Table 4.

Results of SS2, SMR, SMR-multi, COLOC, and COLOC2 applied to the MUC20/MUC4 locus in primary human nasal epithelia (HNE) at chromosome 3

Gene and tissue	SS2 stage 1 test		SS2 stage 2 test		SMR		SMR-multi		COLOC	COLOC2
	p value	Adjusted p value	p value	Adjusted p value	p value	Adjusted p value	p value	Adjusted p value	CLPP	CLPP1a	CLPP2
MUC20 and HNE	0.083	1	N/A	N/Ab	N/A	N/A	N/A	N/A	0.1057	0.0666	0.0005
MUC4 and HNE	3.16 × 10−7	1.78 × 10−4	1.31 × 10−5	1.49 × 10−3	2.65 × 10−3	0.379	2.07 × 10−4	0.0296	0.7573	0.9482c	0.0007

Colocalization analyses are conducted for all genes within a 1 Mb region on either side of the peak lung GWAS-associated variant and 14 CF-related tissues. In total, there are 564 gene-by-tissue pairs. Raw p values and adjusted p values by 564 gene-by-tissue pairs are both demonstrated for the SS2, SMR, and SMR-multi. The eQTL evidence for conducting the SS2 is the eQTL p value based on the −log10(eQTL p) scale for a specified gene and tissue. SMR and Multi-SNP-based SMR test (SMR-multi) are conducted under the default setting such that a SNP is picked only if the eQTL p value is less than 5 × 10⁻⁸. N/As are listed for MUC20 since no SNP has eQTL p value less than 5 × 10⁻⁸. For COLOC and COLOC2, the colocalization posterior probability (CLPP) is calculated, and a high posterior probability (>0.8) suggests strong colocalization evidence. For COLOC2, we show both the CLPP calculated based on the likelihood from the single gene and tissue (CLPP1) and the CLPP calculated based on the likelihood from 564 gene-by-tissue pairs (CLPP2).

^aThis method has been shown with inflation in Table 1. CLPP1 > 0.8 suggests colocalization.

^bThe stage 1 SS2 test p value (0.083) for MUC20 and HNE does not pass the significant threshold (0.05) and therefore, the stage 2 SS2 test p value is not applicable (N/A).

^cThis method has been shown with inflation in Table 1.