Table 1. Genetic Correlation and Genetic Overlap Estimations Between 24 Pairwise Traits^a.

Trait pair	Genetic correlation				Genetic overlap
	Genetic correlation (SE)	P value for LDSC	Intercept (SE)	P value for intercept	PM 11	PARb	P value for GPA
IBD-MDDc,d	0.1706 (0.0407)	2.82 × 10−5	0.0003 (0.0055)	9.57 × 10−1	0.0116	0.0473	1.41 × 10−3
IBD-PTSD	0.1742 (0.0377)	7.39 × 10−2	0.0049 (0.0051)	3.37 × 10−1	0.0038	0.0189	2.27 × 10−1
IBD-SCZd	0.0359 (0.0403)	3.73 × 10−1	0.0004 (0.0062)	9.49 × 10−1	0.0167	0.0605	6.07 × 10−15
IBD-ADHD	–0.0045 (0.0599)	9.40 × 10−1	0.0121 (0.0057)	3.38 × 10−2	0.0121	0.0512	5.16 × 10−2
IBD-BIPd	0.0221 (0.0478)	6.45 × 10−1	0.0064 (0.0063)	3.10 × 10−1	0.0194	0.0828	3.80 × 10−28
IBD-ANd	–0.0296 (0.0630)	6.38 × 10−1	0.0019 (0.0063)	7.63 × 10−1	0.0206	0.0851	8.85 × 10−11
IBS-MDDc,d,e	0.5705 (0.0256)	1.14 × 10−109	0.0795 (0.0066)	2.05 × 10−33	0.1571	0.7791	<1 × 10−300
IBS-PTSDc,d,e	0.4720 (0.0795)	2.87 × 10−9	0.0275 (0.0049)	2.00 × 10−8	0.0422	0.1504	1.27 × 10−5
IBS-SCZc,d	0.1711 (0.0285)	1.85 × 10−9	–0.0025 (0.006)	6.77 × 10−1	0.1246	0.4130	<1 × 10−300
IBS-ADHDc,d	0.2060 (0.0405)	3.73 × 10−7	0.0138 (0.0059)	1.93 × 10−2	0.1155	0.3895	1.67 × 10−87
IBS-BIPc,d,e	0.1269 (0.0305)	3.12 × 10−5	0.0219 (0.0058)	1.59 × 10−4	0.1183	0.4579	3.54 × 10−268
IBS-ANc,d	0.1536 (0.0413)	2.00 × 10−4	0.0003 (0.0064)	9.63 × 10−1	0.1207	0.4059	3.98 × 10−86
PUD-MDDc,d,e	0.4438 (0.0437)	3.31 × 10−24	0.0333 (0.0059)	1.66 × 10−8	0.0987	0.4011	1.04 × 10−102
PUD-PTSDc	0.5448 (0.1120)	1.15 × 10−6	0.0074 (0.0046)	1.08 × 10−1	0.0274	0.1052	3.65 × 10−2
PUD-SCZc,d	0.1306 (0.0402)	1.20 × 10−3	–0.0007 (0.006)	9.07 × 10−1	0.0832	0.2713	7.89 × 10−55
PUD-ADHDc,d	0.4771 (0.0579)	1.63 × 10−16	0.0072 (0.0058)	2.14 × 10−1	0.0886	0.3409	1.27 × 10−37
PUD-BIPd	0.0691 (0.0437)	1.14 × 10−1	0.0023 (0.0054)	6.70 × 10−1	0.0679	0.2491	1.31 × 10−34
PUD-ANd	0.0366 (0.0539)	4.97 × 10−1	0.0014 (0.0056)	8.03 × 10−1	0.0448	0.1441	8.03 × 10−4
GERD–MDDc,d,e	0.4596 (0.0267)	3.50 × 10−66	0.0692 (0.0053)	5.83 × 10−39	0.1762	0.6824	<1 × 10−300
GERD-PTSDc,d	0.4193 (0.0690)	1.24 × 10−9	0.0156 (0.0051)	2.22 × 10−3	0.0538	0.1567	3.43 × 10−4
GERD-SCZd	0.0313 (0.0273)	2.51 × 10−1	0.0107 (0.0062)	8.44 × 10−2	0.1299	0.3596	1.07 × 10−189
GERD-ADHDc,d	0.4919 (0.0371)	3.32 × 10−40	–0.0003 (0.0063)	9.62 × 10−1	0.1543	0.4844	6.81 × 10−132
GERD-BIPd	0.0332 (0.0308)	2.81 × 10−01	0.0048 (0.0059)	4.16 × 10−1	0.1279	0.4050	1.27 × 10−174
GERD-ANd	0.0179 (0.0386)	6.43 × 10−1	0.0038 (0.0063)	5.46 × 10−1	0.1265	0.3597	1.24 × 10−61

Abbreviations: ADHD, attention-deficit/hyperactivity disorder; AN, anorexia nervosa; BIP, bipolar disorder; GERD, gastroesophageal reflux disease; GPA, genetic analysis incorporating pleiotropy and annotation method; IBD, inflammatory bowel disease; IBS, irritable bowel syndrome; LDSC, linkage disequilibrium score regression; MDD, major depressive disorder; PAR, pleiotropy association ratio; PM 11, proportion of genetic variants associated with both traits; PTSD, posttraumatic stress disorder; PUD, peptic ulcer disease; SCZ, schizophrenia.

^a Genetic correlation and genetic overlap were estimated by LDSC and GPA methods, respectively. Bonferroni-corrected significance threshold was set at P < 2.83 × 10⁻³ (.05/24), producing a final union set of 22 pairwise traits with significant genetic correlation or genetic overlap for subsequent analysis.

^b We introduced PAR as PM 11/(PM 10 + PM 01 + PM 11) to represent the proportion of pleiotropic single-nucleotide variations (SNVs) associated with both traits against the proportion of SNVs associated with at least 1 trait.

^c Pairwise trait with significant genetic correlation.

^d Pairwise trait with significant genetic overlap.

^e Genome-wide association study summary data with potentially significant sample overlap.