Gene Page: LEMD2
Summary ?
| GeneID | 221496 |
| Symbol | LEMD2 |
| Synonyms | NET25|dJ482C21.1 |
| Description | LEM domain containing 2 |
| Reference | MIM:616312|HGNC:HGNC:21244|Ensembl:ENSG00000161904|HPRD:13984|Vega:OTTHUMG00000014535 |
| Gene type | protein-coding |
| Map location | 6p21.31 |
| Pascal p-value | 1.79E-7 |
| Sherlock p-value | 0.481 |
| eGene | Anterior cingulate cortex BA24 Caudate basal ganglia Cerebellar Hemisphere Cerebellum 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 | |
| GSMA_I | Genome scan meta-analysis | Psr: 0.033 |
Section I. Genetics and epigenetics annotation
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs9461864 | chr6 | 33481468 | LEMD2 | 221496 | 0.12 | cis | ||
| rs16883896 | chr6 | 34255630 | LEMD2 | 221496 | 0.19 | cis | ||
| rs17629180 | chr6 | 34285608 | LEMD2 | 221496 | 0.04 | cis | ||
| rs17696583 | chr6 | 34291764 | LEMD2 | 221496 | 0.09 | cis | ||
| rs4713782 | chr6 | 34401280 | LEMD2 | 221496 | 0.11 | cis | ||
| rs16829545 | chr2 | 151977407 | LEMD2 | 221496 | 1.332E-5 | trans | ||
| rs3845734 | chr2 | 171125572 | LEMD2 | 221496 | 0.04 | trans | ||
| rs16955618 | chr15 | 29937543 | LEMD2 | 221496 | 1.637E-6 | trans | ||
| rs4711347 | 6 | 33735292 | LEMD2 | ENSG00000161904.7 | 1.567E-7 | 0 | 21621 | gtex_brain_ba24 |
| rs12173787 | 6 | 33735471 | LEMD2 | ENSG00000161904.7 | 3.913E-7 | 0 | 21442 | gtex_brain_ba24 |
| rs7774620 | 6 | 33736285 | LEMD2 | ENSG00000161904.7 | 1.517E-7 | 0 | 20628 | gtex_brain_ba24 |
| rs4711348 | 6 | 33736295 | LEMD2 | ENSG00000161904.7 | 2.041E-7 | 0 | 20618 | gtex_brain_ba24 |
| rs747694 | 6 | 33736490 | LEMD2 | ENSG00000161904.7 | 1.517E-7 | 0 | 20423 | gtex_brain_ba24 |
| rs943471 | 6 | 33738314 | LEMD2 | ENSG00000161904.7 | 1.518E-8 | 0 | 18599 | gtex_brain_ba24 |
| rs2296744 | 6 | 33740382 | LEMD2 | ENSG00000161904.7 | 1.536E-8 | 0 | 16531 | gtex_brain_ba24 |
| rs4711349 | 6 | 33740592 | LEMD2 | ENSG00000161904.7 | 1.533E-8 | 0 | 16321 | gtex_brain_ba24 |
| rs4713679 | 6 | 33742403 | LEMD2 | ENSG00000161904.7 | 1.829E-7 | 0 | 14510 | gtex_brain_ba24 |
| rs12196293 | 6 | 33749151 | LEMD2 | ENSG00000161904.7 | 2.375E-8 | 0 | 7762 | gtex_brain_ba24 |
| rs12190029 | 6 | 33749152 | LEMD2 | ENSG00000161904.7 | 2.294E-8 | 0 | 7761 | gtex_brain_ba24 |
| rs6922275 | 6 | 33749739 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | 7174 | gtex_brain_ba24 |
| rs943474 | 6 | 33749834 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | 7079 | gtex_brain_ba24 |
| rs943475 | 6 | 33749978 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | 6935 | gtex_brain_ba24 |
| rs943478 | 6 | 33750940 | LEMD2 | ENSG00000161904.7 | 1.658E-8 | 0 | 5973 | gtex_brain_ba24 |
| rs943479 | 6 | 33752013 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | 4900 | gtex_brain_ba24 |
| rs2395402 | 6 | 33753673 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | 3240 | gtex_brain_ba24 |
| rs9394167 | 6 | 33754396 | LEMD2 | ENSG00000161904.7 | 1.575E-8 | 0 | 2517 | gtex_brain_ba24 |
| rs398065692 | 6 | 33755116 | LEMD2 | ENSG00000161904.7 | 1.82E-8 | 0 | 1797 | gtex_brain_ba24 |
| rs6457741 | 6 | 33756026 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | 887 | gtex_brain_ba24 |
| rs6929696 | 6 | 33759290 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | -2377 | gtex_brain_ba24 |
| rs4711355 | 6 | 33759906 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | -2993 | gtex_brain_ba24 |
| rs9357164 | 6 | 33761021 | LEMD2 | ENSG00000161904.7 | 1.581E-8 | 0 | -4108 | gtex_brain_ba24 |
| rs4711347 | 6 | 33735292 | LEMD2 | ENSG00000161904.7 | 1.042E-6 | 0 | 21621 | gtex_brain_putamen_basal |
| rs7774620 | 6 | 33736285 | LEMD2 | ENSG00000161904.7 | 1.055E-6 | 0 | 20628 | gtex_brain_putamen_basal |
| rs4711348 | 6 | 33736295 | LEMD2 | ENSG00000161904.7 | 2.234E-6 | 0 | 20618 | gtex_brain_putamen_basal |
| rs747694 | 6 | 33736490 | LEMD2 | ENSG00000161904.7 | 9.901E-7 | 0 | 20423 | gtex_brain_putamen_basal |
| rs943471 | 6 | 33738314 | LEMD2 | ENSG00000161904.7 | 9.224E-9 | 0 | 18599 | gtex_brain_putamen_basal |
| rs2296744 | 6 | 33740382 | LEMD2 | ENSG00000161904.7 | 9.034E-9 | 0 | 16531 | gtex_brain_putamen_basal |
| rs4711349 | 6 | 33740592 | LEMD2 | ENSG00000161904.7 | 9.284E-9 | 0 | 16321 | gtex_brain_putamen_basal |
| rs4713678 | 6 | 33742097 | LEMD2 | ENSG00000161904.7 | 4.639E-8 | 0 | 14816 | gtex_brain_putamen_basal |
| rs4713679 | 6 | 33742403 | LEMD2 | ENSG00000161904.7 | 2.02E-8 | 0 | 14510 | gtex_brain_putamen_basal |
| rs12196293 | 6 | 33749151 | LEMD2 | ENSG00000161904.7 | 5.123E-9 | 0 | 7762 | gtex_brain_putamen_basal |
| rs12190029 | 6 | 33749152 | LEMD2 | ENSG00000161904.7 | 1.37E-8 | 0 | 7761 | gtex_brain_putamen_basal |
| rs6922275 | 6 | 33749739 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | 7174 | gtex_brain_putamen_basal |
| rs943474 | 6 | 33749834 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | 7079 | gtex_brain_putamen_basal |
| rs943475 | 6 | 33749978 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | 6935 | gtex_brain_putamen_basal |
| rs943478 | 6 | 33750940 | LEMD2 | ENSG00000161904.7 | 9.519E-9 | 0 | 5973 | gtex_brain_putamen_basal |
| rs943479 | 6 | 33752013 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | 4900 | gtex_brain_putamen_basal |
| rs2395402 | 6 | 33753673 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | 3240 | gtex_brain_putamen_basal |
| rs9394167 | 6 | 33754396 | LEMD2 | ENSG00000161904.7 | 9.535E-9 | 0 | 2517 | gtex_brain_putamen_basal |
| rs398065692 | 6 | 33755116 | LEMD2 | ENSG00000161904.7 | 1.519E-8 | 0 | 1797 | gtex_brain_putamen_basal |
| rs6457741 | 6 | 33756026 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | 887 | gtex_brain_putamen_basal |
| rs6929696 | 6 | 33759290 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | -2377 | gtex_brain_putamen_basal |
| rs4711355 | 6 | 33759906 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | -2993 | gtex_brain_putamen_basal |
| rs9357164 | 6 | 33761021 | LEMD2 | ENSG00000161904.7 | 9.512E-9 | 0 | -4108 | gtex_brain_putamen_basal |
| rs2281820 | 6 | 33768897 | LEMD2 | ENSG00000161904.7 | 5.599E-8 | 0 | -11984 | gtex_brain_putamen_basal |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 III. Gene Ontology annotation
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005634 | nucleus | IEA | - | |
| GO:0005635 | nuclear envelope | IEA | - | |
| GO:0005637 | nuclear inner membrane | IEA | - | |
| GO:0016020 | membrane | IEA | - | |
| GO:0016021 | integral to membrane | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN | 335 | 193 | All SZGR 2.0 genes in this pathway |
| KINSEY TARGETS OF EWSR1 FLII FUSION UP | 1278 | 748 | All SZGR 2.0 genes in this pathway |
| GYORFFY MITOXANTRONE RESISTANCE | 57 | 35 | All SZGR 2.0 genes in this pathway |
| FIGUEROA AML METHYLATION CLUSTER 3 UP | 170 | 97 | All SZGR 2.0 genes in this pathway |
| BAKKER FOXO3 TARGETS DN | 187 | 109 | All SZGR 2.0 genes in this pathway |
Section VI. microRNA annotation
| miRNA family | Target position | miRNA ID | miRNA seq | ||
|---|---|---|---|---|---|
| UTR start | UTR end | Match method | |||
| miR-124/506 | 424 | 430 | m8 | hsa-miR-506 | UAAGGCACCCUUCUGAGUAGA |
| hsa-miR-124brain | UAAGGCACGCGGUGAAUGCC | ||||
- SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
- Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.