Study ID Samples (size)
Cell type
Genotyping
Phenotyping
eQTL
exSNPs exGenes
associations
HA
HapMap CEU (30)
LCL
HapMap Project
Illumina Human WG-6
3858
3686
239
HapMap CHB (45)
4066
3780
253
HapMap JPT (45)
5254
5061
274
HapMap YRI (30)
3524
3283
306
624
545
209
21116
12121
2632
Custom ink-jet microarray
4362
2527
3824
Affymetrix GeneChip
4453
3699
722
Human Exon 1.0
5027
4086
1659
554
544
436
Fibroblast
522
508
424
T-cell
546
540
429
37694
29948
2752
BR
Caucasians (193)
Brain Cortex Affymetrix 500K
Illumina HumanRefseq-8
AS
Childhood Asthma (206)
LCL
Affymatrix HG-U133
1. Illumina Human-1
2. Illumina HumanHap 300
LV
Caucasian liver donors (427) Liver cell
1. Illumina 650Y
2. Affymetrix 500K
HA2
30 HapMap CEU (30)
LCL
HapMap Project
30 HapMap YRI (30)
3C
Caucasians (75)
LCL
Illumina 550K
Illumina Human WG-6
MO
German (1490)
Monocyte
Affymetrix 6.0
Illumina Human HT-12
HRC
HapMap CEU (60)
LCL
HapMap Project
RNA-Seq
8908
3896
930
HRY
HapMap YRI (69)
LCL
HapMap Project
RNA-Seq
799
779
786
BR2
Caucasians (150)
Cerebellum
Illumina Infinium
Illumina HumanRef-8
5243
4399
317
Frontal
HumanHap 550
5512
5198
329
cortex
5335
4059
385
Temporal
3411
3284
275
cortex
Pons
SKN
Healthy skin individuals (57)
Skin
Perlegen Sciences array
Affymatrix HG-U133
5410
4782
222
LV2
Liver donors (266)
Liver cell
1. Illumina 610
1. Agilent-014850
1170
1161
1170
33740
28956
6063
22453
20333
5449
211977 149684
3945
2. Illumina HumanHap 550 2. Illumina HumanRef-8
IM
British (288)
MuTHER Caucasian female twins
(~160)
Monocyte
Illumina Human
Illumina HumanHT-12
B-cell
OmniExpress-12
LCL
Illumina
Skin
1. HumanHap 300
103537
82933
2495
Adipose
2. HumanHap 610Q
138885 109689
3136
176848 109763
1251
390813 281446
3048
Illumina Human HT-12
3. 1M-Duo
4. 1.2MDuo 1M
MRC
Childhood Asthma (MRCA:
LCL
405) & Atopic Dermatitis
1. Illumina Human-1
1. Affymetrix HG-U133
2. Illumina HumanHap 300 2. Illumina Human WG-6
(MRCE: 950)
E-GEUV
1000 Genome - EUR (373)
LCL
1000 Genome - YRI (89)
LCL
1000 Genome Project
Illumina HiSeq 2000
19314
16932
472
References:
HA - Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, et al. 2007. Population genomics of human
gene expression. Nat Genet 39: 1217–1224
BR - Myers AJ, Gibbs JR, Webster J a, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, et al. 2007. A survey of genetic human cortical
gene expression. Nat Genet 39: 1494–1499.
AS - Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, Wong KCC, Taylor J, Burnett E, Gut I, Farrall M, et al. 2007. A genome-wide association study of
global gene expression. Nat Genet 39: 1202–1207.
LV - Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, et al. 2008. Mapping the genetic architecture of
gene expression in human liver. PLoS Biol 6: e107.
3C - Dimas ASA, Deutsch S, Stranger BEB, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Arcelus MG, Sekowska M, et al. 2009. Common
regulatory variation impacts gene expression in a cell type–dependent manner. Science 325: 1246–1250.
MO - Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, Castagne R, Maouche S, Germain M, Lackner K, Rossmann H, et al. 2010. Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS One 5: e10693.
HRC - Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. 2010. Transcriptome genetics using
second generation sequencing in a Caucasian population. Nature 464: 773–777.
HRY - Pickrell JK, Marioni JC, Pai A a, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK. 2010. Understanding
mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768–772.
BR2 - Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls M a, Lai S-L, Arepalli S, Dillman A, Rafferty IP, Troncoso J, et al. 2010. Abundant
quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6: e1000952.
SKN - Ding J, Gudjonsson JE, Liang L, Stuart PE, Li Y, Chen W, Weichenthal M, Ellinghaus E, Franke A, Cookson W, et al. 2010. Gene expression in skin
and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals. Am J Hum Genet 87: 779–789.
LV2 - Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, Ramirez J, Liu W, Lin YS, Moloney C, et al. 2011. Identi fication, replication,
and functional fine-mapping of expression quantitative trait Loci in primary human liver tissue. PLoS Genet 7: e1002078.
IM - Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC. 2012. Genetics of gene expression in
primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet 44: 502–510.
MuTHER - Grundberg E, Small KS, Hedman Å K, Nica AC, Buil A, Keildson S, Bell JT, Yang T-P, Meduri E, Barrett A, et al. 2012. Mapping cis- and transregulatory effects across multiple tissues in twins. Nat Genet 44: 1084–1089.
MRC - Liang L, Morar N, Dixon AL, Lathrop GM, Abecasis GR, Moffatt MF, Cookson WOC. 2013. A cross-platform analysis of 14,177 expression quantitative
trait loci derived from lymphoblastoid cell lines. Genome Res 23: 716–726.
E-GEUV - Lappalainen T, Sammeth M, Friedlä nder MR, ’t Hoen PAC, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, et al.
2013. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501: 506–511.