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. Author manuscript; available in PMC: 2010 Sep 21.
Published in final edited form as: Nature. 2009 Apr 28;459(7246):528–533. doi: 10.1038/nature07999

Table 3.

Genotyped and imputed markers (other than those on 5p14.1) with suggestive association signals (P<1×10−5) in the two discovery cohorts

Chr SNP Position Locus Gene Type MACH
Rsq* 		Minor /
major
allele		 MAF
(AGRE)		 Z score†
(AGRE)		 Case
MAF
(ACC)		 Control
MAF
(ACC)		 Odds
ratio†
(ACC)		 P value
(combined)
3 rs3755827 62335411 3p14.2 Near FEZF2 Genotyped C/T 0.13 3.37 0.14 0.11 1.27 3.5×10−6
6 rs9395885 53853436 6p12.1 LRRC1 Imputed 0.99 T/C 0.08 2.27 0.10 0.07 1.43 5.8×10−6
6 rs9349688 53870051 6p12.1 LRRC1 Genotyped G/A 0.09 2.10 0.10 0.07 1.43 8.1×10−6
6 rs9384952 116066757 6q22.1 Between HS3ST5
and FRK 		Genotyped C/T 0.41 2.33 0.42 0.37 1.20 9.4×10−6
10 rs9651325 68649859 10q21.3 CTNNA3 Imputed 0.97 A/G 0.11 −3.24 0.09 0.12 0.80 9.2×10−6
10 rs807023 102760072 10q24.31 Near LZTS2 Genotyped A/C 0.14 1.12 0.15 0.10 1.48 7.8×10−6
12 rs10774538 118888180 12q24.23 Near CCDC64 Genotyped T/C 0.13 −2.51 0.12 0.15 0.77 6.2×10−6
13 rs9521337 108823637 13q33.3 Near MYO16 Imputed 0.98 T/G 0.13 2.41 0.14 0.11 1.34 6.8×10−6
13 rs4771632 108846743 13q33.3 Near MYO16 Imputed 0.99 A/G 0.13 2.32 0.14 0.11 1.32 9.5×10−6
13 rs7996916 108855628 13q33.3 Near MYO16 Imputed 0.99 A/C 0.12 3.07 0.15 0.12 1.27 5.5×10−6
13 rs1328250 108856632 13q33.3 Near MYO16 Imputed 1.00 T/C 0.12 3.07 0.14 0.12 1.27 5.9×10−6
13 rs4771633 108858788 13q33.3 Near MYO16 Imputed 1.00 G/A 0.12 2.98 0.14 0.12 1.26 9.2×10−6
13 rs9521354 108865125 13q33.3 Near MYO16 Genotyped C/A 0.13 3.38 0.14 0.12 1.25 5.8×10−6
13 rs9521355 108865183 13q33.3 Near MYO16 Genotyped T/C 0.13 3.20 0.14 0.12 1.25 7.1×10−6
13 rs1328244 108881899 13q33.3 Near MYO16 Genotyped C/T 0.08 3.92 0.10 0.08 1.31 8.2×10−7
14 rs12897470 39895590 14q21.1 Between FBXO33
and LRFN5 		Imputed 0.99 A/G 0.50 3.39 0.51 0.47 1.17 2.6×10−6
14 rs7147817 39901754 14q21.1 Between FBXO33
and LRFN5 		Genotyped G/A 0.54 3.38 0.54 0.50 1.20 2.7×10−7
14 rs17783432 76141161 14q24.3 Between ESRRB
and VASH1 		Genotyped T/G 0.15 1.97 0.15 0.11 1.36 9.4×10−6
16 rs7206043 8412954 16p13.2 Between A2BP1
and C16orf68 		Imputed 0.98 G/A 0.41 −3.03 0.39 0.43 0.84 4.8×10−6
16 rs9932538 19116070 16p12.3 SYT17 Genotyped G/A 0.16 1.97 0.17 0.12 1.47 1.9×10−7
20 rs6131030 44241393 20q13.12 CDH22 Genotyped A/G 0.42 3.24 0.41 0.37 1.17 6.5×10−6
X rs11798405 4940801 Xp22.32 Between PRKX
and NLGN4X 		Genotyped G/A 0.09 2.71 0.10 0.06 1.66 9.0×10−7
X rs5972577 32390211 Xp21.1 DMD Genotyped A/G 0.33 3.90 0.35 0.30 1.26 2.7×10−7
X rs6646569 119125802 Xq24 Near RHOXF1 Genotyped T/C 0.13 2.49 0.14 0.09 1.56 9.7×10−7
*

MACH Rsq estimates the squared correlation between imputed and true genotypes, and a value less than 0.3 flags poorly imputed SNPs.

†

The Z score and odds ratio are calculated with respect to the major allele.