Appendix 3.

Summary statistics for differentially expressed exons between Rejectors and Non-rejectors

Exon ID	Transcript ID	Exon fold change†	Exon p-value†	Transcript fold change‡	Transcript p-value‡	Transcript/SNP name	Exon start/SNP location	Exon stop
2950312	2950307	1.063	0.555	−1.083	0.326	HLA-DOA	33,081,985	33,082,504
2950313	2950307	1.122	0.397	−1.083	0.326	HLA-DOA	33,082,838	33,082,870
2950314	2950307	1.069	0.372	−1.083	0.326	HLA-DOA	33,082,939	33,082,970
2950317	2950307	−1.065	0.638	−1.083	0.326	HLA-DOA	33,083,111	33,083,291
2950322	2950307	−1.060	0.395	−1.083	0.326	HLA-DOA	33,083,777	33,083,802
2950323	2950307	−1.011	0.905	−1.083	0.326	HLA-DOA	33,083,818	33,083,847
2950324	2950307	1.017	0.84	−1.083	0.326	HLA-DOA	33,083,857	33,083,987
2950325	2950307	1.127	0.383	−1.083	0.326	HLA-DOA	33,084,068	33,084,099
2950326	2950307	−1.048	0.748	−1.083	0.326	HLA-DOA	33,085,222	33,085,260
2950327	2950307	−1.532	0.0153	−1.083	0.326	HLA-DOA	33,085,305	33,085,362
	untranslated					rs6457699	33,089,625
	untranslated					rs9276994	33,092,233
	untranslated					rs6933994	33,095,098
	untranslated					rs9296068	33,096,673
	untranslated					rs9277015	33,101,244
2950331	2950329	1.129	0.545	−1.166	0.419	HLA-DPA1	33,140,788	33,140,818
2950332	2950329	−1.161	0.517	−1.166	0.419	HLA-DPA1	33,140,836	33,140,861
2950333	2950329	−1.246	0.204	−1.166	0.419	HLA-DPA1	33,140,925	33,141,014
2950338	2950329	−1.302	0.0128	−1.166	0.419	HLA-DPA1	33,144,437	33,144,544
2950340	2950329	−1.114	0.31	−1.166	0.419	HLA-DPA1	33,144,774	33,144,804
2950341	2950329	−1.014	0.875	−1.166	0.419	HLA-DPA1	33,144,844	33,144,876
2950342	2950329	1.030	0.792	−1.166	0.419	HLA-DPA1	33,144,929	33,144,963
2950343	2950329	−1.114	0.479	−1.166	0.419	HLA-DPA1	33,144,969	33,144,999
2950345	2950329	1.057	0.565	−1.166	0.419	HLA-DPA1	33,145,413	33,145,477
2950346	2950329	1.346	0.113	−1.166	0.419	HLA-DPA1	33,145,573	33,145,641
2950348	2950329	1.035	0.723	−1.166	0.419	HLA-DPA1	33,149,238	33,149,262

^†Exon fold change, or splicing index, is calculated as the ratio of mean gene-level normalized intensities between rejectors and non-rejectors. Negative values indicate exon skipping or repression, whereas positive values indicate exon enrichment. The p-values are calculated using a Student’s two-sample t -test on gene-level normalized intensities. Orange cells indicate p<.05.

^‡Transcript fold change is calculated as the ratio of the mean gene-level intensities between rejectors and non-rejectors. All exons within a transcript have identical gene-level intensities, but different exon-level intensities. The p-values are calculated using a Student’s two-sample t -test on gene-level intensities.