Gene Page: SETD4
Summary ?
| GeneID | 54093 |
| Symbol | SETD4 |
| Synonyms | C21orf18|C21orf27 |
| Description | SET domain containing 4 |
| Reference | HGNC:HGNC:1258|Ensembl:ENSG00000185917|HPRD:10743|Vega:OTTHUMG00000086483 |
| Gene type | protein-coding |
| Map location | 21q22.13 |
| Pascal p-value | 0.056 |
| Sherlock p-value | 0.386 |
| Fetal beta | 0.549 |
| DMG | 1 (# studies) |
| eGene | Anterior cingulate cortex BA24 Cerebellar Hemisphere Cortex Frontal Cortex BA9 Nucleus accumbens basal ganglia Myers' cis & trans Meta |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:GWASdb | Genome-wide Association Studies | GWASdb records for schizophrenia | |
| 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 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg17969117 | 21 | 37432493 | SETD4 | 6E-9 | -0.01 | 3.2E-6 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs317216 | 0 | SETD4 | 54093 | 0.18 | trans | |||
| rs2845740 | 21 | 37364666 | SETD4 | ENSG00000185917.9 | 1.031E-7 | 0 | 87021 | gtex_brain_ba24 |
| rs67241603 | 21 | 37365144 | SETD4 | ENSG00000185917.9 | 5.069E-7 | 0 | 86543 | gtex_brain_ba24 |
| rs73198863 | 21 | 37365288 | SETD4 | ENSG00000185917.9 | 5.832E-8 | 0 | 86399 | gtex_brain_ba24 |
| rs111213017 | 21 | 37365435 | SETD4 | ENSG00000185917.9 | 2.6E-7 | 0 | 86252 | gtex_brain_ba24 |
| rs73198866 | 21 | 37365870 | SETD4 | ENSG00000185917.9 | 1.434E-6 | 0 | 85817 | gtex_brain_ba24 |
| rs73198867 | 21 | 37365871 | SETD4 | ENSG00000185917.9 | 1.439E-6 | 0 | 85816 | gtex_brain_ba24 |
| rs368058024 | 21 | 37366222 | SETD4 | ENSG00000185917.9 | 5.322E-7 | 0 | 85465 | gtex_brain_ba24 |
| rs62637211 | 21 | 37366371 | SETD4 | ENSG00000185917.9 | 5.795E-7 | 0 | 85316 | gtex_brain_ba24 |
| rs2835218 | 21 | 37366403 | SETD4 | ENSG00000185917.9 | 5.241E-7 | 0 | 85284 | gtex_brain_ba24 |
| rs62230784 | 21 | 37366433 | SETD4 | ENSG00000185917.9 | 5.241E-7 | 0 | 85254 | gtex_brain_ba24 |
| rs12233318 | 21 | 37366802 | SETD4 | ENSG00000185917.9 | 5.213E-7 | 0 | 84885 | gtex_brain_ba24 |
| rs12233319 | 21 | 37366807 | SETD4 | ENSG00000185917.9 | 5.213E-7 | 0 | 84880 | gtex_brain_ba24 |
| rs2835219 | 21 | 37366925 | SETD4 | ENSG00000185917.9 | 4.342E-7 | 0 | 84762 | gtex_brain_ba24 |
| rs12233320 | 21 | 37366959 | SETD4 | ENSG00000185917.9 | 5.198E-7 | 0 | 84728 | gtex_brain_ba24 |
| rs2835220 | 21 | 37367098 | SETD4 | ENSG00000185917.9 | 5.193E-7 | 0 | 84589 | gtex_brain_ba24 |
| rs2835221 | 21 | 37367160 | SETD4 | ENSG00000185917.9 | 5.167E-7 | 0 | 84527 | gtex_brain_ba24 |
| rs4817756 | 21 | 37368393 | SETD4 | ENSG00000185917.9 | 5.106E-7 | 0 | 83294 | gtex_brain_ba24 |
| rs4817757 | 21 | 37368454 | SETD4 | ENSG00000185917.9 | 4.847E-7 | 0 | 83233 | gtex_brain_ba24 |
| rs1984353 | 21 | 37368542 | SETD4 | ENSG00000185917.9 | 5.089E-7 | 0 | 83145 | gtex_brain_ba24 |
| rs1984018 | 21 | 37369086 | SETD4 | ENSG00000185917.9 | 1.078E-6 | 0 | 82601 | gtex_brain_ba24 |
| rs2835224 | 21 | 37370030 | SETD4 | ENSG00000185917.9 | 1.61E-9 | 0 | 81657 | gtex_brain_ba24 |
| rs201772229 | 21 | 37371138 | SETD4 | ENSG00000185917.9 | 3.217E-9 | 0 | 80549 | gtex_brain_ba24 |
| rs11700546 | 21 | 37371139 | SETD4 | ENSG00000185917.9 | 3.211E-9 | 0 | 80548 | gtex_brain_ba24 |
| rs2835225 | 21 | 37371140 | SETD4 | ENSG00000185917.9 | 3.217E-9 | 0 | 80547 | gtex_brain_ba24 |
| rs62230786 | 21 | 37374082 | SETD4 | ENSG00000185917.9 | 5.611E-11 | 0 | 77605 | gtex_brain_ba24 |
| rs62230787 | 21 | 37376480 | SETD4 | ENSG00000185917.9 | 6.112E-11 | 0 | 75207 | gtex_brain_ba24 |
| rs61738607 | 21 | 37377631 | SETD4 | ENSG00000185917.9 | 6.568E-10 | 0 | 74056 | gtex_brain_ba24 |
| rs62230788 | 21 | 37380337 | SETD4 | ENSG00000185917.9 | 2.148E-9 | 0 | 71350 | gtex_brain_ba24 |
| rs7277791 | 21 | 37383227 | SETD4 | ENSG00000185917.9 | 4.111E-9 | 0 | 68460 | gtex_brain_ba24 |
| rs8134590 | 21 | 37384027 | SETD4 | ENSG00000185917.9 | 1.136E-8 | 0 | 67660 | gtex_brain_ba24 |
| rs11701590 | 21 | 37384730 | SETD4 | ENSG00000185917.9 | 4.111E-9 | 0 | 66957 | gtex_brain_ba24 |
| rs743420 | 21 | 37387402 | SETD4 | ENSG00000185917.9 | 3.054E-8 | 0 | 64285 | gtex_brain_ba24 |
| rs62230790 | 21 | 37388911 | SETD4 | ENSG00000185917.9 | 4.111E-9 | 0 | 62776 | gtex_brain_ba24 |
| rs4817759 | 21 | 37389559 | SETD4 | ENSG00000185917.9 | 8.219E-9 | 0 | 62128 | gtex_brain_ba24 |
| rs2835231 | 21 | 37390598 | SETD4 | ENSG00000185917.9 | 8.219E-9 | 0 | 61089 | gtex_brain_ba24 |
| rs2835232 | 21 | 37393427 | SETD4 | ENSG00000185917.9 | 8.219E-9 | 0 | 58260 | gtex_brain_ba24 |
| rs2835233 | 21 | 37393582 | SETD4 | ENSG00000185917.9 | 8.219E-9 | 0 | 58105 | gtex_brain_ba24 |
| rs62230791 | 21 | 37394607 | SETD4 | ENSG00000185917.9 | 4.111E-9 | 0 | 57080 | gtex_brain_ba24 |
| rs67503416 | 21 | 37394690 | SETD4 | ENSG00000185917.9 | 2.958E-8 | 0 | 56997 | gtex_brain_ba24 |
| rs4817760 | 21 | 37395301 | SETD4 | ENSG00000185917.9 | 3.606E-8 | 0 | 56386 | gtex_brain_ba24 |
| rs4817761 | 21 | 37395556 | SETD4 | ENSG00000185917.9 | 2.518E-8 | 0 | 56131 | gtex_brain_ba24 |
| rs62230812 | 21 | 37398552 | SETD4 | ENSG00000185917.9 | 3.155E-10 | 0 | 53135 | gtex_brain_ba24 |
| rs34033502 | 21 | 37398954 | SETD4 | ENSG00000185917.9 | 2.882E-9 | 0 | 52733 | gtex_brain_ba24 |
| rs8130966 | 21 | 37401413 | SETD4 | ENSG00000185917.9 | 2.15E-9 | 0 | 50274 | gtex_brain_ba24 |
| rs62230813 | 21 | 37403432 | SETD4 | ENSG00000185917.9 | 1.838E-9 | 0 | 48255 | gtex_brain_ba24 |
| rs62230814 | 21 | 37403546 | SETD4 | ENSG00000185917.9 | 2.15E-9 | 0 | 48141 | gtex_brain_ba24 |
| rs34259635 | 21 | 37403570 | SETD4 | ENSG00000185917.9 | 2.15E-9 | 0 | 48117 | gtex_brain_ba24 |
| rs144356767 | 21 | 37404404 | SETD4 | ENSG00000185917.9 | 6.372E-10 | 0 | 47283 | gtex_brain_ba24 |
| rs62230815 | 21 | 37404487 | SETD4 | ENSG00000185917.9 | 2.674E-8 | 0 | 47200 | gtex_brain_ba24 |
| rs878606 | 21 | 37406692 | SETD4 | ENSG00000185917.9 | 1.666E-10 | 0 | 44995 | gtex_brain_ba24 |
| rs7275820 | 21 | 37409414 | SETD4 | ENSG00000185917.9 | 2.107E-9 | 0 | 42273 | gtex_brain_ba24 |
| rs35353247 | 21 | 37409587 | SETD4 | ENSG00000185917.9 | 5.305E-9 | 0 | 42100 | gtex_brain_ba24 |
| rs7280551 | 21 | 37409609 | SETD4 | ENSG00000185917.9 | 2.132E-9 | 0 | 42078 | gtex_brain_ba24 |
| rs56249518 | 21 | 37409835 | SETD4 | ENSG00000185917.9 | 3.252E-10 | 0 | 41852 | gtex_brain_ba24 |
| rs2835241 | 21 | 37411380 | SETD4 | ENSG00000185917.9 | 3.241E-10 | 0 | 40307 | gtex_brain_ba24 |
| rs2255734 | 21 | 37411909 | SETD4 | ENSG00000185917.9 | 2.15E-9 | 0 | 39778 | gtex_brain_ba24 |
| rs2255858 | 21 | 37412752 | SETD4 | ENSG00000185917.9 | 3.241E-10 | 0 | 38935 | gtex_brain_ba24 |
| rs2835242 | 21 | 37413532 | SETD4 | ENSG00000185917.9 | 2.056E-9 | 0 | 38155 | gtex_brain_ba24 |
| rs2835243 | 21 | 37413946 | SETD4 | ENSG00000185917.9 | 2.107E-9 | 0 | 37741 | gtex_brain_ba24 |
| rs10581489 | 21 | 37415766 | SETD4 | ENSG00000185917.9 | 3.834E-10 | 0 | 35921 | gtex_brain_ba24 |
| rs2835245 | 21 | 37416708 | SETD4 | ENSG00000185917.9 | 2.107E-9 | 0 | 34979 | gtex_brain_ba24 |
| rs12483151 | 21 | 37419578 | SETD4 | ENSG00000185917.9 | 3.155E-10 | 0 | 32109 | gtex_brain_ba24 |
| rs12482541 | 21 | 37419743 | SETD4 | ENSG00000185917.9 | 2.107E-9 | 0 | 31944 | gtex_brain_ba24 |
| rs2835253 | 21 | 37419745 | SETD4 | ENSG00000185917.9 | 2.132E-9 | 0 | 31942 | gtex_brain_ba24 |
| rs880221 | 21 | 37420785 | SETD4 | ENSG00000185917.9 | 3.155E-10 | 0 | 30902 | gtex_brain_ba24 |
| rs11088331 | 21 | 37421872 | SETD4 | ENSG00000185917.9 | 3.155E-10 | 0 | 29815 | gtex_brain_ba24 |
| rs56279140 | 21 | 37424361 | SETD4 | ENSG00000185917.9 | 3.155E-10 | 0 | 27326 | gtex_brain_ba24 |
| rs2835258 | 21 | 37424365 | SETD4 | ENSG00000185917.9 | 2.107E-9 | 0 | 27322 | gtex_brain_ba24 |
| rs11702405 | 21 | 37424690 | SETD4 | ENSG00000185917.9 | 1.12E-8 | 0 | 26997 | gtex_brain_ba24 |
| rs78393308 | 21 | 37424695 | SETD4 | ENSG00000185917.9 | 2.111E-8 | 0 | 26992 | gtex_brain_ba24 |
| rs11702407 | 21 | 37424700 | SETD4 | ENSG00000185917.9 | 2.111E-8 | 0 | 26987 | gtex_brain_ba24 |
| rs62230821 | 21 | 37425116 | SETD4 | ENSG00000185917.9 | 3.155E-10 | 0 | 26571 | gtex_brain_ba24 |
| rs2835259 | 21 | 37425302 | SETD4 | ENSG00000185917.9 | 3.155E-10 | 0 | 26385 | gtex_brain_ba24 |
| rs62230822 | 21 | 37429945 | SETD4 | ENSG00000185917.9 | 1.516E-10 | 0 | 21742 | gtex_brain_ba24 |
| rs2835263 | 21 | 37430245 | SETD4 | ENSG00000185917.9 | 3.147E-10 | 0 | 21442 | gtex_brain_ba24 |
| rs2026259 | 21 | 37430627 | SETD4 | ENSG00000185917.9 | 2.107E-9 | 0 | 21060 | gtex_brain_ba24 |
| rs143347702 | 21 | 37430817 | SETD4 | ENSG00000185917.9 | 2.215E-9 | 0 | 20870 | gtex_brain_ba24 |
| rs2051395 | 21 | 37431265 | SETD4 | ENSG00000185917.9 | 2.107E-9 | 0 | 20422 | gtex_brain_ba24 |
| rs7280136 | 21 | 37432910 | SETD4 | ENSG00000185917.9 | 1.587E-10 | 0 | 18777 | gtex_brain_ba24 |
| rs6517325 | 21 | 37434978 | SETD4 | ENSG00000185917.9 | 2.999E-8 | 0 | 16709 | gtex_brain_ba24 |
| rs76910698 | 21 | 37435108 | SETD4 | ENSG00000185917.9 | 1.283E-7 | 0 | 16579 | gtex_brain_ba24 |
| rs2835264 | 21 | 37435965 | SETD4 | ENSG00000185917.9 | 1.725E-9 | 0 | 15722 | gtex_brain_ba24 |
| rs11702262 | 21 | 37437223 | SETD4 | ENSG00000185917.9 | 7.984E-9 | 0 | 14464 | gtex_brain_ba24 |
| rs1005696 | 21 | 37443480 | SETD4 | ENSG00000185917.9 | 4.797E-7 | 0 | 8207 | gtex_brain_ba24 |
| rs1005695 | 21 | 37443565 | SETD4 | ENSG00000185917.9 | 2.885E-7 | 0 | 8122 | gtex_brain_ba24 |
| rs998384 | 21 | 37445526 | SETD4 | ENSG00000185917.9 | 4.168E-10 | 0 | 6161 | gtex_brain_ba24 |
| rs998383 | 21 | 37445739 | SETD4 | ENSG00000185917.9 | 4.168E-10 | 0 | 5948 | gtex_brain_ba24 |
| rs2835267 | 21 | 37447025 | SETD4 | ENSG00000185917.9 | 4.797E-7 | 0 | 4662 | gtex_brain_ba24 |
| rs2835268 | 21 | 37449136 | SETD4 | ENSG00000185917.9 | 1.496E-8 | 0 | 2551 | gtex_brain_ba24 |
| rs7278930 | 21 | 37450210 | SETD4 | ENSG00000185917.9 | 4.346E-7 | 0 | 1477 | gtex_brain_ba24 |
| rs2835270 | 21 | 37450583 | SETD4 | ENSG00000185917.9 | 4.346E-7 | 0 | 1104 | gtex_brain_ba24 |
| rs59397717 | 21 | 37451725 | SETD4 | ENSG00000185917.9 | 4.758E-9 | 0 | -38 | gtex_brain_ba24 |
| rs62229264 | 21 | 37452213 | SETD4 | ENSG00000185917.9 | 5.573E-9 | 0 | -526 | gtex_brain_ba24 |
| rs4816518 | 21 | 37453307 | SETD4 | ENSG00000185917.9 | 1.914E-8 | 0 | -1620 | gtex_brain_ba24 |
| rs4817768 | 21 | 37455338 | SETD4 | ENSG00000185917.9 | 2.017E-6 | 0 | -3651 | gtex_brain_ba24 |
| rs5843741 | 21 | 37456659 | SETD4 | ENSG00000185917.9 | 1.924E-6 | 0 | -4972 | gtex_brain_ba24 |
| rs11908841 | 21 | 37457401 | SETD4 | ENSG00000185917.9 | 1.919E-6 | 0 | -5714 | gtex_brain_ba24 |
| rs11701331 | 21 | 37458392 | SETD4 | ENSG00000185917.9 | 1.675E-8 | 0 | -6705 | gtex_brain_ba24 |
| rs2835275 | 21 | 37460001 | SETD4 | ENSG00000185917.9 | 1.675E-8 | 0 | -8314 | gtex_brain_ba24 |
| rs62229266 | 21 | 37460271 | SETD4 | ENSG00000185917.9 | 6.498E-10 | 0 | -8584 | gtex_brain_ba24 |
| rs7280896 | 21 | 37460906 | SETD4 | ENSG00000185917.9 | 5.488E-9 | 0 | -9219 | gtex_brain_ba24 |
| rs988082 | 21 | 37462482 | SETD4 | ENSG00000185917.9 | 1.165E-6 | 0 | -10795 | gtex_brain_ba24 |
| rs7278507 | 21 | 37463631 | SETD4 | ENSG00000185917.9 | 1.282E-6 | 0 | -11944 | gtex_brain_ba24 |
| rs11088334 | 21 | 37466829 | SETD4 | ENSG00000185917.9 | 7.921E-9 | 0 | -15142 | gtex_brain_ba24 |
| rs4817771 | 21 | 37467226 | SETD4 | ENSG00000185917.9 | 3.621E-7 | 0 | -15539 | gtex_brain_ba24 |
| rs11088335 | 21 | 37470335 | SETD4 | ENSG00000185917.9 | 3.951E-9 | 0 | -18648 | gtex_brain_ba24 |
| rs11702763 | 21 | 37470704 | SETD4 | ENSG00000185917.9 | 6.338E-9 | 0 | -19017 | gtex_brain_ba24 |
Section II. Transcriptome annotation
General gene expression (GTEx)
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
ST1: fetal (13 - 26 postconception weeks), 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 |
|---|---|---|---|
| BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS | 882 | 572 | All SZGR 2.0 genes in this pathway |
| KAAB HEART ATRIUM VS VENTRICLE DN | 261 | 183 | All SZGR 2.0 genes in this pathway |
| KRIGE RESPONSE TO TOSEDOSTAT 6HR DN | 911 | 527 | All SZGR 2.0 genes in this pathway |
| KRIGE RESPONSE TO TOSEDOSTAT 24HR DN | 1011 | 592 | All SZGR 2.0 genes in this pathway |
| SANSOM APC TARGETS REQUIRE MYC | 210 | 123 | All SZGR 2.0 genes in this pathway |
| BOYLAN MULTIPLE MYELOMA D CLUSTER UP | 27 | 19 | All SZGR 2.0 genes in this pathway |
| BOYLAN MULTIPLE MYELOMA D UP | 89 | 62 | All SZGR 2.0 genes in this pathway |
| WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D | 658 | 397 | All SZGR 2.0 genes in this pathway |
| FORTSCHEGGER PHF8 TARGETS UP | 279 | 155 | All SZGR 2.0 genes in this pathway |