 / rs11001919 / EUR / G/A / Proxy / rs2116830 / 0.987 / 0.920 / Jiao et al. BMC Med Genomics 2011.
HS6ST3 / 13 / rs9556582 / EUR / A/G / Proxy / rs7989336 / 0.946 / 0.934 / Berndt et al. Nat. Genet. 2013.
MRPS33P4 / 20 / rs6126579 / EUR / G/A / Proxy / rs13041126 / 1.000 / 1.000 / Berndt et al. Nat. Genet. 2013.
RPTOR / 17 / rs12940622 / EUR / G/A / Proxy / rs7503807 / 0.976 / 0.932 / Berndt et al. Nat. Genet. 2013.
ADCY9 / 16 / rs2531995 / EUR / T/C / Hit / NA / NA / Berndt et al. Nat. Genet. 2013.
PRKCH / 14 / rs4899048 / EUR / A/G / Proxy / rs1957894 / 1.000 / 1.000 / Wheeler et al. Nat. Genet. 2013.
LEPR / 1 / rs10889560 / EUR / A/C / Proxy / rs11208659 / 0.974 / 0.791 / Wheeler et al. Nat. Genet. 2013.
PACS1 / 11 / rs537497 / EUR / G/A / Proxy / rs564343 / 1.000 / 1.000 / Wheeler et al. Nat. Genet. 2013.
RMST / 12 / rs7963407 / EUR / C/T / Proxy / rs11109072 / 0.767 / 1.000 / Wheeler et al. Nat. Genet. 2013.
LPIN2 / 18 / rs680813 / EUR / C/T / Proxy / rs643507 / 0.811 / 1.000 / Melen et al. Clin. Exp. Allergy 2013.
CREBRF / 5 / rs12513649 / EUR / G/C / Hit / NA / NA / Minster et al. Nat. Genet. 2016.

Abbreviations: EUR, Europeans; EAS, East Asians; AFR, Africans.

aHit/Proxy: Indicates whether the index SNP used in the final analysis was a GWAS hit or a proxy to a GWAS hit.

bRsquared discovery: the R2 value between the index SNP and the GWAS hit within the ethnicity of the discovery population (EAS, EUR, or AFR) in 1000G

cRsquared discovery: the R2 value between the index SNP and the GWAS hit within the MXL population in 1000G