Table S1. Technical details of genotyping, quality control criteria and SNP imputation methods

Study / deCODE / Rotterdam / Framingham / TwinsUK
Array type / Infinium HapMap 300 / Illumina HapMap550v3 / Affymetrix GeneChip® Human Mapping 500 / Infinium HapMap 300
Genotyping calling algorithm / Illuminus / Beadstudio / Illluminus
Exclusion of SNPs used for imputation / Call rate<98% / Call rate<98% / call rate <97% / Call rate<98%
Imputation method / IMPUTE / MACH / MACH / IMPUTE
Imputation backbone (NCBI build) / HapMap CEU release 22 build 36 / HapMap CEU release 22 build 36 / HapMap CEU release 22 build 35 / HapMap CEU release 22 build 36
Data handling and statistical tests / R, SNPTEST / MACH2QTL / R / PLINK and R

Table S2. SNPs selected for replication

SNP rs number / Chr / Locus / P-value discovery
rs4730250 / 7 / DUS4L / 5.06x10-8
rs6957186 / 7 / COG5 / 1.21x10-7
rs12535761 / 7 / COG5 / 1.29x10-7
rs763386 / 7 / COG5 / 1.30x10-7
rs10953541 / 7 / BCAP29 / 6.16x10-7
rs7785962 / 7 / BCAP29 / 7.42x10-7
rs3749132 / 2 / ARHGAP25 / 3.58x10-6
rs886827 / 7 / GLI3 / 6.84x10-6
rs1886695 / 20 / CPNE1 / 9.25x10-6
rs3746410 / 20 / CPNE1 / 1.06x10-5
rs10071956 / 5 / Integenic / 1.16x10-5
rs6816070 / 4 / LDB2 / 1.39x10-5
rs661924 / 10 / NEBL / 1.46x10-5
rs436354 / 5 / ZDHC11 / 1.51x10-5
rs1994104 / 12 / Integenic / 1.51x10-5
rs3787166 / 20 / CPNE1 / 1.72x10-5
rs9857056 / 3 / Integenic / 1.72x10-5
rs1823429 / 3 / Integenic / 1.85x10-5
SNP rs number / Minor allele / Chr / Position / Gene / MAF / OR (95% CI)
Random effects / p-value
rs4730250 / G / 7 / 106994931 / DUS4L / 0.17 / 1.18 (1.11-1.26 / 5.5x10-7
rs10953541 / T / 7 / 107031781 / BCAP29 / 0.24 / 1.17 (1.09-1.23) / 7.9x10-7
rs3749132 / A / 2 / 68907001 / ARHGAP25 / 0.07 / 1.18 (1.00-1.38) / 0.041
rs886827 / C / 7 / 42285581 / GLI3 / 0.27 / 1.07 (0.92-1.25) / 0.37
rs1886695 / G / 20 / 33643949 / CPNE1 / 0.16 / 0.88 (0.81-0.96) / 5x10-3
rs10071956 / T / 5 / 173093290 / Intergenic / 0.38 / 1.12 (1.05-1.20) / 3.4x10-4
rs6816070 / G / 4 / 16089455 / LDB2 / 0.42 / 0.91 (0.86-0.95) / 1.3x10-4
rs661924 / T / 10 / 21353562 / NEBL / 0.39 / 1.12 (1.04-1.20) / 1.82x10-4
rs436354 / G / 5 / 783271 / ZDHC11 / 0.17 / 1.21 (0.99-1.31) / 0.06
rs1994104 / T / 12 / 83040643 / intergenic / 0.13 / 0.90 (0.77-1.05) / 0.18
rs9857056 / G / 3 / 181698548 / intergenic / 0.12 / 1.16 (0.97-1.39) / 0.10

Table S3. Summary Odds ratio for the top hits using random effects (RE) models

Table S4. Conditional analysis of the two top hits (effect of rs10953541 given that rs4730250 exists in the model)

Group / effect / p-value
deCODE / 0.153 / 0.088
Rotterdam / 0.10 / 0.414