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Table 1 The top SNPs that CS-LMM identifies in an alcoholism study with four known associations

From: Discovering weaker genetic associations guided by known associations

RankSNPChrChr PositionEst. Coe.MAFGeneDisease [Literature]
1rs17898914993292624.2E30.15ADH1BALC [27]
2rs759072022160339351.7E30.29PECRALC [28]; AD [29]
3rs283587221376549701.5E30.25KCNJ6ALC [30]; DS [31]
4rs44788581314110781.4E30.44SERINC2ALC [32]
5rs1789924499353129-2.2E-40.33ADH1CALC [33]
6rs698499339632-2.2E-40.33ADH1CALC [33]
7rs2851300499358667-2.2E-40.33  
8rs104830382137652469-1.6E-40.25KCNJ6ALC [30]; DS [31]
9rs13446942216028914-1.3E-40.32PECRALC [28]; AD [29]
10rs4147536499317955-7.6E-50.30ADH1BALC [27]
11rs124825702137705475-5.9E-50.28KCNJ6ALC [30]; DS [31]
12rs8579752137629311-5.8E-50.28KCNJ6ALC [30]; DS [31]
13rs4147544499213357-5.7E-50.45ADH6ALC [34]
14rs7028602137636327-5.6E-50.26KCNJ6ALC [30]; DS [31]
15rs28358532137642590-5.6E-50.26KCNJ6ALC [30]; DS [31]
16rs7178592137640500-5.6E-50.26KCNJ6ALC [30]; DS [31]
17rs11499823499353592-5.6E-50.12ADH1CALC [33]
18rs28359102137713604-5.5E-50.30KCNJ6ALC [30]; DS [31]
19rs4355398499237168-3.8E-50.25  
20rs2187483499212946-9.7E-70.38ADH6ALC [34]
21rs28358312137614931-6.9E-70.30  
  1. The SNPs are ranked by the absolute values of their estimated coefficients. The first four SNPs with the largest coefficients in the upper panel are known SNPs that our model CS-LMM takes as prior knowledge. The rest SNPs in the lower panel are ones predicted by the model. The MAFs reported in the table are calculated using the case-control alcoholism GWAS data. The information of whether a SNP is located within a region of a gene is taken from the Database for Single Nucleotide Polymorphisms (dbSNP) [35], and listed in the ’Gene’ column. Abbreviations: ALC, Alcoholism; AD, Alzheimer’s Disease; DS, Down Syndrome; 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 Alcoholism Study for details