Table 4

Comparison of point-wise and proxy MA of dBGaP GWAS for known type II diabetes genes
PubMed ID Genea rs-Catalogueb p-Cataloguec rs-Naived p-Naivee rs-Proxyf p-Proxyg p-Imputeh Q(Na/Pro)i Q(Pro/Imp)j
20581827 BCL11A rs243021 3.0E-15 rs243021 3.3E-03 rs11697597 3.3E-03 3.2E-03 1 1.03
20818381 C2CD4A,C2CD4B rs7172432 9.0E-14 rs335302 1.2E-03 rs7172432 1.2E-03 1.98E-04 1 6.04
20581827 CDKAL1 rs10440833 2.0E-22 rs12336110 2.1E-03 rs6950237 2.1E-03 1.0E-03 1 2.10
19401414 CDKN2A, CDKN2B rs2383208 2.0E-29 rs2383208 2.2E-03 rs2383208 8.4E-04 5.2E-04 2.6 1.60
20581827 CENTD2 rs1552224 1.0E-22 rs1552224 1.1E-01 rs1552224 3.4E-02 4.8E-03 3.33 7.08
17463249 FTO rs8050136 7.0E-14 rs8050136 8.0E-03 rs8050136 6.7E-04 9.4E-04 11.9 0.71
20581827 HHEX,IDE rs5015480 1.0E-15 rs5015480 9.6E-03 rs5015480 2.0E-03 4.9E-04 4.8 4.10
20581827 HMGA2 rs1531343 4.0E-09 rs12741948 3.3E-02 rs1122590 1.4E-02 9.1E-05 2.43 149.8
17463249 IGF2BP2 rs4402960 9.0E-16 rs4402960 2.3E-03 rs4402960 7.2E-04 1.2E-04 3.21 6.12
20581827 IRS1 rs7578326 5.0E-20 rs7578326 4.2E-02 rs7578326 1.7E-03 8.8E-04 24.65 1.95
18372903 JAZF1 rs864745 5.0E-14 rs864745 1.6E-03 rs864745 1.9E-04 1.1E-04 8.47 1.78
17463249 KCNJ11 rs5215 5.0E-11 rs5215 8.1E-02 rs4646410 3.1E-03 9.6E-04 26.16 3.24
18711367 KCNQ1 rs2237892 2.0E-42 rs2237892 2.1E-02 rs2237892 2.7E-04 3.5E-04 78.57 0.77
19734900 LOC64673, IRS1 rs2943641 9.0E-12 rs2943641 7.8E-02 rs2943641 1.7E-03 8.8E-04 45.94 1.95
20418489 RBMS1, ITGB6 rs7593730 4.0E-08 rs7593730 1.8E-05 rs7593730 3.4E-06 3.6E-06 5.15 0.94
20581827 SLC30A8 rs3802177 1.0E-08 rs2466295 2.4E-02 rs2466295 1.0E-02 5.3E-05 2.35 193.6
20862305 SPRY2 rs1359790 6.0E-09 rs17249026 4.5E-02 rs17249026 4.5E-02 2.1E-03 1 21.6
19734900 TCF7L2 rs7903146 1.0E-30 rs7903146 3.2E-19 rs7903146 1.5E-22 4.4E-23 2126.7 3.40
18372903 THADA rs7578597 1.0E-09 rs2236705 1.5E-02 rs7578597 6.7E-03 2.4E-03 2.18 2.79
18372903 TSPAN8,LGR5 rs7961581 1.0E-09 rs4581087 1.1E-02 rs4581087 1.2E-02 2.4E-03 0.70 4.83
19734900 WFS1, PPP2R2C rs4689388 1.0E-08 rs4689388 5.5E-03 rs4689388 1.6E-03 7.7E-04 3.44 2.08
20581827 ZFAND6 rs11634397 2.0E-09 rs11634397 2.6E-02 rs11634397 2.6E-02 1.0E-02 1 2.46

aEach gene region is listed only once, even if listed several times in the GWAS catalogue.

bMost significant SNP according to GWAS catalog [1].

cp-value according to GWAS catalog.

dMost significant SNP with naïve MA on intersection of marker panels of 6 dbGaP GWAS described before.

ep-value refering to SNP from previous column.

fMost significant SNP with proxy MA on 6 dbGaP GWAS.

gp-value refering to SNP from previous column.

hp-value of the correslonding SNP calculated by imputation/snptest.

iImprovement with proxy algorithm: quotient of columns “p-Pointwise” and “p-Proxy”.

jImprovement with imputation: quotient of columns “p-Proxy” and “p-Impute”.

Meesters et al.

Meesters et al. BMC Bioinformatics 2012 13:231   doi:10.1186/1471-2105-13-231

Open Data