Table 3. Summary statistics of significantly associated regions identified by aMAT in the multi-trait analysis of a set of volume related IDPs.

Locus	SNP	CHR	BP	A1	A2	MAF	aMAT P	Nearest Gene
1	rs72688340	1	47,983,839	G	A	0.171	2.5 × 10−9	AL356458.1
2	rs6665134	1	180,949,628	C	A	0.401	1.7 × 10−10	STX6
3	rs476557	1	215,140,251	A	C	0.475	4.3 × 10−8	RP11-323K10.1
4	rs1504	2	37,066,018	T	G	0.447	1.4 × 10−8	AC007382.1
5	rs13070564	3	190,629,975	G	T	0.383	8.8 × 10−13	GMNC
6	rs10031823	4	103,125,031	T	C	0.395	1.3 × 10−8	SLC39A8
6	rs34333163	4	103,283,117	A	G	0.075	4.4 × 10−16	SLC39A8
7	rs1922930	6	1,364,691	A	C	0.118	3.8 × 10−8	RP4-668J24.2
8	rs77126132	7	54,966,738	G	A	0.089	1.8 × 10−8	SNORA73
9	rs2707521	7	120,940,436	C	T	0.377		CPED1
10	rs2974298	8	42,376,477	T	C	0.493	2.5 × 10−9	SLC20A2
11	rs10217651	9	118,923,652	A	G	0.386	1.7 × 10−14	PAPPA
11	rs35565319	9	119,065,043	C	T	0.072	6.7 × 10−16	PAPPA
11	rs7030607	9	119,245,183	G	A	0.36	6.7 × 10−9	ASTN2
12	rs12783517	10	21,878,407	C	T	0.299	1.3 × 10−8	MLLT10
13	rs4962692	10	126,424,823	G	A	0.414	2.7 × 10−10	FAM53B
14	rs1187159	11	92,009,792	T	C	0.413	5.1 × 10−11	NDUFB11P1
15	rs73123652	12	65,874,956	T	C	0.106	1.1 × 10−12	MSRB3
16	rs4301837	12	102,336,310	T	C	0.496	6.9 × 10−9	DRAM1
16	rs17797222	12	102,913,946	A	G	0.224	3.6 × 10−13	RP11-210L7.1
17	rs12146713	12	106,476,805	T	C	0.093	3.2 × 10−9	NUAK1
18	rs77956314	12	117,323,367	T	C	0.083	1.2 × 10−9	HRK
19	rs10129414	14	56,193,272	G	A	0.438	2.0 × 10−9	RP11-813I20.2
20	rs2464469	15	58,362,025	G	A	0.412	2.1 × 10−13	ALDH1A2
21	rs13330163	16	70,660,243	A	G	0.453	3.0 × 10−12	IL34
22	rs12920553	16	87,227,046	G	T	0.418	3.5 × 10−10	C16orf95
23	rs6121038	20	30,254,773	T	G	0.291	5.2 × 10−10	BCL2L1
24	rs1004764	22	38,474,852	G	A	0.377	4.2 × 10−9	SLC16A8

Independent lead SNPs are defined by $r^2<0.1$ and distinct loci are >250 kb apart. SNP, CHR, BP, A1, A2 are the lead SNP, chromosome, position, reference allele, and alternate allele, respectively. The MAF is the minor allele frequency and obtained from the 1000 genomes reference panel (Phase 3). aMAT P is the P-value for the aMAT test. SNPs in bold correspond to the novel SNPs that were ignored by standard GWAS for any IDP at the genome-wide significance level 5 × 10⁻⁸.