Table 1 TMT AD network mod-QTLs

SNP	CHR	BP	A1	Nearest coding gene to SNP	Beta	P value	Module	mod-QTL	Module protein within 1 Mb of SNP
rs28716042	8	125,418,451	G	TMEM65	0.04	3.7 × 10⁻⁹	M3 oligo/myelination	trans	NA
rs112028701	13	104,134,726	T	SLC10A2	−0.04	3.1 × 10⁻⁸	M22 post-synaptic density	trans	NA
rs11021075	11	94,940,421	T	SESN3	0.02	4.9 × 10⁻⁸	M26 complement/acute phase	trans	NA
rs1733609	7	81,536,375	A	CACNA2D1	0.02	1.6 × 10⁻⁸	M11 cell–ECM interaction	trans	NA
rs429358	19	45,411,941	C	APOE	0.02	3.2 × 10⁻⁸	M42 matrisome	cis	APOE
rs6940448	6	3,810,805	G	FAM50B	−0.02	1.4 × 10⁻⁸	M8 protein transport	cis	TUBB2A
rs1553484	6	91,507,934	A	MAP3K7	−0.02	6.4 × 10⁻⁹	M29 glycosylation/ER	trans	NA
rs2352535	4	114,127,905	T	ANK2	0.02	2.4 × 10⁻⁸	M27 ECM	trans	NA

SNPs associated with the first eigenprotein of a protein module at a genome-wide significant level (P < 5 × 10⁻⁸ using Bonferroni correction) were referred to as protein co-expression mod-QTLs. mod-QTLs located within 1 Mb of one of the module proteins were defined as proximal (cis) mod-QTLs; otherwise, they were categorized as distal (trans) mod-QTLs. The associations were determined using linear regression and were adjusted for cognitive diagnosis, sex, ten genetic PCs and genotyping chip. A1, allele; BP, base pair; CHR, chromosome; NA, not applicable.

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