Genes Identified by expression imputation


Gene Location Tissuea BETAb P value GVARc Adjusted BETA Adjusted OR
GNL3chr3:52715172-52728508Cerebellum0.0371.39-e110.1150.0121.012
THOC7chr3:63819546-63849579Cerebellum-0.1135.77-e100.010-0.0110.989
NAGAchr22:42454358-42466846Cerebellum0.1221.12-e090.0090.0111.011
TAC3chr12:57403784-57422667Cerebellum-0.8688.03-e080.000-0.0150.985
CHRNA2chr8:27317279-27337400Cerebellum-0.0161.63-e070.395-0.0100.990
ACTR5chr20:37377085-37400834Cerebellum0.2083.88-e070.0190.0291.029
INO80Echr16:30006615-30017114Frontal cortex0.1307.25-e120.0090.0121.013
PLPPR5chr1:99355801-99470449Frontal cortex-0.6722.58-e090.006-0.0530.948
FAM205Achr9:34723052-34729464Frontal cortex0.0431.21-e080.0610.0111.011
AC110781.3chr7:1878222-1889567Thyroid0.3421.31-e130.0020.0141.014
IMMP2Lchr7:110303106-111202588Thyroid-0.0737.09-e120.046-0.0160.984
IGSF9Bchr11:133778459-133826880Thyroid-0.0243.05-e070.156-0.0100.991
NMRAL1chr16:4511681-4545764Thyroid0.0384.03-e070.0600.0091.009
HIF1Achr14:62162231-62214976DLPFC11.1307.52-e140.0000.1481.159
TIMM29chr19:11039424-11040917DLPFC11.2079.27-e140.0000.1681.183
ST7-OT4chr7:116593953-116738860DLPFC10.1705.79-e130.0010.3181.374
H2AFY2chr10:71812552-71872036DLPFC10.9623.60-e120.0000.1911.211
STARD3chr17:37793318-37819737DLPFC10.7405.90-e120.0010.3041.355
CTC-471F3.5chr19:40529291-40531409DLPFC8.5351.11-e110.0000.1041.110
SF3A1chr22:30727977-30752936DLPFC8.6511.32-e110.0000.0831.086
ZNF512chr2:27805897-27858041DLPFC10.3121.32-e110.0010.2611.298
FURINchr15:91411822-91426688DLPFC-0.0842.22-e110.022-0.0120.988
INHBA-AS1chr7:41733514-41818986DLPFC8.3992.24-e110.0000.1271.135
SF3B1chr2:198254508-198299815DLPFC0.0996.14-e110.0140.0121.012
EFTUD1P1chr15:84748920-84795356DLPFC-0.0921.81-e100.017-0.0120.988
MLH1chr3:37034823-37107380DLPFC2.8402.10-e100.0010.0691.071
GATAD2Achr19:19496635-19619740DLPFC-0.0442.18-e100.071-0.0120.988
METTL1chr12:58162254-58166576DLPFC9.3572.23-e100.0000.1661.181
DMC1chr22:38914954-38966291DLPFC7.2294.48-e100.0000.1301.139
RAD51Dchr17:33426811-33448541DLPFC7.6122.11-e090.0000.1111.117
REREchr1:8412457-8877702DLPFC2.8476.32-e090.0000.0361.037
PCCBchr3:135969148-136056738DLPFC-0.0442.05-e080.054-0.0100.990
CLCN3chr4:170533784-170644824DLPFC0.1412.96-e080.0050.0101.010
ATG101chr12:52463758-52471279DLPFC8.0864.90-e080.0070.6952.005
JRKchr8:143738874-143763386DLPFC0.0321.25-e070.0910.0101.010
PTPRUchr1:29563028-29653325DLPFC-0.0771.60-e070.016-0.0100.990
MARCKSchr6:114178541-114184648DLPFC0.3982.05-e070.0010.0151.015
TCF4chr18:52889562-53332018Anterior cingulate cortex-0.0595.22-e130.051-0.0130.987
DGKDchr2:234263153-234380750Anterior cingulate cortex-0.9372.63-e110.001-0.0220.979
C1QTNF4chr11:47611216-47616211Anterior cingulate cortex-0.1731.37-e090.010-0.0170.983
PITPNAchr17:1421012-1466110Anterior cingulate cortex-0.2431.77-e070.002-0.0100.990
FXR1chr3:180585929-180700541Caudate basal ganglia0.4395.40-e120.0010.0171.017
ZDHHC1chr16:67428322-67450736Caudate basal ganglia0.3545.36-e080.0010.0111.012
PDE4Dchr5:58264865-59817947Cerebellar hemisphere0.3656.81-e110.0010.0131.013
DRD2chr11:113280318-113346413Cerebellar hemisphere-0.1822.47-e100.004-0.0120.988
PITPNM2chr12:123468027-123634562Cerebellar hemisphere-0.0652.21-e090.028-0.0110.989
RINT1chr7:105172532-105208124Cerebellar hemisphere0.0866.32-e090.0160.0111.011
SRMSchr20:62172163-62178857Cerebellar hemisphere-0.4403.08-e080.001-0.0110.989
SETD6chr16:58549383-58554431Cerebellar hemisphere-0.0431.05-e070.054-0.0100.990
APOPT1chr14:104029299-104073860Cortex-0.0741.24-e100.026-0.0120.988
VSIG2chr11:124617368-124622134Cortex-0.0926.01-e090.013-0.0110.989
SDCCAG8chr1:243419320-243663394Cortex-0.0693.88-e070.002-0.0030.997
PIK3C2Achr11:17099277-17229530Cortex-0.0404.04-e070.365-0.0240.976
AS3MTchr10:104629273-104661656Frontal cortex0.5945.65-e170.0010.0171.017
FOXN2chr2:48541776-48606433Hippocampus-0.2502.65-e070.021-0.0360.964
RASIP1chr19:49223844-49243978Nucleus accumbens basal ganglia0.0553.80-e080.0340.0101.010
TCF23chr2:27371872-27376378Nucleus accumbens basal ganglia-0.0764.83-e080.019-0.0100.990
TTC14chr3:180319918-180335616Nucleus accumbens basal ganglia-0.0894.84-e080.013-0.0100.990
TYW5chr2:200794698-200820459Putamen basal ganglia-0.0802.63-e130.035-0.0150.985
SNX19chr11:130745331-130786404Putamen basal ganglia0.0311.31-e120.1790.0131.013
CIARTchr1:150254930-150259505Putamen basal ganglia0.0906.78-e100.0170.0121.012
SH2D7chr15:78370150-78397251Putamen basal ganglia0.0967.89-e090.0130.0111.011
DGUOKchr2:74153953-74186088Putamen basal ganglia0.2558.26-e080.0020.0111.011
C12orf76chr12:110465872-110511491Putamen basal ganglia0.0312.27-e070.0950.0101.01
LRRC37Achr17:44370099-44415160Putamen basal ganglia-0.0352.69-e070.076-0.0100.991
AC005841.1chr12:2958397-2966213Pituitary0.1623.28-e090.0050.0111.011
RPS17chr15:82821158-82824972Pituitary0.0354.03-e080.0820.0101.010
BTN1A1chr6:26501449-26510650Caudate basal ganglia-0.2611.67-e22---
VARS2chr6:30881982-30894236Anterior cingulate cortex0.0757.48-e15---
HIST1H3Hchr6:27777842-27778314Putamen basal ganglia-1.1063.22-e10---
NUDT3chr6:34247456-34360451Nucleus accumbens basal ganglia0.1046.55-e09---
Gene Location Tissue BETA P value GVAR Adjusted BETA Adjusted OR

Where does this data come from?

Huckins et al. applied dorso-lateral prefrontal cortex (DLPFC) and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. They identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We collected these gene set into our database. More details about the gene expression imputation study can be found in the original study (Huckins et al. 2019. Gene Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. Nature Genetics, 51:659-674. [PMID: 30911161])


aTissue -12 GTEx-brain eQTL data and CommondMind Consortium (CMC) DLPFC eQTL data were used by the PrediXcan method.
bBETA -effect sizes (BETA) refer to predicted GREX in cases compared with controls. Effect sizes and odds ratios are also shown adjusted to ‘unit’ variance in gene expression. OR, odds ratio.
cGVAR -genetic variance.
If you used this data, please cite the original reference. [PMID: 30911161]