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Table 2 Variants associated with habitual coffee consumption

From: GWAS of habitual coffee consumption reveals a sex difference in the genetic effect of the 12q24 locus in the Japanese population

Variant Chr Position Gene EA NEA Population EAF Beta SE (Beta) P association I 2 P heterogeneity
rs518341 1 78,896,492 GIPC2– PTGFR G A Discovery 0.315 0.133 0.030 6.4 × 10− 6
      Replication 0.317 0.009 0.030 0.77
      Meta-analysis 0.316 0.072 0.021 5.9 × 10−4 88.6 3.1 × 10−3
rs11722777 4 7,590,819 SORCS2 A G Discovery 0.816 −0.167 0.037 6.4 × 10−6
      Replication 0.821 −0.075 0.038 0.05
      Meta-analysis 0.819 −0.123 0.027 3.9 × 10−6 66.3 0.08
rs10941308 5 36641,007 SLC1A3 A G Discovery 0.115 0.189 0.043 9.3 × 10−6
      Replication 0.118 −0.026 0.044 0.55
      Meta-analysis 0.117 0.084 0.031 5.8 × 10−3 92.0 4.2 × 10−4
rs10648495 6 162,128,756 PRKN CTCTTT C Discovery 0.463 −0.130 0.028 4.5 × 10−6
      Replication 0.459 0.040 0.029 0.16
      Meta-analysis 0.461 −0.046 0.020 0.02 94.4 2.4 × 10−5
rs10252701 7 17,280,513 AHR C A Discovery 0.322 −0.194 0.031 3.2 × 10−10
      Replication 0.308 −0.146 0.032 4.0 × 10−6
      Meta-analysis 0.315 −0.171 0.022 1.0 × 10−14 15.1 0.28
rs79105258 12 111,718,231 CUX2 A C Discovery 0.268 0.211 0.032 4.4 × 10−11
      Replication 0.298 0.137 0.031 1.3 × 10−5
      Meta-analysis 0.283 0.173 0.022 9.5 × 10−15 63.2 0.10
  1. Chr Chromosome number, EA Effect allele, NEA Non-effect allele, EAF Effect allele frequency, SE Standard error