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. Author manuscript; available in PMC: 2014 Jun 26.
Published in final edited form as: Hum Genet. 2013 Jan 25;132(5):523–536. doi: 10.1007/s00439-013-1269-4

Table 2.

Previously identified variants for MSKCC dataset (a) and FGFR2 haplotype (b).

a)
SNP Chr Gene MA Dataset MAFA MAFU P-value OR Pooled P-value Pooled OR Fisher Meta P I2/Q
rs2180341 6q22.33 ECHDC1; RNF146 C MSKCC 0.28 0.19 6.86×10-4 1.64 4.77×10-3 1.28 6.40×10-3 56%/4.6
BCFR 0.25 0.22 2.51×10-1 1.20
NYUMC 0.25 0.24 7.48×10-1 1.05
rs6569479 6q22.33 ECHDC1; RNF146 A MSKCC 0.27 0.19 5.81×10-3 1.50 1.06×10-2 1.25 2.94×10-2 15%/2.4
BCFR 0.25 0.22 2.70×10-1 1.19
NYUMC 0.26 0.24 5.74×10-1 1.09
rs6569480 6q22.33 ECHDC1; RNF146 A MSKCC 0.27 0.19 1.77×10-3 1.58 5.62×10-3 1.27 1.19×10-2 39%/3.3
BCFR 0.25 0.22 2.70×10-1 1.19
NYUMC 0.26 0.24 5.82×10-1 1.09
rs7776136 6q22.33 ECHDC1; RNF146 A MSKCC 0.27 0.19 2.58×10-3 1.56 7.85×10-3 1.26 1.68×10-2 38%/3.2
BCFR 0.25 0.22 2.54×10-1 1.19
NYUMC 0.26 0.24 6.60×10-1 1.07
rs1078806 10q FGFR2 C MSKCC 0.44 0.39 7.66×10-2 1.25 1.70×10-6 1.43 9.64×10-6 25%/2.7
BCFR 0.46 0.38 7.72×10-3 1.43
NYUMC 0.48 0.35 1.05×10-4 1.69
rs7203563 16p13.3 A2BP1 C MSKCC 0.12 0.08 2.26×10-2 1.60 4.10×10-2 1.30 5.50×10-3 75%/8.0
BCFR 0.11 0.07 2.43×10-2 1.70
NYUMC 0.07 0.09 1.93×10-1 0.72
rs3012642 Xq13.1 PHKA1; HDAC8 G MSKCC 0.06 0.03 2.44×10-2 2.01 8.91×10-3 1.64 3.84×10-2 18%/2.4
BCFR 0.06 0.03 5.37×10-2 1.86
NYUMC 0.03 0.03 9.85×10-1 0.99
b)
SNP Chromosome Gene Minor Allele Dataset MAF (cases) MAF (controls) P-value OR Pooled P-value Pooled OR Meta P-value
rs11200014 10q FGFR2 A NYUMC 0.48 0.35 1.23×10-4 1.68 N/A N/A N/A
rs2981579 10q FGFR2 A NYUMC 0.48 0.36 1.67×10-4 1.66 N/A N/A N/A
rs1078806 10q FGFR2 G MSKCC 0.44 0.39 7.66×10-2 1.25 1.70×10-6 1.43 9.64×10-6
BCFR 0.46 0.38 7.72×10-3 1.43
NYUMC 0.48 0.35 1.05×10-4 1.69
rs1219648 10q FGFR2 G NYUMC 0.48 0.36 2.67×10-4 1.63 N/A N/A N/A
rs2420946 10q FGFR2 T NYUMC 0.48 0.37 9.57×10-3 1.56 N/A N/A N/A
rs2981582 10q FGFR2 A NYUMC 0.48 0.37 9.57×10-3 1.56 N/A N/A N/A

MA=minor allele; MAF=minor allele frequency for Cases (“A”) and Controls (“U”); p-values based on χ2 test on allele counts between cases and controls. All 3 datasets were combined for pooled P-values and Ors and Fisher Meta-analysis. Cochran Q and I2 statistics for heterogeneity are reported (“I2/Q”).