Table 2.
Genomic Annotation Characteristics at 22 EA-Associated Type 2 Diabetes Quantitative Traits Loci with Substantially Reduced 99% Credible Sets Based on Trans-ethnic Fine Mapping
| Locusb | # SNPsc | Syn |
dbSNP |
Intronic | eQTL | TF Motif |
ENCODE23 |
Promoter | Enhancer | DHS |
Islet Regulome Browser13a |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Non-Syn | TFBS | PIACTd | |||||||||
| Fasting Glucose-Associated Loci | |||||||||||
| FOXA2 | 2 | 0 | 0 | 1 | 0 | 2 | 2 | 2 | 2 | 2 | AT |
| GCK | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 1 | PT |
| KL | 147 | 1 | 0 | 53 | 24 | 122 | 19 | 18 | 94 | 36 | PIACT |
| ADCY5 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | T |
| GCKR | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | I |
| PROX1 | 5 | 0 | 0 | 0 | 6 | 5 | 1 | 1 | 4 | 1 | PAT |
| DPYSL5 | 50 | 1 | 1 | 37 | 23 | 44 | 7 | 9 | 42 | 24 | PIACT |
| IGF2BP2 | 38 | 0 | 0 | 30 | 32 | 34 | 8 | 8 | 35 | 15 | PIACT |
| CDKN2B-ANRIL | 5 | 0 | 0 | 0 | 3 | 5 | 0 | 0 | 4 | 2 | AT |
| ADRA2 | 26 | 0 | 0 | 0 | 1 | 22 | 0 | 1 | 12 | 6 | IT |
| TCF7L2 | 4 | 0 | 0 | 3 | 0 | 2 | 0 | 1 | 3 | 2 | AT |
| FADS1 | 16 | 0 | 0 | 12 | 16 | 15 | 7 | 6 | 16 | 10 | PAT |
| DGKB-TMEM195 | 10 | 0 | 0 | 0 | 2 | 8 | 0 | 3 | 10 | 0 | A |
| CRY2 | 2 | 0 | 0 | 1 | 2 | 2 | 0 | 1 | 2 | 0 | PACT |
| Fasting Insulin-Associated Loci | |||||||||||
| ARL15 | 22 | 0 | 0 | 22 | 18 | 18 | 3 | 3 | 17 | 5 | IT |
| PPP1R3B | 1 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | – |
| COBLL1-GRB14 | 3 | 0 | 1 | 0 | 3 | 3 | 1 | 0 | 1 | 0 | T |
| IRS1 | 13 | 0 | 0 | 0 | 13 | 11 | 1 | 0 | 7 | 2 | C |
| GCKR | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | I |
| FAM13A | 21 | 0 | 0 | 21 | 18 | 15 | 3 | 8 | 20 | 6 | PIACT |
| ANKRD55-MAP3K1 | 200 | 0 | 0 | 0 | 63 | 161 | 20 | 17 | 147 | 67 | IAT |
| UHRF1BP1 | 9 | 0 | 0 | 8 | 9 | 8 | 2 | 0 | 4 | 5 | PAT |
| PPARG | 11 | 0 | 1 | 10 | 11 | 8 | 2 | 4 | 11 | 5 | – |
Abbreviations are as follows: Syn, synonymous SNP; non-syn, non-synonymous SNP; eQTL, expression quantitative trait loci; TF motif, transcription factor motif; TFBS, transcription factor binding site; DHS, DNase l-hypersensitive sites.
The information was obtained on December 1, 2014.
For ease of comparison to previous studies, the loci (13 fasting glucose, 8 fasting insulin, and 1 more for both) are named based on the historically identified nearest protein-coding gene or genes to the index SNP in EA.
#SNPs: the number of SNPs in trans-ethnic analysis-based 99% credible set.
PIACT: P, I, A, C, and T represent promoter, inactive enhancer, active enhancer, CTCF insulator, and transcription factor binding site (TFBS), respectively.