. 2012 Sep 7;91(3):422–434. doi: 10.1016/j.ajhg.2012.07.010

Table 3.

The Ranking of the Causal Variants via Different Statistics

Phenotype	Discovery SNP	Number of Candidate SNVs^a	Causal SNV	MAF	Rank of the Causal SNV^b
Phenotype	Discovery SNP	Number of Candidate SNVs^a	Causal SNV	MAF	D′	r²	P_LD	PhastCons	Sorting Score
Crohn disease	rs17221417	1,658	rs2066844	0.048	1,306	26	34	42	1
Crohn disease	rs17221417	1,658	rs2066845	0.023	1,306	89	38	35	2
Crohn disease	rs2076756	1,523	rs2066845	0.023	1,195	68	27	31	1
Crohn disease	rs2076756	1,523	rs2066844	0.048	1,195	13	19	37	2
Ribavirin-induced hemolytic anemia	rs6051702	1,289	rs1127354	0.081	829	86	49	1	1
Ribavirin-induced hemolytic anemia	rs6051702	1,289	rs7270101	0.128	776	22	39	10	2
Therapeutic warfarin dose	rs4917639	1,966	rs1799853	0.134	1,586	7	26	10	2
Bladder cancer	rs11892031	516	rs17863783	0.015	256	102	20	73	37^c
Hearing loss	rs870729	1,477	rs80338945	0.002	964	1145	150	7	5
Hearing loss	rs7329467	999	rs35887622	0.015	574	55	12	70	6

The following abbreviations are used: SNV, single-nucleotide variant; MAF, minor allele frequency; and P_LD, preferential linkage disequilibrium.

Candidate SNVs are the ones obtained at step 1 of the preferential LD approach.

The rank of the causal variant is the number of candidate SNVs with an equal or better value of the corresponding statistic than the causal variant.

The rank of rs17863783 shown here is different from the rank shown on Table 2 because the 14 candidate SNVs with larger sorting scores than rs17863783 did not pass the permutation test at step 3.