Identification of candidate protective variants for common diseases and evaluation of their protective potential

Butler, Joe M.; Hall, Neil; Narendran, Niro; Yang, Yit C.; Paraoan, Luminita

doi:10.1186/s12864-017-3964-3

BMC Genomics

Table 2 Candidate protective nsSNPs

From: Identification of candidate protective variants for common diseases and evaluation of their protective potential

	Disease	Gene	rsID	Chr	Position	Anc	Der	OR^b	SNPs in high LD set	Mean iHS	GWAS
1	Multiple sclerosis	IL7R	rs6897932	5	35,874,575	C	T	1.12	6	−1.462	[34]
2	Glaucoma (primary open-angle)	COL11A1	rs3753841	1	103,379,918	G	A	1.20	22	−1.270	[35]
3	Type 2 diabetes	SLC30A8	rs13266634	8	118,184,783	C	T	1.16	5	−1.218	[36]^a
4	Psoriasis	TYK2	rs12720356	19	10,469,975	A	C	1.40	1	−1.197	[37]
5	Acute lymphoblastic leukemia (childhood)	KCNE4	rs12621643	2	223,917,983	T	G	1.48	3	−1.167	[38]
6	Ulcerative colitis	IL17REL	rs5771069	22	50,435,480	G	A	1.11	10	−1.121	[39]
7	Esophageal cancer and gastric cancer	PLCE1	rs3765524	10	96,058,298	T	C	1.35	23	−0.897	[40]
8	IgA nephropathy	TNFSF13	rs3803800	17	7,462,969	A	G	1.21	23	−0.819	[41]
9	Systemic lupus erythematosus	WDFY4	rs7097397	10	50,025,396	G	A	1.30	18	−0.767	[42]
10	Esophageal cancer	PLCE1	rs2274223	10	96,066,341	G	A	1.34	38	−0.740	[43]
11	AMD	CFB	rs641153	6	31,914,180	G	A	2.44	13	−0.723	-
12	Inflammatory bowel disease	CD6	rs11230563	11	60,776,209	C	T	1.09	21	−0.705	[44]
13	Behcet’s disease	KLRC4	rs2617170	12	10,560,957	T	C	1.28	46	−0.657	[45]
14	Coronary heart disease	ZC3HC1	rs11556924	7	129,663,496	C	T	1.09	6	−0.649	[46]
15	Type 1 diabetes	TYK2	rs2304256	19	10,475,652	C	A	1.16	7	−0.627	[47]
16	Obesity	GIPR	rs1800437	19	46,181,392	G	C	1.1	10	−0.606	[48]
17	AMD	C2	rs9332739	6	31,903,804	G	C	1.82	9	−0.551	-
18	Type 2 diabetes	PPARG	rs1801282	3	12,393,125	C	G	1.14	11	−0.537	[49]
19	Inflammatory bowel disease	TUBD1	rs1292053	17	57,963,537	G	A	1.08	41	−0.498	[44]
20	Migraine	MMP17	rs6598163	12	132,325,239	G	A	1.15	22	−0.493	[50]
21	Glaucoma (exfoliation)	LOXL1	rs3825942	15	74,219,582	G	A	20.1	26	−0.453	[51]
22	Inflammatory bowel disease	IL23R	rs11209026	1	67,705,958	G	A	2.01	2	−0.410	[52]
23	Multiple sclerosis	MPV17L2	rs874628	19	18,304,700	A	G	1.11	8	−0.292	[53]
24	Rheumatoid arthritis	RTKN2	rs3125734	10	63,958,112	T	C	1.20	12	−0.263	[54]
25	Interstitial lung disease	LRRC34	rs6793295	3	169,518,455	C	T	1.30	19	−0.228	[55]
26	Obesity	SH2B1	rs7498665	16	28,883,241	G	A	1.07	27	−0.210	[48]
27	Breast cancer	ANKLE1	rs8100241	19	17,392,894	G	A	1.14	11	−0.185	[56]
28	Systemic lupus erythematosus	BANK1	rs10516487	4	102,751,076	G	A	1.38	8	−0.184	[57]
29	Ovarian cancer	ANKLE1	rs2363956	19	17,394,124	T	G	1.10	13	−0.153	[58]
30	Rheumatoid arthritis	NFKBIE	rs2233434	6	44,232,920	G	A	1.20	32	−0.114	[59]
-	Hypertension	LPL	rs328	8	19,819,724	C	G	-	28	−0.031	-
31	Type 2 diabetes	WFS1	rs1801214	4	6,303,022	T	C	1.13	8	0.314	[60]
32	Type 2 diabetes	THADA	rs7578597	2	43,732,823	T	C	1.15	49	0.379	[61]
33	Psoriasis	IL13	rs20541	5	131,995,964	G	A	1.27	8	0.872	[62]
34	Prostate cancer	MLPH	rs2292884	2	238,443,226	G	A	1.14	40	0.883	[63]

^adenotes the nsSNP has been detected by more than one GWAS in the catalog, we only report the first chronologically
^bOR for ancestral allele

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ISSN: 1471-2164

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