Table 1 Known transcriptional regulators associated with identified eQTL hotspots
HotspotLocationStickleback Ensembl_IDHuman Ensembl_IDGene NameDescription
Chr04aCisENSGACG00000017632ENSG00000133884DPF2Double PHD fingers 2
Chr04aCisENSGACG00000017819ENSG00000156603MED19Mediator complex subunit 19
Chr04aCisENSGACG00000017706ENSG00000168002POLR2GPolymerase (RNA) II subunit G
Chr04aCisENSGACG00000017981ENSG00000155827RNF20Ring finger protein 20
Chr04aHotspotENSGACG00000017062ENSG00000175602CCDC85BCoiled-coil domain containing 85B
Chr04aHotspotENSGACG00000017113ENSG00000131264CDX4Caudal type homeobox 4
Chr04aHotspotENSGACG00000016877ENSG00000145214DGKQDiacylglycerol kinase θ
Chr04aHotspotENSGACG00000016862ENSG00000088881EBF4Early B-cell factor 4
Chr04aHotspotENSGACG00000016923ENSG00000126500FLRT1Fibronectin leucine rich transmembrane protein 1
Chr04aHotspotENSGACG00000017059ENSG00000175592FOSL1FOS like 1, AP-1 transcription factor subunit
Chr04aHotspotENSGACG00000017029ENSG00000184481FOXO4Forkhead box O4
Chr04aHotspotENSGACG00000016896ENSG00000161021MAML1Mastermind like transcriptional coactivator 1
Chr04aHotspotENSGACG00000016876ENSG00000109320NFKB1Nuclear factor κ B subunit 1
Chr04aHotspotENSGACG00000017076ENSG00000174576NPAS4Neuronal PAS domain protein 4
Chr04aHotspotENSGACG00000017018ENSG00000123728RAP2CRAP2C, member of RAS oncogene family
Chr04aHotspotENSGACG00000017237ENSG00000147274RBMXRNA binding motif protein, X-linked
Chr04aHotspotENSGACG00000017181ENSG00000134595SOX3SRY-box 3
Chr04aHotspotENSGACG00000016868ENSG00000131508UBE2D2Ubiquitin conjugating enzyme E2 D2
Chr04aHotspotENSGACG00000016930ENSG00000185670ZBTB3Zinc finger and BTB domain containing 3
Chr04aHotspotENSGACG00000017211ENSG00000152977ZIC1Zic family member 1
Chr04aHotspotENSGACG00000017212ENSG00000156925ZIC3Zic family member 3
Chr04aTransENSGACG00000019192ENSG00000105856HBP1HMG-box transcription factor 1
Chr04aTransENSGACG00000018763ENSG00000168310IRF2Interferon regulatory factor 2
Chr04aTransENSGACG00000010116ENSG00000163904SENP2SUMO1/sentrin/SMT3 specific peptidase 2
Chr04aTransENSGACG00000019776ENSG00000234495TRIM27Tripartite motif containing 27
Chr04bHotspotENSGACG00000018659ENSG00000112983BRD8Bromodomain containing 8
Chr04bHotspotENSGACG00000018605ENSG00000198791CNOT7CCR4-NOT transcription complex subunit 7
Chr04bHotspotENSGACG00000018730ENSG00000170619COMMD5COMM domain containing 5
Chr04bHotspotENSGACG00000018655ENSG00000147257GPC3Glypican 3
Chr04bHotspotENSGACG00000018752ENSG00000171720HDAC3Histone deacetylase 3
Chr04bHotspotENSGACG00000018614ENSG00000179111HES7Hes family bHLH transcription factor 7
Chr04bHotspotENSGACG00000018626ENSG00000101928MOSPD1Motile sperm domain containing 1
Chr04bHotspotENSGACG00000018642ENSG00000156531PHF6PHD finger protein 6
Chr04bHotspotENSGACG00000018664ENSG00000138814PPP3CAProtein phosphatase 3 catalytic subunit α
Chr04bHotspotENSGACG00000018680ENSG00000185129PURAPurine rich element binding protein A
Chr04bHotspotENSGACG00000018663ENSG00000184584TMEM173Transmembrane protein 173
Chr04bTransENSGACG00000018210ENSG00000121060TRIM25Tripartite motif containing 25
Chr04bTransENSGACG00000001351ENSG00000116830TTF2Transcription termination factor 2
Chr06CisENSGACG00000012317ENSG00000266412NCOA4Nuclear receptor coactivator 4
Chr06CisENSGACG00000001371ENSG00000167380ZNF226Zinc finger protein 226
Chr06HotspotENSGACG00000011981ENSG00000197223C1DC1D nuclear receptor corepressor
Chr06TransENSGACG00000018659ENSG00000112983BRD8Bromodomain containing 8
Chr06TransENSGACG00000005983ENSG00000168036CTNNB1Catenin (cadherin-associated protein), β 1, 88 kDa
Chr06TransENSGACG00000004982ENSG00000065883CDK13Cyclin-dependent kinase 13
Chr06TransENSGACG00000008525ENSG00000100644HIF1AHypoxia inducible factor 1, α subunit
Chr06TransENSGACG00000013704ENSG00000096968JAK2Janus kinase 2
Chr06TransENSGACG00000009631ENSG00000107938EDRF1Erythroid differentiation regulatory factor 1
Chr06TransENSGACG00000018816ENSG00000196670ZFP62ZFP62 zinc finger protein
Chr07Cis/hotspotENSGACG00000018669ENSG00000137462TLR2Toll-like receptor 2
Chr07HotspotENSGACG00000000325ENSG00000135625EGR4Early growth response 4
Chr07HotspotENSGACG00000018606ENSG00000109670FBXW7F-box And WD repeat domain containing 7, E3 ubiquitin protein ligase
Chr07HotspotENSGACG00000000304ENSG00000170448NFXL1Nuclear transcription factor, X-box binding-like 1
Chr07HotspotENSGACG00000000370ENSG00000164985PSIP1PC4 and SFRS1 interacting protein 1
Chr07HotspotENSGACG00000018586ENSG00000074966TXKTyrosine kinase
Chr07TransENSGACG00000000333ENSG00000173801JUPJunction plakoglobin
Chr08HotspotENSGACG00000014457ENSG00000162733DDR2Discoidin domain receptor tyrosine kinase 2
Chr08HotspotENSGACG00000014404ENSG00000187764SEMA4DSema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (Semaphorin) 4D
Chr08HotspotENSGACG00000014374ENSG00000178078STAP2Signal transducing adaptor family member 2
Chr08TransENSGACG00000006033ENSG00000125686MED1Mediator complex subunit 1
Chr08TransENSGACG00000017475ENSG00000137699TRIM29Tripartite motif containing 29
Chr08TransENSGACG00000003512ENSG00000148204CRB2Crumbs 2, cell polarity complex component
Chr08TransENSGACG00000006901ENSG00000136999NOVNephroblastoma overexpressed
Chr09CisENSGACG00000019842ENSG00000128272ATF4Activating transcription factor 4
Chr09CisENSGACG00000019868ENSG00000103423DNAJA3DnaJ heat shock protein family (Hsp40) member A3
Chr09HotspotENSGACG00000019898ENSG00000162961DPY30Dpy-30 histone methyltransferase complex regulatory subunit
Chr09HotspotENSGACG00000019915ENSG00000132664POLR3FPolymerase (RNA) III (DNA directed) polypeptide F, 39 kDa
Chr09HotspotENSGACG00000020002ENSG00000112658SRFSerum response factor
Chr09HotspotENSGACG00000019873ENSG00000011243AKAP8LA-kinase anchoring protein 8 like
Chr12aCisENSGACG00000000816ENSG00000126767ELK1ELK1, member of ETS oncogene family
Chr12aHotspotENSGACG00000000295ENSG00000146109ABT1Activator of basal transcription 1
Chr12aHotspotENSGACG00000000248ENSG00000106785TRIM14Tripartite motif containing 14
Chr12aTransENSGACG00000019625ENSG00000164134NAA15N(α)-acetyltransferase 15, NatA auxiliary subunit
Chr12aTransENSGACG00000001088ENSG00000111581NUP107Nucleoporin 107 kDa
Chr12bCisENSGACG00000006074ENSG00000185513L3MBTL1L(3)mbt-like
Chr12bCisENSGACG00000004938ENSG00000012504NR1H4Nuclear receptor subfamily 1, group h, member 4
Chr12bHotspotENSGACG00000011155ENSG00000101017CD40CD40 molecule, TNF receptor superfamily member 5
Chr12bHotspotENSGACG00000010943ENSG00000110925CSRNP2Cysteine-serine-rich nuclear protein 2
Chr12bHotspotENSGACG00000011240ENSG00000163349HIPK1Homeodomain interacting protein kinase 1
Chr12bHotspotENSGACG00000011086ENSG00000101096NFATC2Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2
Chr12bHotspotENSGACG00000010788ENSG00000123358NR4A1Nuclear receptor subfamily 4, group A, member 1
Chr12bHotspotENSGACG00000010925ENSG00000184271POU6F1POU class 6 homeobox 1
Chr12bHotspotENSGACG00000010838ENSG00000181852RNF41Ring finger protein 41, E3 ubiquitin protein ligase
Chr12bHotspotENSGACG00000011124ENSG00000101115SALL4Spalt-like transcription factor 4
Chr12bHotspotENSGACG00000011135ENSG00000182463TSHZ2Teashirt zinc finger homeobox 2
Chr12bHotspotENSGACG00000010929ENSG00000135457TFCP2Transcription factor CP2
Chr12bHotspotENSGACG00000011187ENSG00000204859ZBTB48Zinc finger and BTB domain containing 48
Chr12bHotspotENSGACG00000011128ENSG00000020256ZFP64Zinc finger protein 64
Chr12bHotspotENSGACG00000010636ENSG00000126895AVPR2Arginine vasopressin receptor 2
Chr12bHotspotENSGACG00000011168ENSG00000171680PLEKHG5Pleckstrin homology and RhoGEF domain containing G5
Chr12bHotspotENSGACG00000011023ENSG00000134242PTPN22Protein tyrosine phosphatase, nonreceptor type 22
Chr12bTransENSGACG00000011682ENSG00000162761LIMX1ALIM homeobox transcription factor 1, α
Chr12cCisENSGACG00000013344ENSG00000101997CCDC22Coiled-coil domain containing 22
Chr12cCisENSGACG00000013103ENSG00000196924FLNAFilamin A, α
Chr12cCisENSGACG00000005361ENSG00000116670MAD2L2Mitotic spindle assembly checkpoint protein MAD2B
Chr12cCis/hotspotENSGACG00000004839ENSG00000188157AGRNAgrin
Chr12cHotspotENSGACG00000004256ENSG00000101126ADNPActivity-dependent neuroprotector homeobox
Chr12cHotspotENSGACG00000004544ENSG00000009307CSDE1Cold shock domain containing E1, RNA-binding
Chr12cHotspotENSGACG00000004732ENSG00000101412E2F1E2F transcription factor 1
Chr12cHotspotENSGACG00000004740ENSG00000078747ITCHItchy E3 ubiquitin protein ligase
Chr12cHotspotENSGACG00000004213ENSG00000197780TAF13TAF13 RNA Polymerase II, TATA box binding protein (TBP)-associated factor, 18 kDa
Chr12cHotspotENSGACG00000004773ENSG00000122691TWIST2Twist homolog 2
Chr12cHotspotENSGACG00000004763ENSG00000111424VDRVitamin D (1,25- dihydroxyvitamin D3) receptor
Chr12cHotspotENSGACG00000004734ENSG00000131061ZNF341Zinc finger protein 341
Chr12cHotspotENSGACG00000004662ENSG00000197114ZGPATZinc finger, CCCH-type with G patch domain
Chr12cHotspotENSGACG00000004338ENSG00000088832FKBP1AFK506 Binding Protein 1A
Chr16CisENSGACG00000005831ENSG00000153234NR4A2Nuclear receptor subfamily 4, group A, member 2
Chr16TransENSGACG00000012487ENSG00000125845BMP2Bone morphogenetic protein 2
  • Human orthologs of stickleback genes were identified using BioMart. Location is as follows: “Hotspot”: annotated gene is in genomic region of hotspot; “Cis”: gene is cis-regulated by hotspot at chromosome-wide P < 0.01; “Trans”: gene is trans-regulated by hotspot at genome-wide P < 0.021. Chr, chromosome.