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Table 2 The top SNPs that CS-LMM identifies in an AD study with two known associations

From: Discovering weaker genetic associations guided by known associations

RankSNPChrChr PositionEst. Coe.MAFGeneDisease [Literature]
1rs207565019448923620.210.18APOEAD [38]
2rs15758019448920090.020.27TOMM40AD [39]
3rs1002792643412927-8.3E-110.14RGS12SCZ [40]
4rs1264198943418113-7.8E-110.14RGS12SCZ [40]
5rs308823143420484-7.5E-110.13RGS12SCZ [40]
6rs1051252317690449195.2E-110.28ABCA9AD [41]
7rs407694912340663994.2E-110.18SLC35F3 
8rs87441843440342-3.9E-110.19HGFAC 
9rs684241943475572-3.2E-110.16DOK7 
10rs1684438343445516-2.9E-110.21HGFAC 
11rs1213150812340171931.7E-110.17SLC35F3 
12rs1250682143282833-1.6E-110.16  
13rs1148517512224378681.4E-110.23  
14rs5845071064897881.2E-110.24PRKCQ 
15rs125636921216818264-1.2E-110.30ESRRGALC [42, 43]
16rs644673143283024-1.1E-110.26  
17rs79840511370233817-8.1E-120.25  
18rs232777120132957343.0E-120.29ISM1 
19rs754865112340128122.4E-120.20SLC35F3 
20rs43306748133209259-1.2E-120.24WISP1 
21rs16885750556578982-8.1E-130.12C5orf67 
22rs93841231885712693.6E-130.31LPP 
  1. The SNPs are ranked by the absolute values of their estimated coefficients. The first two SNPs with largest coefficients are known SNPs the model takes as a prior knowledge. The rest are SNPs predicted by the model. The MAFs reported in the table are calculated using the AD GWAS data. The information of whether a SNP is located within a region of a gene is taken from the dbSNP. Abbreviations: ALC, Alchoholism; AD, Alzheimer’s Disease; SCZ, Schizophrenia; Est. Coe.: Estimated Coefficients. Note that the literature support may refer to how the genes that the corresponding SNPs reside in are related to the phenotype, instead of the SNPs themselves. See discussions in Section Alzheimer’s Disease Study for details.