eQTLs catalog

Version 20200324

The expression Qualitative Traits Loci (eQTLs) are genetic polymorphisms associated with changes in gene expression levels and they have been successfully used to interpret the molecular role of Genome Wide Association Studies (GWAS) variants. Up to date few eQTLs databases exist but they collect only a small portion of the available datasets. We collected several studies and here is the description of the most important features.

Project_ID	PubMed_ID	Year	FinalSource	SampleSize(min)	SampleSize(mean)	SampleSize(max)	Population	eQTLs	Tested genes	#eGenes	BodyDistrict	SampleType	SampleSize
Andiappan et al., 2015	26259071	2015	Andiappan et al., 2015	114	114	114	CHB	871	NA	784	Blood	Neutrophils	114
Aterido et al., 2014	24959711	2014	Aterido et al., 2014	26	26	26	CEU	74	NA	60	Blood	CD4_T-Cells\|LCLs	26
Battle et al., 2013	24092820	2013	Battle et al., 2013	922	922	922	EUR	10813	13,857	11009	Blood	Whole_Blood	922
Borel et al., 2010	21147911	2010	Borel et al., 2010	180	180	180	Western_EUR	57	121 (miRNAs)	36	Blood	Fibroblasts	180
Chen et al., 2016	27863251	2016	Chen et al., 2016	197	197	197	UK	19600	NA	12706	Blood	Monocytes, neutrophils, t-cells	197
Dimas et al., 2009	19644074	2009	Pritchard db	75	75	75	EUR	1102	NA	971	Blood	Fibroblasts\|Lymphocytes\|T-Cells	75
Ding et al., 2010	21129726	2010	Dinget al., 2010	53	55	57	EA	41	NA	27	Skin	Psoriatic_Lesional_Skin\|Psoriatic_Uninvolved_Skin\|Skin_normal	53\|57
Dixon et al., 2007	17873877	2007	Dixon et al., 2007	378	378	378	British	1998	14,819	1433	Blood	LCLs	378
eQTLGen	eqtlgen.org	2019	eQTLGen Consortium	31684	31684	31684	Multipop	17925	NA	17109	Blood	Whole_Blood	31684
Fadista et al., 2014	25201977	2014	Fadista et al., 2014	89	89	89	EUR	653	NA	557	Pancreas	Islets_of_Langerhans	89
Fairfax et al., 2012	22446964	2012	Fairfax et al., 2012	283	283	283	UK (Oxforshire)	14849	NA	9258	Blood	B-Cell\|Monocytes	283
Fairfax et al., 2014	24604202	2014	Fairfax et al., 2014	261	341	414	EUR	32557	15421 probes	9637	Blood	Monocytes_Ifn_TopVarV1\|Monocytes_Ifn_TopVarV2\|Monocytes_Lps24Hrs_TopVar2\|Monocytes_Lps24Hrs_TopVarV1\|Monocytes_Lps2Hrs_TopVarV1\|Monocytes_Lps2Hrs_TopVarV2\|Monocytes_Naive_TopVarV1\|Monocytes_Naive_TopVarV2	261\|322\|367\|414
Fehrmann et al., 2011	21829388	2011	Fehrmann et al., 2011	1469	1469	1469	EUR	9686	19,609	7593	Blood	Whole_Blood	1469
Gaffney et al., 2012	22293038	2012	Pritchard db	210	210	210	CEU\|YRI\|CHB\|JPT	1881	8,526	1835	Blood	LCLs	210
GEUVADIS	24037378	2013	Lappalainen et al. 2013	89	231	373	EUR\|YRI	3643	13,703	3279	Blood	LCLs	373\|89
Gibbs et al., 2010	20485568	2010	Gibbs et al., 2010	142	145	150	Caucasian	1062	NA	966	Brain	Brain_Cerebellum\|Brain_Frontal_Cortex\|Brain_Pons\|Brain_Temporal_Cortex	142\|143\|144\|150
Grundberg et al., 2009	19654370	2009	Grundberg et al., 2009	95	95	95	Swedish	264	NA	259	Bone	Osteoblasts	95
Grundberg et al., 2011	21283786	2011	Grundberg et al., 2011	106	110	113	Swedish	487	18,144 RefSeq transcripts	479	Bone\|Bones	Osteoblast_BMP-2\|Osteoblast_DEX\|Osteoblast_PGE2\|Osteoblasts_treated_with_bmp\|Osteoblasts_treated_with_BMP2\|Osteoblasts_treated_with_dexamethasone\|Osteoblasts_treated_with_pge-2\|Osteoblasts_treated_with_PGE2\|Osteoblasts_untreated\|Osteoblasts_with_treatment_interaction	106\|113
GTex (V6p) 2016	25954001	2016	GTEx Consortium	70	163	361	European,AfricanAmerican,Asian	135017	NA	27998	Adipose_Tissue\|Adrenal_Gland\|Blood\|Blood_Vessel\|Brain\|Breast\|Esophagus\|Heart\|Large_Intestine\|Liver\|Lung\|Muscle\|Nerve\|Ovary\|Pancreas\|Pituitary\|Prostate\|Skin\|Small_Intestine\|Spleen\|Stomach\|Testis\|Thyroid\|Uterus\|Vagina	Adipose_Subcutaneous\|Adipose_Visceral_Omentum\|Adrenal_Gland\|Artery_Aorta\|Artery_Coronary\|Artery_Tibial\|Brain_Anterior_cingulate_cortex_BA24\|Brain_Caudate_basal_ganglia\|Brain_Cerebellar_Hemisphere\|Brain_Cerebellum\|Brain_Cortex\|Brain_Frontal_Cortex_BA9\|Brain_Hippocampus\|Brain_Hypothalamus\|Brain_Nucleus_accumbens_basal_ganglia\|Brain_Putamen_basal_ganglia\|Breast_Mammary_Tissue\|Cells_EBV-transformed_lymphocytes\|Cells_Transformed_fibroblasts\|Colon_Sigmoid\|Colon_Transverse\|Esophagus_Gastroesophageal_Junction\|Esophagus_Mucosa\|Esophagus_Muscularis\|Heart_Atrial_Appendage\|Heart_Left_Ventricle\|Liver\|Lung\|Muscle_Skel et al., \|Nerve_Tibial\|Ovary\|Pancreas\|Pituitary\|Prostate\|Skin_Not_Sun_Exposed_Suprapubic\|Skin_Sun_Exposed_Lower_leg\|Small_Intestine_Terminal_Ileum\|Spleen\|Stomach\|Testis\|Thyroid\|Uterus\|Vagina\|Whole_Blood	100\|103\|114\|118\|124\|126\|127\|149\|157\|159\|169\|170\|183\|185\|190\|196\|197\|218\|241\|256\|272\|278\|285\|298\|302\|338\|361\|70\|72\|77\|79\|81\|82\|85\|87\|89\|92\|93\|96\|97
GTex (V7) 2017	gtexportal.org	2017	GTEx Consortium	80	214	491	White,AfricanAmerican,AmericanIndian;Asian;Unknown	218213	NA	31346	Adipose_Tissue\|Adrenal_Gland\|Blood\|Blood_Vessel\|Brain\|Breast\|Cells_Transformed_fibroblasts\|Connective_tissue\|Esophagus\|Female_reproductive_system\|Heart\|Large_Intestine\|Liver\|Lung\|Male_reproductive_system\|Muscle\|Nerve\|Pancreas\|Pituitary\|Salivary_Gland\|Skin\|Small_Intestine\|Spleen\|Stomach\|Thyroid	Adipose_Subcutaneous\|Adipose_Visceral_Omentum\|Adrenal_Gland\|Artery_Aorta\|Artery_Coronary\|Artery_Tibial\|Brain_Amygdala\|Brain_Anterior_cingulate_cortex_BA24\|Brain_Caudate_basal_ganglia\|Brain_Cerebellar_Hemisphere\|Brain_Cerebellum\|Brain_Cortex\|Brain_Frontal_Cortex_BA9\|Brain_Hippocampus\|Brain_Hypothalamus\|Brain_Nucleus_accumbens_basal_ganglia\|Brain_Putamen_basal_ganglia\|Brain_Spinal_cord_cervical_c-1\|Brain_Substantia_nigra\|Breast_Mammary_Tissue\|Cells_EBV-transformed_lymphocytes\|Cells_Transformed_fibroblasts\|Colon_Sigmoid\|Colon_Transverse\|Esophagus_Gastroesophageal_Junction\|Esophagus_Mucosa\|Esophagus_Muscularis\|Heart_Atrial_Appendage\|Heart_Left_Ventricle\|Liver\|Lung\|Minor_Salivary_Gland\|Muscle_Skeletal\|Nerve_Tibial\|Ovary\|Pancreas\|Pituitary\|Prostate\|Skin_Not_Sun_Exposed_Suprapubic\|Skin_Sun_Exposed_Lower_leg\|Small_Intestine_Terminal_Ileum\|Spleen\|Stomach\|Testis\|Thyroid\|Uterus\|Vagina\|Whole_Blood	385\|313\|175\|267\|152\|388\|88\|109\|144\|125\|154\|136\|118\|111\|108\|130\|111\|83\|80\|251\|117\|300\|203\|246\|213\|358\|335\|264\|272\|153\|383\|85\|491\|361\|122\|220\|157\|132\|335\|414\|122\|146\|237\|225\|399\|101\|106\|369
GTex (V8) 2019	gtexportal.org	2019	GTEx Consortium	73	310	706	White,AfricanAmerican,AmericanIndian;Asian;Unknown	280157	NA	30587	Adipose_Tissue\|Adrenal_Gland\|Blood\|Blood_Vessel\|Brain\|Breast\|Cells_Transformed_fibroblasts\|Esophagus\|Female_reproductive_system\|Heart\|Kidney\|Large_Intestine\|Liver\|Lung\|Male_reproductive_system\|Muscle\|Nerve\|Pancreas\|Pituitary\|Salivary_Gland\|Skin\|Small_Intestine\|Spleen\|Stomach\|Thyroid	Adipose_Subcutaneous\|Adipose_Visceral_Omentum\|Adrenal_Gland\|Cells_EBV-transformed_lymphocytes\|Whole_Blood\|Artery_Aorta\|Artery_Coronary\|Artery_Tibial\|Brain_Amygdala\|Brain_Anterior_cingulate_cortex_BA24\|Brain_Caudate_basal_ganglia\|Brain_Cerebellar_Hemisphere\|Brain_Cerebellum\|Brain_Cortex\|Brain_Frontal_Cortex_BA9\|Brain_Hippocampus\|Brain_Hypothalamus\|Brain_Nucleus_accumbens_basal_ganglia\|Brain_Putamen_basal_ganglia\|Brain_Spinal_cord_cervical_c-1\|Brain_Substantia_nigra\|Breast_Mammary_Tissue\|Cells_Cultured_fibroblasts\|Esophagus_Gastroesophageal_Junction\|Esophagus_Mucosa\|Esophagus_Muscularis\|Ovary\|Uterus\|Vagina\|Heart_Atrial_Appendage\|Heart_Left_Ventricle\|Kidney_Cortex\|Colon_Sigmoid\|Colon_Transverse\|Liver\|Lung\|Prostate\|Testis\|Muscle_Skeletal\|Nerve_Tibial\|Pancreas\|Pituitary\|Minor_Salivary_Gland\|Skin_Not_Sun_Exposed_Suprapubic\|Skin_Sun_Exposed_Lower_leg\|Small_Intestine_Terminal_Ileum\|Spleen\|Stomach\|Thyroid	581\|469\|233\|147\|670\|387\|213\|584\|129\|147\|194\|175\|209\|205\|175\|165\|170\|202\|170\|126\|114\|396\|483\|330\|497\|465\|167\|129\|141\|372\|386\|73\|318\|368\|208\|515\|221\|322\|706\|532\|305\|237\|144\|517\|605\|174\|227\|324\|574
Hao et al., 2010	20084173	2010	Hao et al., 2010	59	59	59	AfricanAmericans	70		1	Liver	Liver	59
Hao et al., 2012	23209423	2012	Hao et al., 2012	1111	1111	1111	EA	1523	NA	1451	Lung	lung	1111
Heap et al., 2009	19128478	2009	Heap et al., 2009	110	155	200	UK	813	NA	778	Blood	Leukocytes_Celiac\|Leukocytes	110\|200
Idaghdour et al., 2010	19966804	2010	Idaghdour et al., 2009	194	194	194	Morocco	341	NA	306	Blood	Leukocytes	194
Innocenti et al., 2011	21637794	2011	Pritchard db	532	532	532	EUR\|African\|unspecified	1966	NA	1966	Liver	Liver	532
Inouye et al., 2010	20844574	2010	Inouye et al., 2010	518	518	518	EUR	3	NA	3	Blood	Whole_Blood	518
Kabakchiev et al., 2013	23474282	2013	Kabakchiev et al., 2013	173	173	173	White\|Asian\|Black	7027	19,047	2864	Small_Intestine	Ileum	173
Kompass et al., 2011	21226949	2011	Kompass et al., 2011	52	52	52	Norway	48	NA	54	Endometrium	Endometrial_Tumor	52
Koopmann et al., 2014	24846176	2014	Koopmann et al., 2014	129	129	129	EUR	412	18,402 transcripts	383	Heart	left ventricular samples that were collected from non-diseased human donor hearts	129
Kwan et al., 2008	18193047	2008	Kwan et al., 2008	60	60	60	EA	313	NA	302	Blood	LCLs	60
Lee et al., 2014	24604203	2014	Lee et al., 2014	122	209	295	EUR\|AfrAmr\|EastAsn	943	NA	373	Blood	Dendritic_Cells	295\|122\|117 534
Li et al., 2013	23374354	2013	Li et al., 2013	48	110	171	EUR	998	NA	1000	Breast	ErNegative_Breast\|ErPositive_Breast	171\|48
Mangravite et al., 2012	23995691	2012	Pritchard db	480	480	480	AFR-AME\|CEU	825	NA	808	Blood	LCLs	480
Mehta et al., 2013	22692066	2012	Mehta et al., 2013	322	322	322	Caucasian	343	NA	319	Blood	Whole_Blood	322
Montgomery et al., 2010	20220756	2010	Pritchard db	60	60	60	EUR	1046	NA	1040	Blood	LCLs	60
Murphy et al., 2010	20833654	2010	Murphy et al., 2010	200	200	200	EA	1563	NA	1557	Blood	CD4+_lymphocytes	200
MuTHER	21304890	2012	MuTHER	156	161	166	EUR	9433	NA	5917	Adipose_Tissue\|Blood\|Skin	Adipose_Tissue\|LCLs\|Skin	156\|160\|166
Myers et al., 2007	17982457	2007	Myers et al., 2007	193	193	193	EA	210	NA	240	Brain	Brain_Cortex	193
Pala et al., 2017	28394350	2017	Pala et al., 2017	606	606	606	SRD	20410	NA	10850	Blood	Leukocytes	606
Pickrell et al., 2010	20220758	2010	Pritchard db	69	69	69	Nigerian	903	NA	748	Blood	LCLs	69
Qiu et al., 2011	21949713	2011	Qiu et al., 2011	131	131	131	-	1162	NA	1059	Sputum	Sputum	131
Ramasamy et al., 2014	25174004	2014	Ramasamy et al., 2014	101	124	134	EUR	9290	NA	2998	Brain	Brain_AverageAllTissue\|Brain_Cerebellar_Cortex\|Brain_Frontal_Cortex\|Brain_Hippocampus\|Brain_Inferior_Olivary_Nucleus_Medulla\|Brain_Occipital_Cortex\|Brain_Putamen\|Brain_Substantia_Nigra\|Brain_Temporal_Cortex\|Brain_Thalamus\|Brain_White_Matter	101\|119\|122\|124\|127\|129\|130\|131\|134
Rotger et al., 2010	20195503	2010	Rotger et al., 2010	153	153	153	EA	188	NA	190	Blood	HIV-1_CD4+_T-Cells	153
Schadt et al., 2008	18462017	2008	Schadt et al., 2008	427	427	427	Caucasian	3311	NA	2294	Liver	Liver	427
Schmiedel et al., 2018	30449622	2018	Schmiedel et al., 2018	91	91	91	Multipop.	29093	NA	12142	Blood	Activated_naive_CD4Positive_T_cells\|Activated_naive_CD8Positive_T_cells\|Classical_monocytes\|Memory_TREG_cells\|Naive_B_cells\|Naive_CD4Positive_T_cells\|Naive_CD8Positive_T_cells\|Naive_TREG_cells\|NK_cells\|Non_classical_monocytes\|TFH_cells\|TH1_17_cells\|TH17_cells\|TH1_cells\|TH2_cells	91
Schr�der et al., 2011	22006096	2011	Schroder et al., 2011	149	149	149	-	364	NA	304	Liver	Liver	149
Stranger et al., 2007	17873874	2007	Stranger et al., 2007	270	270	270	CEU\|YRI\|CHB\|JPT	1234	NA	640	Blood	LCLs	270
Thibodeau et al., 2015	26611117	2015	Thibodeau et al., 2015	471	471	471	EUR	142	NA	148	Prostate	Prostate	471
Veyrieras et al., 2008	18846210	2008	Pritchard db	210	210	210	Multipop.	1645	NA	1361	Blood	LCLs	210
Webster et al., 2011	19361613	2011	Webster et al., 2011	176	182	188	EUR	623	NA	677	Brain	Brain_Cortex_with_Alzheimers_interaction\|Brain_Cortex_with_no_Alzheimers_interaction	176\|188
Westra et al., 2013	24013639	2013	Westra et al., 2013	5311	5311	5311	-	8077	NA	6663	Blood	Whole_Blood	5311
Zeller et al., 2010	20502693	2010	Pritchard db	1490	1490	1490	Germany	3307	NA	3288	Blood	Monocytes	1490
Zhernakova et al. 2017	27918533	2017	BIOSQTL___Zhernakova	2116	2116	2116	Dutch	40470	NA	20584	Blood	Whole_Blood	2116
Zou et al., 2012	22685416	2012	Zou et al., 2012	400	400	400	Caucasian	2607	NA	681	Brain	Brain_Cerebellum_Alzheimer_cases\|Brain_Cerebellum_Alzheimer_cases_and_controls\|Brain_Cerebellum_in_non-Alzheimer_samples\|Brain_Cerebellum_in_Progressive_Supranuclear_Palsy_cases\|Brain_Temporal_Cortex_Alzheimer_cases\|Brain_Temporal_Cortex_Alzheimer_cases_and_controls\|Brain_Temporal_Cortex_in_non-Alzheimer_samples\|Brain_Temporal_Cortex_in_Progressive_Supranuclear_Palsy_cases	400

Feature	Counts
Projects	55
Datasets	249
Human populations	15
Body districts	29
eQTLs	768,351
eGenes	38,107

Human populations

Body districts

eGenes and year of publication

We collected the results of eQTLs studies published since 2007. In the baplots are reported the number of genes with at least one eQTL (eGenes) found in each study segmented by the year of publication of the study.

In dark blue is reported the number of eGenes found in at least two studies (here called CommonData), in light blue the number of eGenes that are found only in a specific study. Mouse over the bars to see to which study they belong to.

Protein-coding eGenes

lincRNA eGenes

eGenes and sample size

The sample size is a critical experimental feature that determines the power of a study. Knowing the discovery ratio based on the sample size for published datases could be halpful when designing a new experiment

The plots on the right show that sample size is not always fully predictive of the power of studies. In fact other experimental features like the technology and the statistical methods used are relevant.

Mouse over the scatterplots to see to which study the results belong to.