Gene Page:RFT1

Summary?
GeneID 91869
Symbol RFT1
Synonyms CDG1N
Description RFT1 homolog
Reference MIM:611908|HGNC:HGNC:30220|Ensembl:ENSG00000163933|HPRD:15239|Vega:OTTHUMG00000074035
Gene type protein-coding
Map location 3p21.1
Pascal p-value 1.998E-4
Fetal beta -0.445
DMG 1 (# studies)
eGene Caudate basal ganglia
Cerebellar Hemisphere
Cerebellum
Cortex
Frontal Cortex BA9
Nucleus accumbens basal ganglia
Putamen basal ganglia
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
LK:YES Genome-wide Association Study This data set included 99 genes mapped to the 22 regions. The 24 leading SNPs were also included in CV:Ripke_2013

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg21627574 3 53164588 RFT1 1.3E-9 -0.015 1.35E-6 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs10994209 chr10 61877705 RFT1 91869 0.06 trans
rs2564924 3 53103155 RFT1 ENSG00000163933.5 4.421E-7 0.01 61323 gtex_brain_putamen_basal
rs2564923 3 53103262 RFT1 ENSG00000163933.5 2.423E-7 0.01 61216 gtex_brain_putamen_basal
rs34530577 3 53103796 RFT1 ENSG00000163933.5 5.907E-7 0.01 60682 gtex_brain_putamen_basal
rs34597126 3 53104407 RFT1 ENSG00000163933.5 4.443E-7 0.01 60071 gtex_brain_putamen_basal
rs2336723 3 53106047 RFT1 ENSG00000163933.5 1.301E-6 0.01 58431 gtex_brain_putamen_basal
rs2564940 3 53107569 RFT1 ENSG00000163933.5 5.328E-7 0.01 56909 gtex_brain_putamen_basal
rs2581800 3 53109352 RFT1 ENSG00000163933.5 4.972E-7 0.01 55126 gtex_brain_putamen_basal
rs1864367 3 53111704 RFT1 ENSG00000163933.5 2.372E-7 0.01 52774 gtex_brain_putamen_basal
rs2253209 3 53115160 RFT1 ENSG00000163933.5 5.737E-7 0.01 49318 gtex_brain_putamen_basal
rs2336725 3 53118739 RFT1 ENSG00000163933.5 5.737E-7 0.01 45739 gtex_brain_putamen_basal
rs2253685 3 53119703 RFT1 ENSG00000163933.5 5.737E-7 0.01 44775 gtex_brain_putamen_basal
rs2253796 3 53120098 RFT1 ENSG00000163933.5 5.737E-7 0.01 44380 gtex_brain_putamen_basal
rs11130338 3 53120924 RFT1 ENSG00000163933.5 5.737E-7 0.01 43554 gtex_brain_putamen_basal
rs4687701 3 53121276 RFT1 ENSG00000163933.5 5.735E-7 0.01 43202 gtex_brain_putamen_basal
rs2581782 3 53122257 RFT1 ENSG00000163933.5 1.746E-7 0.01 42221 gtex_brain_putamen_basal
rs2581783 3 53122258 RFT1 ENSG00000163933.5 1.743E-7 0.01 42220 gtex_brain_putamen_basal
rs2581784 3 53122370 RFT1 ENSG00000163933.5 5.737E-7 0.01 42108 gtex_brain_putamen_basal
rs2082093 3 53122969 RFT1 ENSG00000163933.5 4.975E-7 0.01 41509 gtex_brain_putamen_basal
rs891368 3 53123273 RFT1 ENSG00000163933.5 5.737E-7 0.01 41205 gtex_brain_putamen_basal
rs1078968 3 53123486 RFT1 ENSG00000163933.5 5.737E-7 0.01 40992 gtex_brain_putamen_basal
rs2564921 3 53125585 RFT1 ENSG00000163933.5 1.553E-6 0.01 38893 gtex_brain_putamen_basal
rs11242 3 53125922 RFT1 ENSG00000163933.5 5.737E-7 0.01 38556 gtex_brain_putamen_basal
rs2581786 3 53126143 RFT1 ENSG00000163933.5 5.789E-7 0.01 38335 gtex_brain_putamen_basal
rs397773232 3 53127135 RFT1 ENSG00000163933.5 6.048E-7 0.01 37343 gtex_brain_putamen_basal
rs2581787 3 53127677 RFT1 ENSG00000163933.5 1.009E-6 0.01 36801 gtex_brain_putamen_basal
rs7640294 3 53130913 RFT1 ENSG00000163933.5 9.117E-7 0.01 33565 gtex_brain_putamen_basal
rs2163167 3 53131772 RFT1 ENSG00000163933.5 1.473E-6 0.01 32706 gtex_brain_putamen_basal
rs2115781 3 53131829 RFT1 ENSG00000163933.5 4.545E-7 0.01 32649 gtex_brain_putamen_basal
rs2115782 3 53131830 RFT1 ENSG00000163933.5 4.877E-7 0.01 32648 gtex_brain_putamen_basal

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
死神:胎儿(13 - 26 postconceptionweeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG N GLYCAN BIOSYNTHESIS 46 31 All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF PROTEINS 518 242 All SZGR 2.0 genes in this pathway
REACTOME POST TRANSLATIONAL PROTEIN MODIFICATION 188 116 All SZGR 2.0 genes in this pathway
REACTOME ASPARAGINE N LINKED GLYCOSYLATION 81 54 All SZGR 2.0 genes in this pathway
REACTOME BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 29 17 All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX 795 478 All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 UP 397 206 All SZGR 2.0 genes in this pathway