Extended Data Table 1. Comparison of surrogate variable analyses with direct white cell counts in association models.

The table shows the I values from regression models in the MRCA panel that predict lnIgE at each locus a) before adjusting cell counts; b) after adjusting cell counts using Houseman surrogate variables; c) after adjusting for cell subsets counted in our data. pMethyl measures strength of association to IgE. CD8, CD4 and NK are Tcell subsets, GRAN= granulocytes, EOS=eosinophils, NEU=neutrophil, LYM=lymphocytes, MON=monocytes, BAS=basophils. All models are adjusted for sex, age, methylation, parent/child status, sex*age interaction, and age*parent interaction.

a) Before adjusting cell counts					b) Adjusting for Houseman cell proportions							c) Adjusting for white cell counts
Chr.	Position	Symbol	probe	pMethy	pMethy	pCD8T	pCD4T	pNK	pBCELL	pMON	pGRAN	pMethy	pEOS	pNEU	pLYM	pMON	pBAS
1	9521654	SLC25A33	cg18783781	4.96E-14	5.58E-13	0.3625663	0.6489145	0.0830001	0.0735391	0.7715233	0.2564499	6.14 E-06	0.00065	0.866661	0.678896	0.561016	0.551752
16	54100210	LPCAT2	cg01998785	1.24E-13	3.81E-13	0.1560292	0.3633042	0.034881	0.0300831	0.7239839	0.1881862	2.36E-06	0.0003	0.294806	0.300248	0.445243	0.785135
14	49849865	L2HGDH	cg15996947	7.39E-13	3.81E-11	0.3709841	0.6823007	0.125117	0.1583239	0.9387673	0.3768824	3.21E-05	0.000295	0.38062	0.519495	0.662394	0.890493
10	44815441	ZNF22	cg01614759	4.42E-12	9.09E-11	0.3526504	0.6420391	0.1382946	0.0810812	0.654088	0.3845248	7.61E-05	0.000216	0.305013	0.42021	0.601202	0.937252
3	3127530	IL5RA	cg10159529	5.06E-12	1.70E-10	0.8786628	0.9388517	0.2941882	0.2701973	0.9752202	0.5129874	0.000104	6.81E-05	0.877227	0.802458	0.551635	0.756105
1	172153108	SERPINC1	cg01770400	6.59E-12	1.54E-11	0.1182883	0.3063038	0.0323251	0.0368702	0.574556	0.1896	6.36E-06	0.000109	0.236406	0.186757	0.667289	0.90807
21	42659768	TFF1	cg02643667	7.87E-12	6.81E-11	0.234861	0.4646176	0.0330799	0.0706689	0.797703	0.1753888	9.07E-06	7.18E-06	0.384611	0.725574	0.672431	0.976409
5	132036424	IL4	cg26787239	1.59E-11	2.13E-10	0.5058003	0.9922092	0.1723318	0.1996409	0.7364825	0.6544331	1.25E-05	1.66E-05	0.269226	0.259295	0.614387	0.77939
2	110014086	LIMS3	cg18879041	4.06E-11	2.57E-09	0.3708111	0.7030526	0.1613161	0.2166898	0.9745824	0.474026	0.000865	0.000256	0.280498	0.382954	0.500203	0.963467
13	47774920	RB1	cg13221796	5.66E-10	9.26E-11	0.1278218	0.3641314	0.0353766	0.0458363	0.7786051	0.2987393	2.84E-06	1.83E-05	0.029037	0.081617	0.516731	0.982861
19	60432000	TMEM86B	cg26457013	1.02E-09	4.08E-09	0.3305229	0.5920938	0.036091	0.0792481	0.9078355	0.2711535	0.000691	1.35E-05	0.363948	0.317448	0.558421	0.740734
9	100745613	COL15A1	cg20503329	1.19E-09	3.14E-08	0.4772819	0.7388277	0.1359031	0.1343368	0.9433195	0.4284566	0.001341	1.17E-05	0.443838	0.49736	0.401174	0.959364
1	31166502	SDC3	cg07689731	2.33E-09	4.79E-09	0.5074834	0.7985815	0.0774502	0.0726484	0.7924958	0.4108301	0.002906	1.48E-05	0.415182	0.483806	0.437372	0.932638
21	45317773	ADARB1	cg09676390	1.21E-08	1.32E-07	0.43369	0.6702876	0.0791369	0.1103603	0.9234331	0.3292778	0.000472	3.48E-07	0.432091	0.530921	0.462608	0.820656
9	134926722	CEL	cg03693099	1.84E-08	1.01E-07	0.2926779	0.512945	0.0818301	0.1071869	0.9754856	0.3848947	0.000383	9.27E-06	0.099207	0.18224	0.575481	0.93957
19	12859426	KLF1	cg26136776	3.34E-08	5.42E-07	0.2328607	0.4764967	0.0498737	0.087521	0.7661611	0.2312155	0.008494	4.25E-06	0.308908	0.378613	0.526765	0.764392
X	48529968	GATA1	cg00536175	7.85E-08	5.70E-07	0.6056632	0.9159691	0.163687	0.1102612	0.8082841	0.5675393	0.002444	1.31E-06	0.230592	0.333849	0.423511	0.745501
12	10222881	TMEM52B	cg25494227	1.29E-07	2.79E-07	0.4810187	0.6746518	0.0457622	0.0735827	0.9017706	0.3386288	8.31E-05	2.05E-08	0.349366	0.362883	0.456694	0.75634
9	33229641	SPINK4	cg00079056	1.54E-07	1.23E-06	0.3893041	0.6595419	0.067607	0.090288	0.950103	0.3262354	0.015058	9.70E-07	0.327361	0.481372	0.49343	0.779557
12	15017287	PDE6H	cg09447105	2.16E-07	1.80E-06	0.6038815	0.9752817	0.1325361	0.2619219	0.6725442	0.6818338	0.002327	6.73E-07	0.185319	0.308805	0.650588	0.72691
16	4778723	FLJ25410	cg05215575	3.11E-07	7.40E-08	0.6354446	0.6693211	0.0382164	0.0635217	0.8705757	0.2084314	0.011151	9.08E-08	0.699883	0.891282	0.341595	0.856081
7	142369547	KEL	cg17784922	4.24E-07	9.07E-07	0.6926023	0.9854571	0.0699431	0.1577229	0.8028496	0.5052827	0.001391	3.21E-08	0.505128	0.698535	0.367309	0.99912
7	29199993	CHN2	cg21472642	6.51E-07	7.39E-07	0.5225896	0.8312874	0.0708089	0.0764603	0.9022296	0.4725488	8.45E-06	3.38E-09	0.104506	0.231601	0.595919	0.815002
2	191009029	FLJ20160	cg15998761	9.33E-07	9.09E-06	0.4236314	0.824669	0.1393183	0.1145142	0.8527446	0.4643437	0.043732	5.71E-07	0.331558	0.449501	0.418024	0.785659
6	25862169	SLC17A4	cg21627181	1.14E-06	1.42E-06	0.7663137	0.9149808	0.0591244	0.1414494	0.9511792	0.3972344	0.025202	5.30E-08	0.609342	0.865393	0.467443	0.746032
14	49849874	L2HGDH	cg20189937	1.32E-06	1.16E-05	0.503935	0.9204654	0.0921306	0.1950088	0.8817908	0.5174749	0.007269	1.26E-07	0.297519	0.525586	0.480584	0.958405
17	39822093	ITGA2B	cg17749520	1.37E-06	9.24E-06	0.3677214	0.6752543	0.046072	0.1157269	0.8717913	0.3274826	0.009625	3.11E-07	0.286277	0.406727	0.666483	0.903995
17	39701014	SLC4A1	cg03580247	1.51E-06	1.76E-05	0.4966594	0.7030166	0.1566437	0.1201467	0.7706213	0.4809553	9.19E-05	7.97E-09	0.262889	0.282218	0.522557	0.944193
20	41789039	FAM112A	cg11398517	2.42E-06	2.11E-05	0.431888	0.7316467	0.0506171	0.209415	0.8337169	0.4256838	0.006763	1.86E-07	0.220078	0.444385	0.592602	0.918166
11	56904791	PRG3	cg24459209	3.33E-06	1.29E-05	0.5460024	0.9366639	0.0692143	0.1545826	0.8947187	0.4338765	0.094895	2.69E-07	0.444762	0.62114	0.500854	0.993962
12	7792928	CLEC4C	cg22194129	5.46E-06	0.0001208	0.4977092	0.8378959	0.0710935	0.6019842	0.8886589	0.4447889	0.023532	2.38E-08	0.408481	0.759002	0.521453	0.818552
14	95011802	C14orf49	cg16522484	8.04E-06	0.0001668	0.4308412	0.7282314	0.1486239	0.1112817	0.9482318	0.4206034	0.034072	1.01E-07	0.285777	0.449644	0.49125	0.837548
X	48529554	GATA1	cg22543648	9.51E-06	7.12E-05	0.682124	0.9511741	0.1312401	0.1917101	0.6997158	0.4748147	0.02664	2.00E-08	0.585973	0.689124	0.425854	0.888172
2	11727816	NTSR2	cg25657834	1.02E-05	2.04E-05	0.9354409	0.6331433	0.1373482	0.3261244	0.4920064	0.8015518	5.67E-05	4.84E-10	0.191813	0.526463	0.689339	0.954103
19	48912054	IRGC	cg26251865	1.76E-05	9.19E-06	0.714389	0.9562959	0.0555475	0.1095196	0.6922884	0.4367507	0.011533	1.35E-08	0.495745	0.567965	0.468957	0.977824
19	44919789	CLC	cg18254848	1.77E-05	2.33E-05	0.7122613	0.874791	0.0834931	0.1954486	0.6341788	0.5277066	0.161753	4.77E-08	0.462599	0.67872	0.424877	0.937408
6	10635801	GCNT2	cg26385286	1.78E-05	3.88E-05	0.5747779	0.9758809	0.0654066	0.2046998	0.6574459	0.5308099	0.070861	4.31E-08	0.339931	0.593173	0.451377	0.902264
3	150064527	CPA3	cg13424229	1.89E-05	2.29E-06	0.4329161	0.6962458	0.1048729	0.0674688	0.7084296	0.6214492	0.001236	4.96E-07	0.054043	0.094343	0.451245	0.955257