Table 3

Loci associated with anthropometric traits in GCAT and UK Biobank cohorts

Loci*Chr:position†SNPCohortSingle-trait analysisMultitrait analysis
Weight (kg)Height (cm)BMI (kg/m2)Waist circumference (cm)Hip circumference (cm)P valuesGWAS Catalog‡
βSEP valuesβSEP valuesβSEP valuesβSEP valuesβSEP values
SF3B4, SV2A1:149892872rs11205277GCAT−0.0640.0930.490.550.12 9.1×10−6 0.290.270.270.20.240.40.20.190.290.00092Reported SNP
UK Biobank−0.00170.00240.470.0340.0017 1.1×10−85 0.0170.00214.3×10−16 0.0090.00223.3×10−5 0.0190.00245.1×10−15 3.8×10−53
GCAT-UK Biobank 1.5×10−53
ZRANB2-AS21:71702511rs115213730GCAT1.70.37 4.2×10−6 −0.770.490.123.81.1 0.00033 3.80.95 6.5×10−5 2.80.76 0.0002 1.6×10−8 New loci
UK Biobank0.0210.0068 0.0026 0.00440.00490.370.0190.006 0.0016 0.0170.0061 0.0063 0.0160.0068 0.017 0.00015
GCAT-UK Biobank 1.4×10−9
DPYD, DPYD-IT11:97884058rs140281723GCAT1.90.452×10−5 1.10.60.0716.51.34.3×10−7 5.61.21.1×10−6 3.80.934.7×10−5 8.6×10−11 No association
UK Biobank0.0110.00860.21−0.0150.00620.0120.00040.00760.960.0130.00770.10.00230.00860.790.035
GCAT-UK Biobank 1.9×10−9
PRELID1, RAB24, MXD35:176735612rs111251222GCAT0.060.120.620.780.16 1×10−6 0.840.34 0.014 0.330.310.280.130.250.590.0001Reported loci
UK Biobank−0.00840.00280.00240.0340.002 2.7×10−67 0.0120.0024 1.2×10−6 0.00840.00250.000630.00070.00280.83.5×10−35
GCAT-UK Biobank 2.2×10−36
LMAN2, AC146507.15:176772736rs4976686GCAT0.0490.10.630.710.131.5×10−7 0.790.290.00710.290.260.260.140.210.52.8×10−5 Reported loci
UK Biobank−0.00560.00260.0340.0280.00199.8×10−49 0.010.00238.6×10−6 0.00420.00230.0730.00210.00260.422.7×10−25
GCAT-UK Biobank 4.9×10−27
PIK3R15:67579576rs12657050GCAT−0.290.110.0083−0.330.150.022−10.320.0011−1.30.288.9×10−6 −0.590.230.0091.1×10−6 Unreported locus
UK Biobank−0.00430.00280.13−0.0140.0024.9×10−12 −0.0110.00257.7×10−6 −0.0090.00250.00035−0.00670.00280.0174.1×10−10
GCAT-UK Biobank 2.8×10−13
5:67604628rs695166GCAT−0.270.10.011−0.410.140.0029−1.10.30.00043−1.20.277.4×10−6 −0.690.210.00121.2×10−7
UK Biobank−0.00310.00270.24−0.0150.00192.3×10−14 −0.010.00241×10−5 −0.00830.00240.00051−0.00540.00270.0448.7×10−11
GCAT-UK Biobank 8.4×10−15
GMDS6:1944345rs62391629GCAT0.540.170.00170.520.230.02320.497.9×10−5 1.40.440.00221.70.352.9×10−6 4.9×10−8 Reported locus
UK Biobank0.0130.00510.00850.00850.00360.020.0160.00450.000450.0140.00450.00140.0170.00510.000686.4×10−6
GCAT-UK Biobank 2×10−10
ID4, AL022068.1, –6:19839415rs41271299GCAT−0.110.220.621.40.32×10−6 0.960.640.130.0810.580.890.350.460.450.00048Reported loci
UK Biobank−0.00320.00540.550.0940.00391.4×10−129 0.0490.00481.8×10−24 0.0270.00491.9×10−8 0.0410.00546.8×10−14 2.7×10−77
GCAT-UK Biobank 4.5×10−78
GRM4, HMGA16:34199092rs2780226GCAT0.0290.150.850.910.25.6×10−6 0.890.440.0420.140.390.730.340.310.280.00043Reported SNP
UK Biobank0.000640.00420.880.0670.0037.4×10−109 0.0370.00377.9×10−23 0.0330.00388.3×10–190.020.00422.7×10−6 1.6×10−68
GCAT-UK Biobank 2.7×10−69
HMGA1, SMIM29, AL354740.16:34214322rs1150781GCAT0.0290.150.850.90.29.8×10−6 0.860.440.0490.080.390.840.370.310.240.00059Reported SNP
UK Biobank0.00230.00420.590.0660.003 2.4×10−106 0.0370.00375.7×10−24 0.0340.00387.2×10−20 0.0210.00425.1×10−7 1×10−68
GCAT-UK Biobank 2.3×10−69
EPHA76:94075927rs143547391GCAT1.20.40.00191.70.530.00135.21.16×10−6 3.510.000632.80.820.000823.4×10−8 New locus
UK Biobank−0.0220.00880.014−0.010.00630.1−0.0250.00780.0014−0.0270.00790.00077−0.0270.00880.00253.3×10−5
GCAT-UK Biobank 6.5×10−10
AOC1, KCNH7:150599205rs10216051GCAT−0.440.0999.9×10−6 0.0890.130.5−10.280.00022−1.10.252.6×10−5 −0.840.23.5×10−5 9.5×10−9 R eported loci
UK Biobank0.00730.00250.00390.0120.00182.7×10−11 0.0120.00222.5×10−8 0.00820.00230.000290.00870.00250.000624.2×10−12
GCAT-UK Biobank 4.8×10−17
MAD1L1, –7:2068330rs62444886GCAT−0.760.183.9×10−5 −0.230.250.34−2.30.531.6×10−2.20.474×10−6 −1.60.383.6×10−5 1.9×10−9 Unreported locus
UK Biobank−0.0260.00527.3×10−7 0.00510.00370.17−0.0190.0046−5 4.7×10−5 −0.0210.00471×10−5 −0.0250.00522.5×10−6 9.9×10−10
GCAT-UK Biobank 2.3×10−15
FUBP39:133482006rs11792294GCAT−0.0750.0990.45−0.590.137.1×10−6 −0.690.290.016−0.0790.260.76−0.20.210.320.00029Reported locus
UK Biobank0.00210.00250.39−0.020.00182×10−29 −0.00920.00222.5×10−5 −0.00240.00220.27−0.00320.00250.25.5×10−16
GCAT-UK Biobank 6.3×10−17
CALCUL110:120465796rs12414412GCAT0.0540.170.7510.235.9×10−6 1.10.50.0290.150.440.730.450.350.20.00033Unreported locus
UK Biobank0.0220.00434.3×10−7 0.00740.00310.0170.0220.0386.4×10−9 0.0150.00396.6×10−5 0.0230.00431×10−7 3.7×10−12
GCAT-UK Biobank4×10−13
INS-IGF2, IGF2-AS, –11:2172830rs7948458GCAT−0.370.110.00044−0.420.140.0027−1.40.315.8×10−6 −0.910.270.00091−0.940.221.7×10−5 4.5×10−9 Reported loci
UK Biobank−0.0020.00310.5−0.0220.00224.2×10−24 -0.0140.00273.6×10−7 −0.00440.00270.1−0.0140.00315.8×10−6 2.3×10−16
GCAT-UK Biobank 1.5×10−21
MAP3K914:71268446rs7151024GCAT−0.490.116.3×10−6 0.340.140.017−10.310.0013−1.10.284.4×10−5 −0.930.223.1×10−5 5.7×10−9 New locus
UK Biobank−0.00970.00290.000730.00540.00210.0084−0.00510.00250.042−0.00650.00260.012−0.00580.00290.0440.00015
GCAT-UK Biobank 5.7×10−10
GABRG3-AS1, GABRG315:27398499rs184405367GCAT1.50.321.7×10−6 0.670.420.114.70.912.4×10−7 3.60.819.1×10−6 3.10.651.8×10−6 1.3×10−11 No association
UK Biobank−0.00270.0160.86−0.00150.0110.89−0.00410.0140.77−0.0050.0140.720.00240.0160.881
GCAT-UK Biobank3.5×10−9
SEMA6D15:47923520rs10220751GCAT−0.440.0932×10−6 0.210.120.086−10.270.00015−0.80.240.00086−0.590.190.00227.1×10−8 Reported locus
UK Biobank−0.0110.00242.7×10−6 0.00430.00180.014-0.00710.00220.001−0.00450.00220.039−0.0110.00241.1×10−5 1.6×10−7
GCAT-UK Biobank 8×10−12
GPRC5B-GPR13916:19988852rs9940317GCAT0.430.120.000330.420.160.00851.60.356.3×10−6 1.40.311.2×10−5 1.20.252.7×10−6 3.7×10−10 Reported loci
UK Biobank0.0120.00293.8×10−5 0.00680.00210.000960.0130.00251.4×10−7 0.00790.00260.00220.0110.00290.000123×10−9
GCAT-UK Biobank 1.6×10−15
GPR13916:20046115rs2045457GCAT0.380.10.000160.240.130.0691.30.291.4×10−5 1.20.263.3×10−6 0.930.218.6×10−6 9×10−10 Reported locus
UK Biobank0.0130.00267.6×10−7 0.00570.00190.00240.0140.00232×10−9 0.00680.00230.00380.0110.00265.4×10−5 1.1×10−10
GCAT-UK Biobank 1.4×10−16
ECI1, AC009065.816:2296197rs77407216GCAT−0.390.130.0036−0.70.189.6×10−5 −1.70.396.9×10−6 −0.820.350.018−0.970.280.000535.4×10−8 Reported loci
UK Biobank−0.00210.00350.55−0.0160.00254.4×10−10 −0.010.00310.0011−0.00760.00310.016−0.00680.00310.0513.1×10−7
GCAT-UK Biobank 1.2×10−11
ATAD5, AC130324.217:29165934rs9890032GCAT−0.0980.0950.3−0.610.131.4×10−6 −0.830.270.0023−0.490.240.044−0.410.20.0357×10−6 Reported SNP
UK Biobank– 6.7 × 10−5 0.00250.98−0.0320.00181.8×10−71 -0.0170.00221.6×10−15 −0.0110.00222.2×10−6 −0.0130.00253.8×10−7 1.4×10−43
GCAT-UK Biobank 8.2×10−46
TBX217:59498052rs7214743GCAT0.0840.0950.370.660.132×10−7 0.820.270.00280.430.240.0820.470.20.0163×10−6 Reported locus
UK Biobank−0.00930.00260.000270.0340.00181.3×10−78 0.0110.00233.8×10−7 0.00640.00230.00530.000260.00260.921.9×10−40
GCAT-UK Biobank 5.1×10−43
CABLES118:20758310rs34302357GCAT0.220.120.071−0.750.162.9×10−6 −0.130.350.70.210.310.49−0.0370.250.880.00048Reported locus
UK Biobank−0.00240.00310.43−0.0420.00223.3×10−80 −0.0240.00273.8×10−19 −0.0180.00282.7×10−10 −0.0170.00313.7×10−8 2.9×10−51
GCAT-UK Biobank 6.4×10−52
RIOK3, Y RNA18:21039393rs9954741GCAT0.20.10.05−0.60.148.7×10−6 −0.0250.290.930.140.260.58−0.0320.210.880.00076Reported loci
UK Biobank−0.010.00257.1×10−5 −0.0130.00181.1×10−13 −0.0160.00222.2×10−12 −0.0150.00231.1×10−11 −0.0140.00252.8×10−8 8.9×10−21
GCAT-UK Biobank 2.7×10−21
ADAMTS1019:8670147rs62621197GCAT0.480.190.011−1.20.252.3×10−6 0.290.550.590.370.490.450.20.390.610.00016Reported locus
UK Biobank0.0140.00670.036−0.110.00485.4×10−121 −0.050.00592.6×10−17 −0.0360.0062.4×10−9 −0.0420.00674×10−10 1.9×10−69
GCAT-UK Biobank 1.3×10−70
GDF5, GDF5OS20:34025756rs143384GCAT0.0720.0940.450.590.132.7×10−6 0.740.270.00650.310.240.210.550.190.00521.4×10−5 Reported SNP
UK Biobank−0.00140.00240.580.0640.00188.8×10−292 0.0330.00221.9×10−53 0.00710.00220.00130.0280.00241.6×10−30 8.3×10−168
GCAT-UK Biobank 1.3×10−170
HORMAN, LIF22:30610546rs9608851GCAT0.450.0952×10−6 −0.0290.130.02210.270.000270.820.240.000860.660.20.00075 3.2×10−8 Reported loci
UK Biobank0.0050.00240.0380.00620.00170.000370.00770.00210.000320.00580.00220.0070.00540.00240.0251.7×10−5
GCAT-UK Biobank 3.3×10−10

  • *Loci, a locus was considered as the ±250 000 base pair window flanking the identified SNP.

  • †Chr:position, coordinates on hg19.

  • ‡GWAS Catalog traits, data from GWAS Catalog database (release V.1.0, e90, 27 September 2017).

  • Single-trait and multi trait results are presented. Concordant significant results are marked in violet

  • BMI, body mass index; GWAS, genome-wide association studies.