Haplotype association analysis of genes within the WNT signalling pathways in diabetic nephropathy

Kavanagh, David H; Savage, David A; Patterson, Christopher C; McKnight, Amy Jayne; Crean, John K; Maxwell, Alexander P; McKay, Gareth J

doi:10.1186/1471-2369-14-126

BMC Nephrology

Table 1 Genes included within the analysis on the basis of significant association (P < 0.05) within the GENIE meta-analysis[22] and demonstrating a consistent direction of effect across all four cohorts

From: Haplotype association analysis of genes within the WNT signalling pathways in diabetic nephropathy

Chromosome	Position	Gene	SNP	Direction	Allele	P-value
2	219395841	WNT6	rs6436094	- + ??	A	0.19
2	219411542	WNT6	rs730947	- + −+	A	0.12
2	219427976	WNT6	rs7596898	?-??	T	0.73
2	219428221	WNT6	rs940469	+ − ++	T	0.11
2	219429434	WNT6	rs11695967	+ − ++	T	0.11
2	219434742	WNT6	rs10193725	- + −−	T	0.18
2	219440386	WNT6	rs6754599	- + −+	C	0.36
2	219452118	WNT6	rs3806557	+−−-	A	0.95
2	219454805	WNT6	rs10177996	-+++	T	0.95
2	219458990	WNT6	rs2385199	-+++	A	0.94
2	219464627	WNT6	rs7349332	++−−	T	0.61
3	41205327	CTNNB1	rs2691678	-- + −	A	0.32
3	41205658	CTNNB1	rs7630377	-- + −	T	0.58
3	41209520	CTNNB1	rs9859392	++ − +	C	0.39
3	41215181	CTNNB1	rs3864004	----	A	0.38
3	41218746	CTNNB1	rs3915129	++++	T	0.38
3	41229650	CTNNB1	rs2140090	----	T	0.38
3	41236983	CTNNB1	rs1798802	-- + −	A	0.59
3	41237448	CTNNB1	rs13072632	++++	T	0.38
3	41243358	CTNNB1	rs11564447	+ − +−	T	0.41
3	41247085	CTNNB1	rs1880481	----	A	0.37
3	41249076	CTNNB1	rs11564450	++++	C	0.37
3	41254444	CTNNB1	rs4135385	+−−+	A	0.48
3	41259540	CTNNB1	rs9883073	-- + −	A	0.41
3	41262022	CTNNB1	rs11711946	++ − +	T	0.41
3	41270771	CTNNB1	rs11129896	++++	T	0.20
3	55450313	WNT5A	rs815533	-++−	A	0.73
3	55456115	WNT5A	rs3913369	- + −−	T	0.10
3	55462468	WNT5A	rs751194	-- + −	A	0.15
3	55464838	WNT5A	rs1499890	-- + −	A	0.15
3	55466053	WNT5A	rs629537	+−−-	A	0.82
3	55466476	WNT5A	rs503022	+−−-	A	0.76
3	55467366	WNT5A	rs645486	+ − +−	A	0.46
3	55468554	WNT5A	rs476986	--++	A	0.47
3	55469119	WNT5A	rs6792802	-- + −	T	0.07
3	55471300	WNT5A	rs11706227	+ − ++	T	0.07
3	55472993	WNT5A	rs11710229	- + −−	A	0.06
3	55474704	WNT5A	rs12497254	-- + −	A	0.08
3	55475448	WNT5A	rs10865994	-- + −	A	0.07
3	55476215	WNT5A	rs1829556	++ − +	T	0.08
3	55482321	WNT5A	rs556874	-++−	T	0.13
3	55486715	WNT5A	rs472631	+−−-	A	0.73
3	55494897	WNT5A	rs648872	+ − ++	A	0.77
3	55495818	WNT5A	rs566926	+ − ++	T	0.59
3	55506307	WNT5A	rs557077	+−−-	A	0.63
3	55506999	WNT5A	rs1160047	---+	A	0.39
3	121176301	GSK3B	rs6771023	++++	T	0.05
3	121225411	GSK3B	rs6770314	----	A	0.04
3	121232101	GSK3B	rs9851174	----	A	0.04
3	121246776	GSK3B	rs7652172	----	T	0.04
3	121255730	GSK3B	rs968824	++++	A	0.04
3	121273402	GSK3B	rs334536	++++	A	0.05
3	121274994	GSK3B	rs334535	----	T	0.05
3	121292295	GSK3B	rs334559	----	A	0.05
4	108110470	DKK2	rs17509845	++++	A	0.01
7	120715028	WNT16	rs2952556	----	A	<0.01
7	120723242	WNT16	rs10241888	----	A	<0.01
7	120727672	WNT16	rs2707521	----	T	0.01
7	120732453	WNT16	rs1547960	++++	A	<0.01
7	120739818	WNT16	rs10231005	----	A	<0.01
14	58700292	DAAM1	rs6573249	----	T	0.04
14	58728544	DAAM1	rs1252906	++++	A	0.02
14	58735687	DAAM1	rs8016570	++++	T	0.03
14	58744616	DAAM1	rs2146009	++++	A	0.01
14	58748939	DAAM1	rs1252989	++++	A	0.01
14	58753987	DAAM1	rs1270988	++++	A	0.01
14	58795556	DAAM1	rs17095967	++++	A	0.02
14	58800998	DAAM1	rs1253005	----	T	0.04
14	58847352	DAAM1	rs7149497	----	A	0.02
14	58870553	DAAM1	rs1957409	----	A	0.03
16	312598	AXIN1	rs3916990	++++	A	0.03
16	68144622	NFAT5	rs17230557	++++	T	0.02
16	68184592	NFAT5	rs17231138	++++	A	0.01
16	68198345	NFAT5	rs17297088	----	T	0.02
16	68200854	NFAT5	rs17297207	++++	A	0.02
16	68207765	NFAT5	rs17231474	++++	A	0.02
16	68224440	NFAT5	rs6499238	----	T	0.02
16	68262239	NFAT5	rs1437137	----	A	0.02
16	68309874	NFAT5	rs689453	----	T	0.02
17	42221887	WNT3	rs199496	++++	A	0.01
17	42223260	WNT3	rs11655598	++++	C	0.05
17	42223596	WNT3	rs199495	----	A	0.02
17	42229159	WNT3	rs11650531	++++	T	0.04
19	51811750	CALM3	rs11083840	++++	T	0.03

Direction of effect represents that observed in the FinnDiane, UK-ROI, US GoKinD George Washington University, US GoKinD Joslin Diabetes Center.? signifies where a marker failed QC in the original collection and was therefore unavailable for meta-analysis.
The P value presented represents the association of the meta-analysed data from all four GENIE cohorts.

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ISSN: 1471-2369

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