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

Table 1.

22 EA-Associated Type 2 Diabetes Quantitative Traits Loci with Substantially Reduced 99% Credible Sets Based on Trans-ethnic Fine Mapping

Locusa Chr 99% Credible Set: European Ancestry Only
 99% Credible Set: Trans-ethnic
 99% Credible Set Reduction
# SNPsb Rangec(bp) # SNPsb Rangec(bp) % SNPsd % Rangee
Fasting Glucose-Associated Loci
FOXA2 20 40 46,365 2 3,872 95.0 91.6
GCK 7 7 25,107 1 1 85.7 100.0
KL 13 696 496,262 147 492,550 78.9 0.7
ADCY5 3 4 31,042 1 1 75.0 100.0
GCKR 2 2 11,663 1 1 50.0 100.0
PROX1 1 11 18,286 6 13,550 45.5 25.9
DPYSL5 2 87 294,065 50 269,667 42.5 –8.3
IGF2BP2 3 64 317,522 38 355,236 40.6 –11.9
CDKN2B-ANRIL 9 7 5,914 5 4,515 28.6 23.7
ADRA2A 10 33 68,716 26 68,110 21.2 0.9
TCF7L2 10 5 36,312 4 15,268 20.0 58.0
FADS1 11 20 58,394 16 57,823 20.0 1.0
DGKB-TMEM195 7 11 143,605 10 2,182 9.1 98.5
CRY2 11 10 57,088 11 14,850 –10.0 74.0
Fasting Insulin-Associated Loci
ARL15 5 319 498,585 22 33,535 93.1 93.3
PPP1R3B 8 8 9,510 1 1 87.5 100.0
COBLL1-GRB14 2 14 51,528 3 11,540 78.6 77.6
IRS1 2 43 137,640 13 68,951 69.8 49.9
GCKR 2 3 11,663 1 1 66.7 100.0
FAM13A 4 43 243,374 21 243,374 51.2 0.0
ANKRD55-MAP3K1 5 417 497,027 218 487,103 47.7 2.0
UHRF1BP1 6 13 217,136 9 136,609 30.8 37.1
PPARG 3 14 60,448 11 56,618 21.4 6.3

The 22 EA-associated T2D QT loci include 13 fasting glucose, 8 fasting insulin, and 1 associated with both. Substantial reduction is defined as greater than 20% reduction in its genomic length or the number of SNPs.

a

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.

b

# SNPs is the number of SNPs included in the 99% credible set.

c

Range is defined as the maximum genomic distance based on hg18 among the SNPs included in the 99% credible set.

d

%SNPs is (the number of SNPs in the EA-based 99% credible set − the number of SNPs in the trans-ethnic analysis-based 99% credible set)/the number of SNPs in the EA-based 99% credible set.

e

%Range is (the range of the EA-based 99% credible set − the range of the trans-ethnic analysis-based 99% credible set)/the range of the EA-based 99% credible set.