Table 1.

Previously Unreported Associations with PLT

rsID	Ref/Alt	Function	Gene	European Ancestry (EA)						Combined All Ancestry (All)
Discovery (n = 108,598)			Replication (n = 19,939)		Combined	Discovery (n = 131,857)			Replication (n = 25,436)		Combined
EAF	Beta	p Value	Beta	p Value	p Value	EAF	Beta	p Value	Beta	p Value	p Value
rs3091242	C/T	intron	TMEM50A	0.54	−0.026	9.68 × 10−8	−0.017	0.124	3.85 × 10−8	0.50	−0.02	1.03 × 10−5	−0.0084	0.390	1.24 × 10−5
rs12566888	G/T	intron	PEAR1∗	0.094	0.040	1.42 × 10−7	0.061	1.26 × 10−3	1.17 × 10−9	0.16	0.034	2.09 × 10−8	0.047	4.31 × 10−4	5.71 × 10−11
rs200731779	C/G	missense	FCER1A	1.5 × 10−5	−2.96	2.48 × 10−7	NA	NA	2.48 × 10−7	1.2 × 10−5	−2.96	2.48 × 10−7	NA	NA	2.48 × 10−7
rs6734238	A/G	intergenic	IL1F10/IL1RN	0.41	0.022	9.55 × 10−6	0.0075	0.487	1.64 × 10−5	0.41	0.026	7.19 × 10−9	0.015	0.117	3.77 × 10−9
rs12692566a	C/A	missense	LY75-CD302∗	0.82	−0.029	9.19 × 10−7	−0.042	2.50 × 10−3	1.23 × 10−8	0.83	−0.026	2.27 × 10−6	−0.05	7.84 × 10−5	3.65 × 10−9
rs78446341	G/A	missense	LY75-CD302∗	0.02	0.092	4.16 × 10−9	0.14	5.01 × 10−5	1.98 × 10−12	0.018	0.094	3.06 × 10−10	0.13	9.23 × 10−5	1.97 × 10−13
rs56106611b	T/G	missense	KALRN∗	0.012	0.11	3.51 × 10−8	0.11	7.14 × 10−3	8.51 × 10−10	0.01	0.11	8.59 × 10−8	0.11	7.37 × 10−3	2.14 × 10−9
rs1470579	A/C	intron	IGF2BP2	0.32	−0.028	1.08 × 10−7	−0.0073	0.562	2.82 × 10−7	0.38	−0.023	6.07 × 10−7	−0.012	0.272	5.15 × 10−7
rs1126673	C/T	ncRNA	LOC100507053	0.69	0.026	6.38 × 10−8	0.019	9.63 × 10−2	1.81 × 10−8	0.71	0.025	1.87 × 10−8	0.014	0.168	1.12 × 10−8
rs1473247b	T/C	intron	RNF145∗	0.27	−0.029	3.01 × 10−8	−0.022	8.32 × 10−2	7.28 × 10−9	0.32	−0.026	1.32 × 10−8	−0.025	1.85 × 10−2	7.66 × 10−10
rs2256183	A/G	intron	MICA	0.56	0.03	6.78 × 10−7	−0.022	0.104	2.60 × 10−6	0.59	0.028	2.13 × 10−7	0.011	0.389	3.20 × 10−7
rs1050331	T/G	3′ UTR	ZMIZ2	0.47	0.037	1.32 × 10−15	0.036	5.80 × 10−4	3.28 × 10−18	0.48	0.035	3.09 × 10−17	0.031	8.80 × 10−4	1.26 × 10−19
rs755109	T/C	intron	HEMGN	0.37	0.028	2.87 × 10−9	0.039	6.84 × 10−4	1.17 × 10−11	0.34	0.028	9.03 × 10−11	0.044	2.18 × 10−5	2.59 × 10−14
rs2068888	G/A	nearGene-3	EXOC6	0.45	−0.023	2.81 × 10−7	−0.012	0.266	2.47 × 10−7	0.44	−0.022	1.19 × 10−7	−0.012	0.212	8.61 × 10−8
rs3794153	C/G	missense	ST5	0.45	−0.027	7.28 × 10−9	−0.026	1.53 × 10−2	3.57 × 10−10	0.40	−0.027	2.19 × 10−9	−0.023	2.47 × 10−2	1.74 × 10−10
rs174583	C/T	intron	FADS2	0.34	0.031	8.79 × 10−9	0.048	1.22 × 10−4	1.03 × 10−11	0.34	0.028	4.72 × 10−9	0.042	1.10 × 10−4	4.42 × 10−12
rs45535039	T/C	3′ UTR	CCDC153	0.28	0.04	4.02 × 10−10	0.071	5.31 × 10−2	8.48 × 10−11	0.28	0.04	2.5 × 10−12	0.056	8.56 × 10−2	6.25 × 10−13
rs11616188	G/A	nearGene3	LTBR	0.42	−0.025	1.26 × 10−8	−0.031	3.59 × 10−3	1.81 × 10−10	0.37	−0.025	7.57 × 10−9	−0.033	1.07 × 10−3	4.20 × 10−11
rs10506328b	A/C	intron	NFE2	0.64	0.033	5.63 × 10−11	0.06	5.88 × 10−8	2.01 × 10−16	0.69	0.038	3.79 × 10−15	0.059	2.33 × 10−8	2.73 × 10−21
rs2279574	C/A	missense	DUSP6	0.54	−0.023	2.47 × 10−7	−0.0082	0.442	4.28 × 10−7	0.50	−0.021	1.57 × 10−7	−0.006	0.531	4.04 × 10−7
rs61745424	G/A	missense	CUX2	0.025	−0.064	2.36 × 10−6	−0.085	6.79 × 10−3	6.49 × 10−8	0.023	−0.068	1.37 × 10−7	−0.073	1.43 × 10−2	6.30 × 10−9
rs2784521	A/G	nearGene-5	DDHD1	0.83	0.025	1.62 × 10−5	0.0096	0.486	2.24 × 10−5	0.76	0.028	2.92 × 10−8	0.01	0.363	5.56 × 10−8
rs55707100	C/T	missense	MAP1A∗	0.032	0.095	7.03 × 10−14	0.073	3.87 × 10−2	9.53 × 10−15	0.028	0.092	6.85 × 10−14	0.082	1.62 × 10−2	3.77 × 10−15
rs10852932	G/T	intron	SMG6∗	0.36	−0.024	1.82 × 10−6	−0.042	8.93 × 10−4	1.42 × 10−8	0.39	−0.025	4.79 × 10−8	−0.036	6.99 × 10−4	2.15 × 10−10
rs76066357	G/C	missense	ITGA2B∗	0.014	−0.17	6.92 × 10−16	−0.19	2.88 × 10−5	1.05 × 10−19	0.013	−0.16	1.92 × 10−15	−0.18	6.00 × 10−5	5.78 × 10−19
rs1801689	A/C	missense	APOH∗	0.036	0.083	6.34 × 10−12	0.13	2.44 × 10−5	1.82 × 10−15	0.032	0.090	8.64 × 10−15	0.12	2.03 × 10−5	1.57 × 10−18
rs892055	A/G	missense	RASGRP4	0.34	0.029	5.30 × 10−10	0.018	9.87 × 10−2	2.01 × 10−10	0.38	0.025	3.49 × 10−9	0.017	8.13 × 10−2	9.96 × 10−10
rs3865444	C/A	5′ UTR	CD33∗	0.32	−0.026	1.11 × 10−6	−0.034	2.52 × 10−3	1.27 × 10−8	0.29	−0.026	2.10 × 10−7	−0.032	3.03 × 10−3	2.59 × 10−9
rs6136489b	T/G	intergenic	SIRPA∗	0.34	−0.033	8.69 × 10−13	−0.028	1.24 × 10−2	4.00 × 10−14	0.39	−0.030	1.8 × 10−12	−0.024	1.30 × 10−2	8.78 × 10−14
rs855791	A/G	missense	TMPRSS6∗	0.56	−0.031	3.96 × 10−11	−0.017	0.130	2.34 × 10−11	0.60	−0.029	2.34 × 10−11	−0.022	3.52 × 10−2	2.97 × 10−12
rs1018448	A/C	missense	ARFGAP3	0.54	−0.028	4.02 × 10−10	−0.0053	0.618	2.62 × 10−9	0.59	−0.025	1.55 × 10−9	−0.0065	0.515	6.13 × 10−9
rs738409	C/G	missense	PNPLA3∗	0.23	−0.042	1.49 × 10−14	−0.042	1.75 × 10−3	1.03 × 10−16	0.22	−0.044	1.33 × 10−18	−0.038	1.61 × 10−3	9.73 × 10−21

We show variants in previously unreported loci (n = 32) and retained after conditional analyses in European ancestry (EA) (p < 2.59 × 10⁻⁷) and all ancestry (All) (p < 2.20 × 10⁻⁷) analyses. Associations in African ancestry (AA) had previously been reported in the literature (Table S10). Asterisks (^∗) indicate variants (20/32) showing evidence of replication (p < 0.05, same direction of effect). If multiple genes/transcripts were annotated to a variant, the transcript most expressed in Eicher et al.³² (Table S22) was selected. Full results and annotations are available in Table S5. Abbreviations are as follows: PLT, platelet count; MPV, mean platelet volume; REF, reference allele; ALT, alternate allele; EAF, effect allele frequency.

^aSurpasses significance threshold after conditioning on rs78446341 (p = 2.48 × 10⁻⁷).⁷

^bPrevious association with MPV.