S5 Table.

Discovery, replication and meta-analysis results for 32 SNPs meeting P<10-5 in discovery association resul
SC
rsID Nearest gene Chr. Position (bp) EA NEA OR (95% CI)
rs9930333 FTO 16 53799977 G T 1.70(1.52,1.90)
rs2168711 MC4R 18 57848531 C T 1.66(1.45,1.89)
rs6748821 TMEM18 2 629601 G A 1.65(1.42,1.91)
rs506589 SEC16B 1 177894287 C T 1.46(1.27,1.67)
rs6738433 ADCY3-DNAJC27 2 25159501 C G 1.43(1.28,1.60)
rs7132908 FAIM2 12 50263148 A G 1.31(1.17,1.47)
rs62107261 FAM150B 2 422144 T C 2.37(1.75,3.20)
rs12507026 GNPDA2 4 45181334 T A 1.30(1.17,1.46)
rs75398113 SNRPC 6 34728071 C G 1.53(1.27,1.85)
rs13135092 SLC39A8 4 103198082 G A 1.58(1.30,1.93)
rs57988840 TFAP2B 6 50817748 T A 1.69(1.39,2.05)
rs4447506 PIK3C3 18 39510074 G A 1.32(1.17,1.48)
rs375252497* SEMA3B 3 50310286 AAATAATAATAAT A 1.35(1.20,1.53)
rs7927262 HIPK3 11 33384447 C T 1.41(1.24,1.60)
rs654240 CCND1 11 69448373 T C 1.35(1.21,1.52)
rs35403928* PRDM6 5 122416569 GT G 1.39(1.23,1.56)
rs516579 MTCL1 18 8801634 G T 1.40(1.22,1.61)
rs397859802* FLJ26850 19 50556007 C CA 1.92(1.45,2.53)
rs2784243 PKHD1 6 51454640 T C 1.30(1.16,1.45)
rs11792928 LMX1B 9 129401550 T C 1.36(1.20,1.53)
rs6711131* BAZ2B 2 160407777 A G 1.31(1.17,1.47)
rs73145387 ABI3BP 3 100813661 C G 2.48(1.67,3.69)
rs599291 SLC44A5 1 75691616 T C 1.31(1.17,1.47)
rs11185396 LOC100129138 1 104754536 C T 1.50(1.26,1.80)
rs2836760 LOC400867 21 40300052 T G 1.65(1.33,2.03)
rs11159277 SPTLC2 14 78032957 A T 1.35(1.20,1.53)
rs10546790 CDH22 20 44910100 C CAT 1.34(1.19,1.52)
rs11319985* CNTN6 3 1377810 T TA 1.29(1.15,1.45)
rs4790399 RAP1GAP2 17 2883199 C T 1.33(1.18,1.51)
rs536093 PDE10A 6 165945641 T C 1.38(1.22,1.58)
rs936249 CACNA1B 9 140971315 T C 2.41(1.66,3.49)
rs1692144 GJA5 1 147281349 C T 1.37(1.19,1.57)

*Interim release used in UKBB for these signals. Nobese=2,799. Nthin=1,212

EA= Effect allele (BMI increasing allele); NEA= Non-effect allele; OR = Odds ratio; 95% CI = 95% confidence interval for the odd
Positions mapped to hg19
Blue line: Conventional genome-wide significant threshold (p<5E-08) in combined analysis.
scovery association results of SCOOP vs STILTS analysis.
SCOOP UKBB
P value EAF Obese EAF Thin proxy rsID OR (95% CI) P value
2.30E-20 49.59% 37.46% 1.46(1.38,1.55) 3.60E-36
8.29E-14 28.90% 19.95% 1.23(1.15,1.32) 2.19E-09
9.45E-11 86.69% 79.84% 1.27(1.18,1.37) 1.31E-09
5.42E-08 23.98% 18.07% 1.25(1.17,1.35) 5.44E-10
1.71E-10 47.31% 43.92% 1.21(1.14,1.28) 2.74E-10
2.26E-06 42.45% 36.27% 1.18(1.11,1.25) 5.43E-08
2.07E-08 96.37% 93.38% 1.54(1.35,1.76) 3.57E-10
3.69E-06 47.29% 40.92% 1.14(1.08,1.21) 8.76E-06
8.91E-06 11.95% 8.04% 1.24(1.12,1.37) 2.07E-05
4.70E-06 10.50% 7.24% 1.25(1.12,1.39) 5.57E-05
1.27E-07 92.53% 88.81% 1.13(1.02,1.24) 1.65E-02
4.21E-06 41.83% 36.39% 1.07(1.01,1.14) 2.60E-02
1.74E-06 37.22% 31.78% 1.13(1.02,1.26) 2.50E-02
1.81E-07 41.78% 35.78% 1.08(0.89,1.32) 4.43E-01
2.99E-07 43.85% 37.39% 1.05(0.99,1.12) 9.25E-02
6.79E-08 39.85% 32.94% 1.05(0.95,1.16) 3.61E-01
2.07E-06 82.14% 77.25% 1.03(0.96,1.11) 4.52E-01
4.49E-06 6.02% 3.44% 1.11(0.86,1.44) 4.28E-01
5.99E-06 61.89% 56.06% 1.07(1.01,1.13) 2.90E-02
1.32E-06 32.13% 26.91% 1.05(0.99,1.12) 1.17E-01
4.30E-06 65.12% 58.62% 1.02(0.92,1.13) 6.81E-01
7.36E-06 98.00% 96.42% 1.15(0.96,1.37) 1.29E-01
2.35E-06 47.71% 41.63% 1.02(0.96,1.08) 4.95E-01
8.13E-06 12.78% 9.21% 1.06(0.97,1.17) 2.13E-01
3.28E-06 10.33% 7.12% 1.03(0.93,1.14) 5.92E-01
1.56E-06 71.04% 66.32% 1.01(0.95,1.08) 6.53E-01
1.91E-06 72.94% 66.87% rs2425853 1.03(0.97,1.10) 3.42E-01
9.85E-06 61.56% 56.63% 0.97(0.88,1.07) 5.75E-01
6.95E-06 74.28% 69.50% 1.02(0.96,1.09) 5.43E-01
1.01E-06 27.05% 21.65% 0.97(0.90,1.03) 3.17E-01
3.81E-06 6.31% 4.63% 1.01(0.88,1.15) 9.30E-01
8.19E-06 81.52% 77.06% 1.04(0.97,1.12) 2.90E-01

fidence interval for the odds ratio; EAF = effect allele frequency. HetPVal= Heterozygosity p-value
UKBB GIANT BMI Tails
EAF Obese EAF Thin proxy rsID r2 OR (95% CI) P value
48.26% 38.93% 1.43(1.34,1.54) 8.10E-25
26.75% 22.90% 1.20(1.10,1.30) 1.80E-05
85.00% 81.69% rs12995480 0.998 1.26(1.14,1.39) 9.90E-06
23.11% 19.16% 1.25(1.14,1.37) 2.70E-06
50.70% 45.96% rs2384054 0.968 1.10(1.03,1.17) 5.70E-03
41.11% 37.39% 1.20(1.10,1.30) 6.60E-06
96.28% 94.36% NA NA NA NA
45.30% 41.98% rs12641981 0.998 1.20(1.12,1.28) 3.10E-07
10.47% 8.52% NA NA NA NA
9.24% 7.52% NA NA NA NA
91.05% 90.04% rs7769978 1 1.20(1.03,1.39) 1.90E-02
39.34% 37.71% 1.10(1.02,1.18) 7.80E-03
34.30% 31.95% NA NA NA NA
97.52% 97.37% NA NA NA NA
41.43% 40.23% 1.08(1.00,1.16) 5.30E-02
37.64% 36.49% NA NA NA NA
80.35% 80.05% rs518561 0.998 1.15(1.04,1.27) 6.40E-03
4.25% 3.78% NA NA NA NA
58.99% 57.34% rs2784187 0.988 1.02(0.95,1.10) 5.40E-01
29.94% 29.01% 1.03(0.95,1.11) 5.00E-01
63.33% 63.04% NA NA NA NA
97.55% 97.19% NA NA NA NA
44.55% 44.01% 1.04(0.97,1.11) 2.20E-01
10.37% 9.65% 1.01(0.89,1.14) 9.20E-01
9.14% 8.91% 1.07(0.93,1.23) 3.50E-01
68.83% 68.55% NA NA NA NA
70.11% 69.59% rs2425853 0.998 1.00(0.93,1.08) 9.90E-01
57.91% 58.39% NA NA NA NA
71.22% 70.85% 0.99(0.91,1.08) 8.30E-01
24.39% 25.03% 1.06(0.97,1.15) 2.00E-01
4.78% 4.77% NA NA NA NA
79.54% 79.06% 0.92(0.84,1.01) 7.00E-02
 Combined analysis
OR (95% CI) P value HetPVal
1.48(1.42,1.54) 8.52E-76 3.34E-02
1.27(1.21,1.33) 2.02E-21 1.12E-04
1.32(1.24,1.39) 7.76E-21 2.81E-03
1.28(1.21,1.35) 3.14E-20 1.21E-01
1.19(1.14,1.24) 3.19E-17 6.25E-03
1.20(1.15,1.26) 1.93E-16 2.52E-01
1.65(1.46,1.87) 1.15E-15 1.07E-02
1.18(1.13,1.23) 5.53E-15 4.06E-02
1.30(1.19,1.42) 5.19E-09 5.56E-02
1.32(1.20,1.45) 1.06E-08 3.59E-02
1.22(1.13,1.31) 3.86E-07 2.87E-04
1.11(1.06,1.16) 1.46E-06 7.85E-03
1.22(1.13,1.32) 1.49E-06 3.05E-02
1.31(1.17,1.45) 1.58E-06 2.87E-02
1.10(1.05,1.15) 2.10E-05 6.81E-04
1.18(1.09,1.28) 2.46E-05 4.77E-04
1.11(1.05,1.18) 9.70E-05 1.11E-04
1.43(1.18,1.73) 2.12E-04 4.77E-03
1.08(1.04,1.13) 3.14E-04 2.55E-03
1.08(1.03,1.13) 8.05E-04 5.19E-04
1.14(1.05,1.23) 8.90E-04 1.33E-03
1.31(1.11,1.54) 1.29E-03 5.19E-04
1.06(1.02,1.11) 3.44E-03 4.01E-04
1.10(1.03,1.18) 6.95E-03 8.13E-04
1.11(1.03,1.20) 9.44E-03 3.30E-04
1.08(1.02,1.14) 9.74E-03 4.58E-05
1.06(1.01,1.11) 1.35E-02 1.57E-04
1.10(1.02,1.18) 1.38E-02 2.03E-04
1.05(1.00,1.10) 4.40E-02 2.50E-04
1.05(1.00,1.10) 6.84E-02 9.29E-06
1.11(0.98,1.27) 9.53E-02 1.62E-05
1.04(0.99,1.10) 1.29E-01 1.68E-05