REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CCR7 G043H7	Biolegend	Cat# 353205; RRID: AB_10918624
CD11c 3.9	eBioscience	Cat# 46-0116-41; RRID: AB_10598361
CD123 6H6	eBioscience	Cat# 25-1239-41; RRID: AB_1257137
CD14 61D3	eBioscience	Cat# 48-0149-41; RRID: AB_1272120
CD24 ML5	Biolegend	Cat# 311121; RRID: AB_10915556
CD27 O323	eBioscience	Cat# 56-0279-41; RRID: AB_11149315
CD3 SK7	eBioscience	Cat# 56-0037-42; RRID: AB_10714978
CD31 WM-59	eBioscience	Cat# 12-0319-41; RRID: AB_10670623
CD38 HIT2	eBioscience	Cat# 17-0389-41; RRID: AB_1834354
CD4 RPA-T4	eBioscience	Cat# 61-0049-41; RRID: AB_2574521
CD8α RPA-T8	eBioscience	Cat# 56-0088-41; RRID: AB_11218867
CD19 HIB19	Biolegend	Cat# 302241; RRID: AB_2561381
CD45Ra HI100	eBioscience	Cat# 47-0458-41; RRID: AB_10853513
CD56 5.1H11	Biolegend	Cat# 362503; RRID: AB_2563912
CXCR5 J252D	Biolegend	Cat# 356903; RRID: AB_2561812
FOXP3 206D	Biolegend	Cat# 320113: RRID: AB_439753
γδTCR B1.1	eBioscience	Cat# 11-9959-41; RRID: AB_10669048
HLA-DR LN3	eBioscience	Cat# 47-9956-41; RRID: AB_1963604
IFNγ 4S.B3	eBioscience	Cat# 47-7319-41; RRID: AB_10853010
IgE IgE21	eBioscience	Cat# 11-6986-41; RRID: AB_10717661
IgM MHM-88	Biolegend	Cat# 314511; RRID: AB_961367
IL-17 eBio64DEC17	eBioscience	Cat# 11-7179-41; RRID: AB_10854885
IL-2 MQ1-17H12	eBioscience	Cat# 46-7029-41; RRID: AB_1834420
IL-4 8D4-8	eBioscience	Cat# 12-7049-41; RRID: AB_1548823
Ki67 B56	BD	Cat# 556027; RRID: AB_2266296
CD127 eBioRDR5	eBioscience	Cat# 13-1278-82; RRID: AB_657595
GM-CSF BVD-21C11	eBioscience	Cat# 502309; RRID: AB_11148950
IL-21 eBio3A3-N2	Biolegend	Cat# 12-7219-41; RRID: AB_1582261
Vα24Jα18 6B11	eBioscience	Cat# 12-5806-41; RRID: AB_1724174
Naive CD4+ T Cell Isolation Kit II, human	Miltenyi Biotec	130-094-131
T Cell Activation/Expansion Kit, human	Miltenyi Biotec	130-091-441
CD24 ML5	BioLegend	Cat# 311103; RRID: AB_314852
IgM SA-DA4	eBioscience	Cat# 12-9998-42; RRID: AB_11150964
CD14 TuK4	eBioscience	Cat# MHCD1418; RRID: AB_10371748
IgD IA6-2	BioLegend	Cat# 348209; RRID: AB_10683460
CD38 HIT2	eBioscience	Cat# 17-0389-42; RRID: AB_1834353
CD27 O323	eBioscience	Cat# 56-0279-42: RRID: AB_11044789
CD19 HIB19	BioLegend	Cat# 302209; RRID: AB_314239
Biological Samples
Serum and PBMCs of healthy volunteers	Carr et al., 2016	N/A
DNA samples of healthy volunteers	This paper	N/A
PBMCs, DNA and RNA samples of healthy volunteers	This paper	N/A
DNA and RNA samples of multiple sclerosis patients	This paper	N/A
Chemicals, Peptides, and Recombinant Proteins
Lymphocyte separation medium	LSM, MP Biomedicals	0850494
Lymphoprep	StemCell Technologies	07861
10% DMSO	Sigma	D2650-100ML
Histopaque-1077	Sigma	10771
Fixation-permeabilization buffer	eBioscience	00-5523-00
PMA	Sigma	P8139
Ionomycin	Sigma	I3909-1ML
GolgiStop	BD Biosciences	554724
Cytofix/Cytoperm	BD Biosciences	55471
IL-2	Peprotech	200-02
IL-12	R&D Systems	219-IL-005
IL-1β	Peprotech	200-01B
IL-6	Peprotech	200-06
IL-23	Peprotech	200-23
EcoRI	New England Biolabs	R0101S
Trizol	Thermo Fisher	15596026
High-Capacity cDNA Reverse Transcription Kit	Thermo Fisher	4374967
Critical Commercial Assays
BAFF Quantikine ELISA kit	R&D Systems	DBLYS0B
V-Plex human Proinflammatory panel MSD	Meso Scale Discovery	K15049D-2
Infinium HTS assay on Global Screening Array bead-chips	Illumina	https://www.illumina.com
Deposited Data
Immune phenotypes of healthy volunteers	Carr et al., 2016	Raw Data Resource
Strand file for Illumina GSA array (“GSAMD-24v1-0_20011747_A1” file)	Developer: Will Rayner	http://www.well.ox.ac.uk/∼wrayner/strand/
1000 Genomes reference datasets [Phase1 (2012); Phase 3 (2014)]	1000 Genomes Project Consortium, 2012, Sudmant et al., 2015	http://www.internationalgenome.org/
T1DGC reference panel for the HLA region, build 37	Jia et al., 2013	https://repository.niddk.nih.gov/studies/t1dgc-special/
ExSNP integrated eQTL database (“All processed eQTL data for each study” file)	Yu et al., 2016	http://www.exsnp.org/
Published dataset for splicing QTLs in whole blood (“ng.3220-S2.xlsx” file)	Zhang et al., 2015b	N/A
Oligonucleotides
DNA detection assays for sjKREC	Thermo Fisher	Custom made
DNA detection assays for sjKREC	Thermo Fisher	Custom made
TaqMan Copy Number Reference Assay for human RNase P	Thermo Fisher	4403326
STON2 Gene Expression Assay	Thermo Fisher	Hs00263833_m1
SEL1L Gene Expression Assay	Thermo Fisher	Hs01071406_m1
LINC01467 Gene Expression Assay	Thermo Fisher	Hs04403614_m1
RPL13A Gene Expression Assay	Thermo Fisher	Hs04194366_g1
SP4 Gene Expression Assay	Thermo Fisher	Hs00162095_m1
SP8 Gene Expression Assay	Thermo Fisher	Hs01941366_s1
LINC01162 Gene Expression Assay	Thermo Fisher	Custom made
LARP1B Gene Expression Assay	Thermo Fisher	Hs00292731_m1
IL6 Gene Expression Assay	Thermo Fisher	Hs00174131_m1
MRPL19 Reference Gene Expression Assay	Thermo Fisher	Hs00608519_m1
POLR2A Reference Gene Expression Assay	Thermo Fisher	Hs00172187_m1
Recombinant DNA
Software and Algorithms
FlowJo v9	Tree Star	https://www.flowjo.com/
QuantaSoft v1.4	Bio-Rad	http://www.bio-rad.com/
R programming language	R Development Core Team, 2015	https://www.R-project.org/
GenomeStudio V2011.1	Illumina team	https://www.illumina.com
PLINK v1.07;v1.9	Purcell et al., 2007	https://www.cog-genomics.org/plink2
SHAPEIT2	Delaneau et al., 2014	http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
IMPUTE v2.0	Howie et al., 2009	http://mathgen.stats.ox.ac.uk/impute/impute_v2.html
SNPTEST v2	Marchini et al., 2007	https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html
SNP2HLA v1.0.3	Jia et al., 2013	http://software.broadinstitute.org/mpg/snp2hla/
PRSice v1.25	Euesden et al., 2015	http://prsice.info/
Locuszoom standalone v1.4	Pruim et al., 2010	https://genome.sph.umich.edu/wiki/LocusZoom_Standalone
SWISS v1.0.05b	Developer: Ryan Welch	https://github.com/statgen/swiss
GEMINI v0.20.1	Paila et al., 2013	https://gemini.readthedocs.io/en/latest/
HaploReg v4 tool	Ward and Kellis, 2012	https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php
RegulomeDB v1.1	Boyle et al., 2012	http://www.regulomedb.org/