Skip to main content
. 2016 Jun 16;99(1):56–75. doi: 10.1016/j.ajhg.2016.05.006

Table 4.

Locus Transferability in African Individuals for 24 EA-Identified Type 2 Diabetes Quantitative Traits Associations

Locusb SNP Information
 Best SNP Association
 adj-ph Effectci % Change in Effectj LDain YRI and CEU
Index SNP in EAc Best SNP in AAd Best SNP Allelese EAFf Effectucg SE p R2YRI D’YRI R2CEU D’CEU
Fasting Glucose-Associated Loci
MTNR1B rs10830963 rs10830963 G/C 0.079 0.089 0.012 9.3 × 10–15 3.5 × 10–3 NA NA 1.00 1.00 1.00 1.00
GCK rs4607517 rs1799884 T/C 0.174 0.047 0.007 2.0 × 10–10 8.6 × 10–3 0.038 19.3 0.47 1.00 1.00 1.00
G6PC2 rs560887 rs830193 C/T 0.816 0.037 0.008 1.2 × 10–6 2.9 × 10–3 0.035 5.2 0.00 0.08 0.07 0.58
FOXA2 rs6048205 rs1203907 T/C 0.505 0.027 0.006 3.7 × 10–6 3.3 × 10–3 0.025 7.7 0.18 0.92 0.66 1.00
RREB1 rs17762454 rs557074 G/T 0.455 0.027 0.006 4.2 × 10–6 4.1 × 10–3 0.025 4.4 0.01 0.48 0.02 0.51
SLC30A8 rs13266634 rs10505311 G/T 0.837 0.036 0.008 5.6 × 10–6 3.7 × 10–3 0.025 30.8 0.19 1.00 NA NA
ADCY5 rs11708067 rs11708067 A/G 0.846 0.036 0.008 6.3 × 10–6 4.5 × 10–3 NA NA 1.00 1.00 1.00 1.00
GCKR rs780094 rs780094 C/T 0.819 0.032 0.008 2.0 × 10–5 1.4 × 10–2 NA NA 1.00 1.00 1.00 1.00
CRY2 rs11605924 rs11038651 T/C 0.828 0.033 0.008 3.8 × 10–5 5.3 × 10–3 0.030 9.4 0.55 0.85 0.12 0.44
MADD rs7944584 rs1052373 T/C 0.481 0.022 0.006 1.4 × 10–4 1.1 × 10–2 0.022 0.0 NA NA 0.15 1.00
PPP1R3B rs4841132 rs7004769 A/G 0.228 0.024 0.007 2.7 × 10–4 2.2 × 10–3 0.018 26.1 0.44 1.00 0.38 1.00
PROX1 rs340874 rs2282387 C/G 0.519 0.021 0.006 4.6 × 10–4 3.4 × 10–3 0.021 –1.2 0.01 0.27 0.00 0.09
IKBKAP rs16913693 rs7038936 C/T 0.669 0.021 0.006 5.3 × 10–4 3.9 × 10–3 NAk NA 0.04 0.29 0.01 0.39
ADRA2A rs10885122 rs12569523 A/T 0.368 0.021 0.006 5.4 × 10–4 3.6 × 10–3 0.020 1.9 0.01 0.11 0.00 0.25
PCSK1 rs13179048 rs7722200 T/C 0.773 0.023 0.007 8.2 × 10–4 7.0 × 10–3 0.023 –0.9 0.04 1.00 0.66 0.83
Fasting Insulin-Associated Loci
COBLL1-GRB14 rs7607980 rs6717858 T/C 0.281 0.036 0.007 8.6 × 10–8 5.3 × 10–3 0.034 6.4 0.06 1.00 0.22 1.00
ARL15 rs4865796 rs6876198 C/T 0.295 0.031 0.007 2.0 × 10–6 3.8 × 10–3 0.030 4.0 0.11 0.89 0.09 0.87
PPP1R3B rs4841132 rs9949 G/A 0.231 0.029 0.007 6.9 × 10–5 2.2 × 10–3 0.027 6.7 0.11 0.51 0.01 0.23
IRS1 rs2943634 rs4413154 G/A 0.041 0.062 0.016 1.2 × 10–4 4.9 × 10–3 0.062 1.3 0.01 1.00 0.08 1.00
ANKRD55-MAP3K1 rs459193 rs7700714 A/G 0.436 0.023 0.006 1.8 × 10–4 2.3 × 10–3 0.024 –3.6 0.00 0.03 0.04 0.29
FAM13A rs3822072 rs17799176 C/G 0.934 0.043 0.012 4.3 × 10–4 5.8 × 10–3 0.043 0.2 0.00 0.22 0.02 0.43
HIP1 rs1167800 rs11465341 C/T 0.035 0.060 0.017 4.5 × 10–4 8.1 × 10–3 0.060 0.0 0.00 1.00 NA NA
MAP3K19 rs1530559 rs13405563 T/C 0.924 0.043 0.013 5.5 × 10–4 8.8 × 10–3 0.045 –3.6 0.00 0.79 0.04 1.00
PDGFC rs4691380 rs17811863 G/A 0.333 0.022 0.006 6.2 × 10–4 4.7 × 10–3 0.020 8.9 0.21 0.49 0.77 0.93
GCKR rs780094 rs780094 C/T 0.817 0.025 0.008 1.9 × 10–3 1.4 × 10–2 NA NA 1.00 1.00 1.00 1.00
a

LD information between the EA index SNP and the best SNP in AA.

b

24 EA-identified T2D QT (14 glucose, 9 fasting insulin, and 1 associated with both) loci with locus-wide significant, p < 0.05/effective number of independent SNPs within each locus, associations. For ease of comparison to previous studies, the loci are named based on the historically identified nearest protein-coding gene or genes to the index SNP in European ancestry.

c

Index SNPs are the most significant SNPs previously reported in MAGIC publications. All of these SNPs reach genome-wide significant level (p < 5 × 10–8) in the original study.

d

The best SNP in AA is the most significant SNP within ±250 kb region of the EA index SNP.

e

AA trait-raising allele/other allele.

f

Frequency of AA trait-raising allele (effect allele) for the best SNP.

g

Effect of AA trait-raising allele ([mmol/L] for fasting glucose and [pmol/L] for fasting insulin per trait-raising allele). This is unconditional association of best SNP in AA samples.

h

Indicates the p value is adjusted for locus-wise multiple comparison and calculated as min(1, P∗the number of effective SNPs). The information for the number of effective SNPs is available in Table S8.

i

Effectuc is the association of the best SNP unconditional on the EA index SNP in AA samples and Effectc is the association of AA best SNP conditional on EA index SNP in AA samples.

j

Percent change in association effect for the best SNP in the AA samples. It is calculated as the (unconditional association effect − conditional association effect)/(unconditional association effect). More detailed information for conditional and unconditional association results are available in Table S8.

k

The association results for EA index SNP is not available in AA.