Table 3.

Combined association and linkage-weighted FDR q-values and genome-wide ranks for SNPs with WFDR q-values genome-wide significant (< 0.05)

Chr	SNP	Base Pair	GMS+CGS F508del/F508del Association P value	FDR q-valuea	FDR rank	WFDR q-valueb	WFDR rank
11	rs93138	9716289	5.08E-06	0.0124	7	0.0383	16
11	rs11032829	34705078	2.29E-06	0.008	3	0.0277	8
11	rs7924717	34732907	2.76E-06	0.008	1	0.0218	6
11	rs10466455	34737512	3.86E-07	0.0124	6	0.0375	14
11	rs7929679	34762425	1.47E-06	0.008	5	0.0282	10
11	rs10836312	34767019	1.56E-07	0.008	2	0.0277	7
11	rs525202	34778524	1.34E-07	0.008	4	0.0277	9
20	rs7265042	53790816	1.14E-03	0.7852	1976	0.0459	18
20	rs6098782	53791974	1.84E-03	0.7349	865	0.0459	17
20	rs910668	53794753	1.09E-03	0.5029	175	0.015	2
20	rs6092176	53799109	1.51E-03	0.5581	255	0.015	5
20	rs6092179	53812440	1.93E-04	0.484	154	0.015	1
20	rs6024437	53813962	1.61E-04	0.7553	1116	0.0353	13
20	rs8125625	53820352	2.49E-04	0.516	207	0.015	3
20	rs6024454	53826840	2.56E-04	0.7615	1348	0.0381	15
20	rs6024460	53828948	1.34E-04	0.7349	854	0.0296	12
20	rs11907114	53862354	2.79E-03	0.554	250	0.015	4
20	rs1326022	54277432	1.16E-03	0.7344	824	0.0296	11

^aBenjamini-Hochberg approach based on association P-value.

^bWeighted FDR using combined linkage information and association P-values.

Rows in bold indicate the top ranked SNPs before incorporating linkage evidence (rs7924717 on chromosome 11) and after (rs6092179 on chromosome 20)