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. Author manuscript; available in PMC: 2012 Jan 20.
Published in final edited form as: Nat Genet. 2011 Jun 26;43(8):753–760. doi: 10.1038/ng.866

Table 1.

Stage 1 and stage 2 results of the SNPs near the IRS1, near the SPRY2 and in the FTO gene that were associated with body fat percentage at genome-wide significant (P < 5 × 10−8) levels

Per allele
change in
body fat %
βa 		Stage 1 Stage 2 Stage 1+2
Locus Meta-analysis Frequency
effect allele		 Explained
variance (%)		 N P N P N P
rs2943650 (near IRS1)
Chr2: 226,814,165 bp
Effect allele: T		 All individuals 64 −0.16 0.03 36,574 7.9×10−9 39,576 1.9×10−4 76,150 3.8×10−11
Europeans 64 −0.16 0.03 29,017 3.1×10−6 39,576 1.9×10−4 68,593 6.0×10−9
Indian-Asians 69 NA NA 7,557 2.7×10−4 NA NA NA NA
Men 64 −0.20 0.06 19,751 4.1×10−8 24,047 3.4×10−5 43,798 2.9×10−11
European men 63 −0.20 0.06 13,216 4.1×10−6 24,047 3.4×10−5 37,263 1.8×10−9
Women 64 −0.06 0.00 16,823 0.0027 15,529 0.47 32,352 9.0×10−3
European women 63 −0.06 0.00 15,801 0.012 15,529 0.47 31,330 0.024
rs534870 (nearSPRY2)
Chr13: 79,857,208 bp
Effect allele: A		 All individuals 68 −0.14 0.02 36,488 3.2×10−6 34,342 2.6×10−3 70,831 6.5×10−8
Europeans 70 −0.14 0.02 28,931 7.9×10−7 34,342 2.6×10−3 63,273 3.2×10−8
Indian-Asians 68 NA NA 7,557 0.52 NA NA NA NA
Men 68 −0.18 0.04 19,726 0.0016 20,537 2.1×10−3 40,263 1.1×10−5
European men 69 −0.18 0.04 13,190 8.6×10−5 20,537 2.1×10−3 33,727 1.6×10−6
Women 69 −0.06 0.01 16,763 9.0×10−4 13,805 0.34 30,568 2.2×10−3
European women 69 −0.06 0.01 15,741 0.0027 13,805 0.34 29,546 0.0048
rs8050136 (FTO)
Chr16: 52,373,776 bp
Effect allele: C		 All individuals 60 −0.33 0.11 36,537 3.9×10−17 34,105 4.4×10−11 70,642 2.7×10−26
Europeans 59 −0.33 0.11 28,980 4.6×10−16 34,105 4.4×10−11 63,085 5.6×10−25
Indian-Asians 68 NA NA 7,557 0.011 NA NA NA NA
Men 60 −0.29 0.10 19,739 2.5×10−8 20,624 6.0×10−7 40,363 1.3×10−13
European men 59 −0.29 0.10 13,204 2.1×10−7 20,624 6.0×10−7 33,828 1.7×10−12
Women 60 −0.39 0.13 16,798 1.2×10−8 13,481 1.6×10−5 30,279 1.1×10−12
European women 59 −0.39 0.13 15,776 2.2×10−8 13,481 1.6×10−5 29,257 2.7×10−12

The effect allele for each locus is the body fat percentage decreasing (major) allele. Chromosomal positions are indicated according to Build 36 and allele coding based on the positive strand.

bp, base pairs; Chr, chromosome; NA, no individuals available for analysis.

a

Effect sizes in % obtained from stage 2 studies only which included only individuals of white European descent.