Table 4

Summary of eQTL in brain from Braineac and GTEx

eQTL
BraineacGTEx
SNPbpRisk alleleChrLocationNearest geneGeneBrain regionp-valueEffect of risk alleleGeneBrain regionp-valueEffect of risk allele
rs766488977087704/4IntronicSCARB2no eQTLno eQTL
rs926887732431147A6IntergenicHLA-DRAHLA-DPA1Frontal cortex3.1×10−5increased expressionHLA-DRB1Cerebellum5.2×10−8Increased expression
Anterior cingulate cortex8.8×10−8
Putamen8.9×10−7
HLA-DQA2Cerebellum1.3×10−6Decreased expression
rs676768116030773/10IntronicVWA2no eQTLno eQTL
rs1078435940445750/12IntronicSLC2A13no eQTLno eQTL
rs2893253107067203/13IntergenicEFNB2no eQTLno eQTL
rs19952844843136C17IntronicWNT3LRRC37A2Temporal cortex3×10−6Decreased expressionRP11–259G18.2Anterior cingulate cortex4×10–14Decreased expression
LRRC37A21.7×10−12
KANSL1-AS14.5×10−12
RP11–259G18.31.6×10−11
LRRC37A2Caudate (basal ganglia)4.5×10−20
KANSL1-AS16.6×10−20
RP11–259G18.21.9×10−19
RP11–259G18.33.5×10−19
LRRC37A5.4×10−7
RP11–259G18.3Cerebellar hemisphere1.1×10−18
LRRC37A25.7×10−17
KANSL1-AS12.3×10−16
RP11–259G18.22×10−13
LRRC37A2×10−10
rs19952844843136C17IntronicWNT3LRRC37A2Temporal cortex3×10−6Decreased expressionRP11–259G18.1Cerebellar hemisphere4.6×10−10Decreased expression
MAPT-AS11.6×10−8
MAPT1.3×10−7Increased expression
RP11–259G18.3Cerebellum2×10−25Decreased expression
KANSL1-AS13.9×10−20
LRRC37A26.2×10−19
RP11–259G18.21.6×10−17
LRRC37A4×10−13
RP11–259G18.11.3×10−12
MAPT8.7×10−12Increased expression
MAPT-AS13.6×10−8Decreased expression
SPPL2C1.3×10−7
KANSL1Hippocampus1×10−5KANSL1-AS1Cortex2.4×10−18
RP11–259G18.35.1×10−18
RP11–259G18.21.3×10−17
LRRC37A22.5×10−14
KANSL1-AS1Frontal cortex1.3×10−20
RP11–259G18.21.5×10−16
LRRC37A22.3×10−16
RP11–259G18.38.4×10−16
MAPT1.3×10−7Increased expression
KANSL1-AS1Hippocampus2.4×10−16Decreased expression
RP11–259G18.33.1×10−13
RP11–259G18.27×10−13
LRRC37A23.7×10−12
KANSL1-AS1Hypothalamus1.3×10−15
rs19952844843136C17IntronicWNT3KANSL1Hippocampus1×10−5Decreased expressionLRRC37A2Hypothalamus7.6×10−15Decreased expression
RP11–259G18.31.6×10−13
RP11–259G18.25.8×10−13
LRRC37A5.6×10−8
KANSL1-AS1Nucleus accumbens (basal ganglia)1.8×10−20
RP11–259G18.31.4×10−18
LRRC37A24.9×10−17
RP11–259G18.23.4×10−16
RP11–259G18.17.3×10−7
KANSL1-AS1Putamen (basal ganglia)2.5×10−19
RP11–259G18.36.9×10−15
LRRC37A23.1×10−14
RP11–259G18.29.6×10−11
LRRC37A1×10−6
RP11–259G18.11.6×10−6
rs135807143803189A17IntronicCRHR1LRRC37A4Cerebellum7.4×10−22Increased expressionLRRC37A4PAnterior cingulate cortex1.9×10−11Increased expression
1.8×10−16RP11–259G18.21.6×10−9Decreased expression
Frontal cortex3.6×10−10RP11–707O23.54.3×10−9
Hippocampus4.7×10−10LRRC37A25.3×10−8
5.3×10−7RP11–259G18.37.5×10−7
Medulla2.7×10−8KANSL1-AS19.7×10−7
Occipital cortex1.9×10−11LRRC37A4PCaudate (basal ganglia)7.3×10−15Increased expression
5.5×10−11LRRC37A21.7×10−14Decreased expression
Putamen2.2×10−6RP11–707O23.54.5×10−13
Substantia nigra7.3×10−11RP11–259G18.23.1×10−12
2.4×10−7KANSL1-AS12.8×10−11
rs135807143803189A17IntronicCRHR1LRRC37A4Temporal cortex3.1×10−12Increased expressionRP11–259G18.3Caudate (basal ganglia)1.1×10−10Decreased expression
1.1×10−7LRRC37A6.3×10−6
Thalamus5.7×10−12LRRC37A4PCerebellar hemisphere1.3×10−15Increased expression
5.2×10−10PLEKHM14.0×10−13
White matter7.7×10−6LRRC37A22.6×10−12Decreased expression
KANSL1Hippocampus6.1×10−7Decreased expressionRP11–259G18.21.5×10−9
RP11–259G18.31.9×10−9
RP11–259G18.12.6×10−9
KANSL1-AS16.1×10−9
LRRC37A2.5×10−8
RP11–798G7.55.9×10−8Increased expression
RP11–707O23.52.8×10−7Decreased expression
FMNL14.2×10−7Increased expression
CTD-2020K17.15.2×10−6
MAPT6.6×10−6
LRRC37A4PCerebellum5.3×10−18
PLEKHM14.2×10−17
RP11–259G18.35.6×10−16Decreased expression
LRRC37A23.3×10−15
RP11–259G18.26.6×10−15
RP11–707O23.52.6×10−13
RP11–259G18.11.5×10−10
LRRC37A1.7×10−10
KANSL1-AS17.1×10−10
RP11–798G7.51.4×10−9Increased expression
MAPT5.4×10−9
rs135807143803189A17IntronicCRHR1KANSL1Hippocampus6.1×10−7Decreased expressionMAPT-AS1Cerebellum6.2×10−8Decreased expression
FMNL12.7×10−6Increased expression
KANSL1-AS1Cortex1.5×10−14Decreased expression
LRRC37A21.6×10−11
RP11–707O23.52.7×10−11
LRRC37A4P3.2×10−11Increased expression
RP11–259G18.35.7×10−11Decreased expression
RP11–259G18.21.3×10−10
CRHR1-IT11.3×10−8
PLEKHM19.4×10−7
RP11–259G18.17.8×10−6
CRHR1Medulla2.9×10−6LRRC37A2Frontal cortex2.5×10−11
LRRC37A4P9.3×10−11Increased expression
RP11–259G18.22.2×10−10Decreased expression
KANSL1-AS18.2×10−10
RP11–707O23.59.8×10−10
RP11–259G18.31.7×10−9
DND1P11.6×10−6
CRHR1-IT12.7×10−6
MAPT4.1×10−6Increased expression
LRRC37A4PHippocampus2.0×10−12
LRRC37A21.6×10−11Decreased expression
RP11–259G18.22.7×10−11
KANSL1-AS14.1×10−11
RP11–707O23.55.8×10−11
RP11–259G18.32.5×10−8
rs135807143803189A17IntronicCRHR1CRHR1Medulla2.9×10−6Decreased expressionCRHR1-IT1Hippocampus4.8×10−8Decreased expression
DND1P12.4×10−6
LRRC37A2Hypothalamus1.1×10−12
RP11–707O23.53.2×10−11
KANSL1-AS18.7×10−10
LRRC37A4P1.8×10−9Increased expression
RP11–259G18.22.1×10−8Decreased expression
RP11–259G18.32.3×10−8
LRRC37A4PNucleus accumbens (basal ganglia)2.2×10−16Increased expression
KANSL1-AS12.3×10−13Decreased expression
RP11–707O23.51.2×10−11
RP11–259G18.34.2×10−11
LRRC37A25.8×10−11
RP11–259G18.28.6×10−9
CRHR1-IT11.0×10−7
LRRC37A4PPutamen (basal ganglia)2.9×10−12Increased expression
LRRC37A21.5×10−10Decreased expression
KANSL1-AS12.9×10−10
RP11–707O23.51.6×10−9
RP11–259G18.34.1×10−9
RP11–259G18.21.7×10−8
CRHR1-IT15.8×10−7
rs1296454356543095/18IntronicZNF532no eQTLno eQTL
rs40550945408836/19IntergenicAPOEno eQTLno eQTL
rs4417745241225364/2IntergenicOTOSno eQTLno eQTL
rs132803271420424/13IntergenicDACH1no eQTLno eQTL
rs244640651679783/15IntronicGLDNno eQTLno eQTL
rs718488273737373C16In orfLOC101927998no eQTLno eQTL
rs685745392254T193′-UTRPVRL2no eQTLno eQTL
rs30266587879627/11IntronicRAB38no eQTLno eQTL
rs1050778971409940/13IntergenicDACH1no eQTLno eQTL

  • eQTL, expression quantitative trait loci.