Table 1 Counts of GWAS hits across runs in the UPE framework, \({{{{\mathcal{C}}}}}_{\ell }\) for each locus ℓ, which represents the number of runs for which the corresponding locus shows at least one association with P < P_GW = 5 × 10⁻⁸ (see details in the Methods section)

From: Unsupervised ensemble-based phenotyping enhances discoverability of genes related to left-ventricular morphology

Chromosome	Region	Candidate gene	Count	Minimum P value	Lead variant	NEA/EA	EAF (%)	\(\bf{\|} \hat{\boldsymbol{\beta} }\| \pm {{{\bf{se}}}}(\hat{\boldsymbol{\beta} })({\boldsymbol{\times 1{0}^{-2}}})\)
10	120591353–122407323	BAG3	35	4.1 × 10⁻¹⁸	rs375034445	A/AT	21.2	5.29 ± 0.79
2	178553183–181312739	TTN	35	1.4 × 10⁻¹⁷	rs2042995	T/C	23.2	5.70 ± 0.77
6	117672972–118963115	PLN	35	2.0 × 10⁻²⁹	rs11153730	T/C	48.6	4.29 ± 0.64
14	23018665–24905123	MYH6	34	2.7 × 10⁻¹⁴	rs365990	A/G	36.9	4.04 ± 0.66
12	113986709–115036602	TBX5	34	2.3 × 10⁻¹¹	rs4767239	G/C	82.5	4.12 ± 0.85
12	110336719–113263518	MYL2	34	2.8 × 10⁻¹⁵	rs35350651	A/AC	51.4	4.36 ± 0.64
4	119933512–120392684	MYOZ2	33	2.4 × 10⁻¹³	4:120304290_GC_G	GC/G	29.0	3.96 ± 0.71
10	73508512–75422550	SYNPO2L	31	2.5 × 10⁻¹⁵	rs3740293	A/C	14.3	5.07 ± 0.92
3	157312028–159477890	SHOX2	30	7.0 × 10⁻¹⁵	rs11706187	A/G	50.1	3.23 ± 0.64
1	154770403–156336133	FDPS	29	9.7 × 10⁻¹³	rs41314549	T/C	2.81	13.7 ± 1.9
17	43056905–45876022	GOSR2	26	8.3 × 10⁻²²	rs17608766	T/C	14.3	5.73 ± 0.90
3	99373762–100592217	FILIP1L^a	25	8.4 × 10⁻¹⁴	rs9811920	G/A	40.8	3.23 ± 0.65
16	4001196–5118345	SRL	24	9.4 × 10⁻¹²	rs889807	T/C	50.8	3.24 ± 0.64
1	21736588–23086883	KDM1A	22	2.0 × 10⁻¹²	rs35001652	G/A	37.3	2.59 ± 0.67
7	45952922–46986720	IGFBP3	22	2.0 × 10⁻¹¹	rs143741275	A/AGTGTGT	42.4	2.59 ± 0.66
5	171074292–172678327	NKX2-5	21	9.0 × 10⁻¹⁴	rs35564079	C/CT	28.5	2.76 ± 0.72
3	13070799–14816900	TMEM43	21	2.7 × 10⁻¹¹	rs900173	T/C	34.0	3.48 ± 0.68
1	144977494–148361253	GJA5	20	1.1 × 10⁻¹⁰	rs12046416	A/G	33.5	2.81 ± 0.68
1	235819436–237555628	ACTN2	20	2.0 × 10⁻¹²	rs12142143	T/C	53.1	4.11 ± 0.65
13	20686720–22242174	FGF9	20	8.8 × 10⁻¹³	rs10628955	G/GAA	47.7	3.95 ± 0.67
4	111256567–113870102	PITX2	19	4.4 × 10⁻¹⁴	rs2723294	C/T	69.5	4.65 ± 0.70
1	14891511–16897730	HSPB7	17	2.3 × 10⁻¹¹	rs1763605	T/G	67.5	2.80 ± 0.68
2	146445570–147277162	ACVR2A/ZEB2	16	2.9 × 10⁻¹¹	rs573709385	A/AT	44.9	1.93 ± 0.65
6	125424383–127540461	HEY2	16	2.9 × 10⁻¹¹	rs11423823	C/CT	50.2	3.23 ± 0.66
2	36122006–38132712	STRN	15	9.9 × 10⁻¹⁶	rs2110944	T/C	52.6	3.71 ± 0.64
16	79134815–80297374	MAF^a	15	5.2 × 10⁻¹¹	rs558328129	A/AT	45.4	2.97 ± 0.70
8	107410754–108648177	ABRA	15	8.1 × 10⁻¹¹	rs72007904	A/AACTATTC	50.0	3.87 ± 0.64
21	27271019–29125226	ADAMTS1	15	1.4 × 10⁻¹⁰	rs2830977	G/A	22.0	4.29 ± 0.78
1	49894177–51713726	RNF11^a	13	3.1 × 10⁻¹¹	rs7555411	C/T	1.42	13.8 ± 2.7
13	98938919–100574095	DOCK9^a	13	1.2 × 10⁻¹⁰	rs34138434	C/A	29.7	4.62 ± 0.72
2	118367466–121303783	EN1^a	13	6.7 × 10⁻¹⁴	rs162746	A/G	67.5	4.01 ± 0.68
12	27799773–29651255	CCDC91^a	12	2.0 × 10⁻¹⁴	rs5797270	G/GT	20.3	3.35 ± 0.81
13	25784362–27284362	WASF3^a	11	9.3 × 10⁻¹¹	rs61944841	G/A	41.3	3.07 ± 0.67
18	19485844–20649472	GATA6	11	6.6 × 10⁻¹¹	rs62094198	T/A	39.6	2.21 ± 0.66
14	19002084–21589402	NDRG2	10	2.5 × 10⁻¹¹	rs12889267	A/G	16.7	3.43 ± 0.85
6	35455756–37572596	CDKN1A	10	3.2 × 10⁻¹³	rs3176326	G/A	19.8	3.47 ± 0.81
7	118351581–121045273	WNT16	10	2.4 × 10⁻¹¹	rs3801387	A/G	28.1	2.79 ± 0.72
16	75977954–77523678	ADAMTS18	10	5.2 × 10⁻¹³	rs62046468	C/T	37.6	4.80 ± 0.66
17	41772087–43056905	SOST	10	5.5 × 10⁻¹¹	rs17881550	G/GC	43.4	3.65 ± 0.65
11	27020461–28481593	CCDC34^a	8	5.7 × 10⁻¹²	rs10835164	C/T	25.6	3.84 ± 0.74
5	120452166–122556905	PRDM6	8	6.2 × 10⁻¹¹	rs463106	T/C	47.2	3.68 ± 0.65
17	67858770–69387817	KCNJ2/SOX9	7	3.6 × 10⁻¹²	rs56229089	G/C	55.7	2.89 ± 0.65
5	63968304–65911286	ADAMTS6	7	1.6 × 10⁻¹¹	rs753963943	ATT/A	42.5	2.88 ± 0.66
18	8498931–11075913	NDUFV2	6	6.1 × 10⁻¹²	rs206524	T/C	70.7	3.01 ± 0.71
11	65898631–68005825	KDM2A	4	2.1 × 10⁻¹¹	rs12785906	G/C	5.84	7.40 ± 1.38
1	1892607–3582736	PRDM16	3	1.7 × 10⁻¹¹	rs781212641	G/GC	9.33	5.68 ± 1.12
4	7539692–8152235	AFAP1	3	1.4 × 10⁻¹¹	rs28542374	G/A	63.5	3.10 ± 0.67
12	76511314–78570570	NAV3	3	2.7 × 10⁻¹²	rs7965680	T/C	55.7	2.43 ± 0.65
17	15019097–16412342	CENPV^a	3	3.4 × 10⁻¹¹	rs7477	A/C	49.8	3.18 ± 0.64

The total number of runs was 36. The lead variant is the one for which the minimum P value occurs. P values are two-sided and derived from a linear association t-statistic (no adjustments were made for multiple comparisons). NEA and EA stand for non-effect and effect allele, respectively, whereas \(\hat{\beta }\) is the standardized effect size estimate. EAF is the frequency of EA. Note that these values correspond to different phenotypes of the ensemble, therefore they are not comparable in terms of the magnitude of the morphological change that they produce. The directions of effect can be understood with the help of Supplementary Table 5.
^aThe genes were annotated based purely on closest proximity to the lead variant in that region (the rest of the genes have additional previous evidence of a link to cardiac physiology as discussed in the text).
Gene names that are in bold mean that the corresponding locus is only discovered with UPE, that is the remaining loci were already found by testing the handcrafted phenotypes or the shape PCs.

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Table 1 Counts of GWAS hits across runs in the UPE framework, \({{{{\mathcal{C}}}}}_{\ell }\) for each locus ℓ, which represents the number of runs for which the corresponding locus shows at least one association with P < P_GW = 5 × 10⁻⁸ (see details in the Methods section)

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