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BMC Bioinformatics

Table 1 Size, location, and the estimated number of SNPs for each of the 10 candidate genes for type 2 diabetes mellitus.

Gene Symbol	Locus-Link	Location	Size (bp) (# exons)^a	Total # SNPs (#/Kb)^b	# SNPs MAF ≥ 5% (density)^c	Func SNPs^d	# SNPs selected for S1
							5' 30 Kb	3' 30 Kb	Gene region	Total
CAPN10	11132	2q37.3	48411(32)	308 (6)	27 (0.6)	1	3	11	25	39
FABP4	2167	8q21	5616 (6)	119 (21)	4 (0.7)	2	1	1	20	22
IL6	3569	7p21	6130 (10)	291 (47)	49 (8.0)	8	3	8	40	51
NOS3	4846	7q36	24637(29)	299 (12)	67 (2.7)	28	7	6	62	75
PPARG	5468	3p25	146974(16)	627 (4)	124 (0.8)	5	0	7	142	149
TNF	7124	6p21.3	2775 (5)	381 (137)	42 (15.1)	6	17	14	20	51
UCP2	7351	11q13	34786 (26)	135 (4)	13 (0.4)	2	4	10	20	34
CRP	1401	1q21-q23	2306 (18)	171 (74)	33 (14.3)	1	5	18	21	44
ESR1	2099	6q25.1	472913 (23)	1403 (3)	207 (0.4)	9	6	16	85*	107
AR	367	Xq11.2	180270 (13)	241 (1)	15 (0.1)	8	1	1	96	98

^aGene statistics from NCBI AceView; number of exons was calculated as number of intron plus 1.
^bIncluding SNPs belonging to all 6 NCBI dbSNP's function classes (i.e. Coding Nonsynonymous, Coding Synonymous, mRNA UTR, Splice site, Intron, and Others) that cover the gene locus as well as the 30-Kb 5' upstream and 30-Kb 3' downstream flanking sequences of the locus.
^cNote that a subset of dbSNP entries do not include information on allele frequency or heterozygosity. The numbers of SNPs reported here indicate those SNPs with MAF information and MAF ≥ 5%, including 30-Kb 5' upstream and 30-Kb 3' downstream flanking regions.
^dDefined as Coding Nonsynonymous, Coding Synonymous, or Splice-site SNPs.
* SNP distance (maximum inter-marker distance between selected SNPs) was controlled at 10 Kb for the ESR1 gene.

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