ARID1A and colorectal carcinoma: We highlighted in Supplementary Fig. S2A spsQTLs where the affected gene’s protein showed negative protein log fold-change (logFC), whereas the mRNA logFC is nonnegative, including CASP8 truncations in UCEC, ARID1A truncations in CRC and UCEC, and ATM truncations in LUAD and UCED.