Targeted genome-wide investigation identifies novel SNPs associated with diabetic nephropathy

McKnight, Amy Jayne; Currie, Diane; Patterson, Chris C.; Maxwell, Alexander P.; Fogarty, Damian G.

doi:10.1007/s11568-010-9133-2

The HUGO Journal

Official Journal of the Human Genome Organisation

Table 2 Chromosome-based genotype results for top ranked SNPs highlighting significance values, associated genes, chromosomal location, amino acid changes and minor allele frequencies as reported in dbSNP

From: Targeted genome-wide investigation identifies novel SNPs associated with diabetic nephropathy

SNP Details						T2DN			T1DN
Reference ID	GeneView (dbSNP)	Chr location	Position on chromosome (bp)	Amino acid change (dbSNP)	Minor allele frequency (dbSNP)	Minor allele frequency (T2DN) (%)	Allelic P value for T2DN	Emprical P_{perm.genotypemodel} T2DN	Genotype method for T1DN	P value for T1DN
rs1543547	RAET1L	6q25.1	150388225	G26R	C > T; C = 7%	41.58	0.00002	0.00004	iPLEX1	0.91
rs1055061	HOMEZ	14q11.2	22814772	Q478R	A > G; A = 3%	3.22	0.0001	0.0001	iPLEX1	0.22
rs4713438	No link established	6p21.3	31254825		A > G; A = 14%	13.83	0.0001	0.0002	TaqMan	0.36
rs2224391^a	FARS2 and LYRM4	6p25.1	5205935	A11S	A > C; A = 68/71%	25.64	0.9	0.0004	TaqMan	0.06
rs9468877	No link established	6p21.3	31250882		A > G; A = 8/13%	10.66	0.0003	0.0004	TaqMan	0.72
rs2243380	ROS1	6q22	117831072	G167R	A > G; A = 8%	8.20	0.003	0.0004	iPLEX1	0.33
rs10751735	AIM1L	1p36.11	26535949	N249S	C > T; C = 55%	46.40	0.003	0.0006	iPLEX1	0.03
rs3825491	MYO16	13q33.3	108459360	A831P	C > G; C = 39/40%	34.75	0.0002	0.0006	iPLEX1	0.75
rs4930979^a	MGC24039	12p11.21	31540093	K52R	C > T; T = 40%	38.40	0.4	0.0007	iPLEX1	0.13
rs12933084	WFDC1	16q24.3	82918034	R217 K	A > G; G = 29/30%	33.96	0.0003	0.0007	iPLEX1	0.11
rs10502001	MMP7	11q21-q22	101903803	H77R	C > T; T = 18%	20.86	0.02	0.0009	iPLEX1	0.73
rs2285372	PLXND1	3q21.3	130787487	S617P	A > G; A = 5%	2.72	0.001	0.001	tagSNP	N/A
rs2301572	PLXND1	3q21.3	130788150	S531G	C > T; T = 5%	2.72	0.001	0.001	iPLEX1	0.69
rs13143848	C4orf17	4q23	100662743	E64G	A > G; A = 36%	28.52	0.02	0.001	iPLEX1	0.15
rs10452600	No link established	6p22	26300481		A > C; A = 10/12%	11.81	0.002	0.001	iPLEX1	0.63
rs2076484	UBD	6p21.3	29631982	S51L	C > T; T mono-morphic	2.96	0.002	0.001	TaqMan	0.03
rs9380215	No link established	6p21.3	31157634		A > G; G = 7%	5.11	0.001	0.001	TaqMan	0.03
rs2857596	No link established	6p21.3	31675401		A > C; C = 31%	31.83	0.001	0.001	TaqMan	0.23
rs10825269	PCDH15	10q21.1	55625616	S380G	C > T; T = 8%	14.22	0.001	0.001	iPLEX1	0.18
rs8141797	SUSD2	22q11-q12	22912041	S466 N	A > G; G = 7/9%	4.79	0.001	0.001	iPLEX1	0.85
rs1129411	SP110	2q37.1	230785969	R112 W	C > T; T = 14%	12.81	0.002	0.002	iPLEX1	0.73
rs11753837	No link established	6p22	26298726		A > G; A = 7%	8.63	0.002	0.002	iPLEX1	0,21
rs11755943	No link established	6p22	26319347		A > G; G = 10/13%	12.04	0.002	0.002	tagSNP	N/A
rs8005245	OR4K17	14q11.2	19655882	N159 K	C > G; C = 40/43%	38.76	0.009	0.002	iPLEX1	0.03
rs1788799	NPC1	18q11-q12	19378943	I642 M	A > G; A = 33%	35.16	0.0006	0.002	iPLEX1	0.50
rs4701997	DNAH5	5p15.2	13947894	L766I	A > T; T = 47%	48.19	0.001	0.003	iPLEX1	0.04
rs2076487	UBD	6p21.3	29631838	G99A	C > G; C = mono-morphic/98%	2.95	0.002	0.003	tagSNP	N/A
rs2076486	UBD	6p21.3	29631851	P95S	C > T; T = mono-morphic	2.95	0.002	0.003	tagSNP	N/A
rs3793524^a	PTPN3	9q31	111259295	P90A	C > G; G = 38/39%	38.74	0.9	0.003	iPLEX1	0.39
rs36012476	ADCK4	19q13.2	45897900	R352T	C > G; G = 17%	4.67	0.0007	0.003	iPLEX1	0.46
rs6917033	UBR2	6p21.1	42735412	T1095P	A > G; A = 38/48%	37.03	0.001	0.004	iPLEX1	0.49
rs9552271	N6AMT2	13q12.11	20220107		C > T; T = 43%	36.57	0.002	0.006	TaqMan	0.71

N/A—not directly assessed because tagged by another SNP (r² > 0.8)
^a HWE for cases,controls: rs2224391 = 0.02, 0.001; rs3793524 = 0.005, 0.01; rs4930979 = 0.004, 0.005

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