. Author manuscript; available in PMC: 2009 Apr 23.

Published in final edited form as: Diabetes. 2007 Mar;56(3):856–862. doi: 10.2337/db06-1305

TABLE 2.

Summary of SNPs typed in Caucasian individual samples for ATF6 region

Location	Name	Gene location	Allele (+ strand)	MAF		OR (95% CI)	P
Location	Name	Gene location	Allele (+ strand)	Case	Control	OR (95% CI)	P
-8150	rs12745240	5′flanking	G/A	0.439	0.362	1.375 (1.025-1.846)	0.03
-6402	rs1417580	5′flanking	C/A	0.482	0.414	1.313 (0.982-1.755)	0.066
-6250	rs1417581	5′flanking	G/C	0.476	0.420	1.257 (0.943-1.676)	0.119
-116	rs2298019	5′flanking	G/A	0.130	0.149	0.853 (0.563-1.292)	0.44
323	rs2271010^*	Intron 1	T/C	0.094	0.092	1.023 (0.616-1.699)	0.925
2088	rs4657101	Intron 1	A/C	0.195	0.249	0.731 (0.517-1.032)	0.082
5124	rs905594^*	Intron 1	C/T	0.336	0.376	0.841 (0.621-1.138)	0.258
10528	rs2340823	Intron 1	T/C	0.042	0.072	0.568 (0.301-1.073)	0.069
10622	rs2340824^*	Intron 1	T/C	0.072	0.089	0.791 (0.46-1.362)	0.376
11906	rs2070151^*	Exon 2 (L35L)	C/T	0.042	0.070	0.585 (0.308-1.109)	0.087
15591	rs1058405	Exon 3 (M67V)	A/G	0.316	0.228	1.568 (1.13-2.175)	0.011
17652	rs2271013^*	Exon 4 (P90P)	T/C	0.069	0.074	0.927 (0.53-1.622)	0.783
20886	rs1027700^*	Intron 4	A/T	0.321	0.241	1.493 (1.083-2.059)	0.021
21477	rs6427630^*	Intron 4	A/G	0.047	0.070	0.653 (0.346-1.23)	0.171
25126	rs2070150^*	Exon 5 (P145A)	C/G	0.047	0.069	0.67 (0.359-1.251)	0.192
25162	rs1135983	Exon 5 (S157P)	C/T	0.045	0.075	0.579 (0.311-1.076)	0.114
27783	rs2134690	Intron 6	G/A	0.122	0.142	0.845 (0.551-1.295)	0.425
29845	rs10917955^*	Intron 6	T/C	0.047	0.069	0.655 (0.351-1.261)	0.195
36092	rs3738326^*	Intron 7	G/A	0.050	0.075	0.648 (0.348-1.204)	0.153
39427	rs11576878^*	Intron 7	A/G	0.320	0.241	1.482 (1.065-2.062)	0.029
42544	rs4656334^*	Intron 7	G/A	0.047	0.072	0.636 (0.337-1.2)	0.146
44829	rs2134697	Intron 7	A/G	0.271	0.274	0.986 (0.712-1.366)	0.936
45050	rs2134696	Intron 7	T/A	0.128	0.138	0.922 (0.597-1.423)	0.706
48255	rs4657109^*	Intron 7	G/A	0.069	0.090	0.758 (0.438-1.313)	0.3
53475	rs3817085^*	Intron 8	G/C	0.071	0.090	0.774 (0.457-1.31)	0.317
61198	rs12403862^*	Intron 9	A/G	0.047	0.069	0.665 (0.351-1261)	0.195
62089	rs4657110^*	Intron 9	C/T	0.069	0.090	0.758 (0.438-1.313)	0.3
69738	rs2340715^*	Intron 9	G/T	0.066	0.092	0.7 (0.409-1.198)	0.172
75405	rs1006310^*	Intron 9	C/T	0.336	0.367	0.873 (0.641-1.189)	0.385
77365	rs1553444^*	Intron 9	T/C	0.135	0.149	0.891 (0.585-1.358)	0.582
84754	rs3767635^*	Intron 10	A/G	0.285	0.313	0.875 (0.639-1.198)	0.408
90465	rs3767633^*	Intron 12	A/T	0.151	0.151	1.002 (0.672-1.495)	0.992
94778	rs1394066^*	Intron 13	A/G	0.155	0.131	1.211 (0.797-1.840)	0.368
97083	rs3767632	Intron 14	G/A	0.343	0.391	0.813 (0.605-1.093)	0.175
98631	rs6427632^*	Intron 14	C/T	0.138	0.132	1.052 (0.684-1.618)	0.818
101978	rs1503815^*	Intron 14	C/T	0.140	0.132	1.074 (0.705-1.634)	0.744
111220	rs12024729^*	Intron 14	T/A	0.069	0.089	0.759 (0.438-1.313)	0.3
113235	rs2340721^*	Intron 14	C/A	0.330	0.362	0.865 (0.636-1.177)	0.344
120274	rs2340722^*	Intron 14	A/G	0.089	0.090	0.998 (0.604-1.648)	0.992
121930	rs4147177	Intron 14	C/T	0.073	0.093	0.762 (0.452-1.287)	0.286
122710	rs1806594^*	Intron 14	C/T	0.128	0.145	0.867 (0.564-1.334)	0.509
127773	rs6427635^*	Intron 14	T/C	0.092	0.090	1.019 (0.609-1.704)	0.939
135657	rs12033967^*	Intron 14	G/A	0.069	0.089	0.759 (0.438-1.313)	0.3
136621	rs2341473^*	Intron 14	G/A	0.082	0.093	0.867 (0.521-1.443)	0.564
144332	rs12079579^*	Intron 14	G/A	0.092	0.082	1.143 (0.686-1.904)	0.602
149202	rs2341479^*	Intron 15	A/C	0.167	0.162	1.036 (0.695-1.543)	0.859
152805	rs4417044^*	Intron 15	C/T	0.195	0.232	0.799 (0.563-1.136)	0.193
159788	rs2341480^*	Intron 15	T/G	0.234	0.263	0.858 (0.609-1.210)	0.361
163581	rs10918215^*	Intron 15	A/G	0.246	0.282	0.832 (0.595-1.162)	0.263
166885	rs7514053^*	Intron 15	G/A	0.244	0.280	0.831 (0.594-1.162)	0.263
168348	rs2341481	Intron 15	A/G	0.237	0.281	0.795 (0.573-1.102)	0.159
172188	rs10737517^*	Intron 15	A/G	0.237	0.263	0.872 (0.620-1.227)	0.411
178133	rs10800151^*	Intron 15	A/G	0.371	0.404	0.869 (0.647-1.167)	0.348
181842	rs10918279^*	Intron 15	C/A	0.220	0.264	0.785 (0.561-1.1)	0.152
188599	rs2341471^*	Intron 15	G/A	0.372	0.396	0.905 (0.668-1.225)	0.514
192418	rs13401	3′UTR	A/G	0.241	0.296	0.767 (0.555-1.06)	0.107
192621	rs1136046	3′UTR	G/A	0.090	0.116	0.752 (0.468-1.208)	0.224
193611	rs2499855	3′flanking	T/C	0.124	0.149	0.803 (0.528-1.221)	0.299
194804	rs11579627	3′flanking	G/A	0.334	0.223	1.751 (1.265-2.423)	0.001
195478	rs2499849^*	3′flanking	C/G	0.223	0.293	0.695 (0.499-0.968)	0.025
199870	rs9783050	3′flanking	A/G	0.376	0.418	0.84 (0.626-1.127)	0.239
200638	rs2490438^*	3′flanking	G/A	0.379	0.315	1.328 (0.979-1.802)	0.076
202745	rs2490433	3′flanking	C/A	0.411	0.340	1.354 (1.008-1.821)	0.054
205069	rs2490431^*	3′flanking	C/T	0.308	0.337	0.876 (0.53-1.237)	0.376

This table summarizes the association data in Utah and Arkansas Caucasians. SNPs that were in complete LD (r² = 1) were typed only in 95 control samples and are not included in this table (see supplemental Table 3S). Likewise, SNPs with low minor allele frequencies (MAFs) (<5%) were generally not tested unless nonsynonymous. Raw counts are available in supplemental Table 3S. Alleles are listed as the major/minor allele. ORs were taken from the allelic association test considering the minor allele as the risk allele. P values are shown for genotypic association by Armitage’s Trend Test.

SNPs also genotyped by the International Type 2 Diabetes 1q Consortium in eight populations but shown here only for the Utah sample. Locations are given with respect to the A of ATG start as 1 and first base upstream as -1, based on NCBI Build 35 (University of California Santa Cruz, May 2004).