Gene Page: LY6G5C
Summary ?
| GeneID | 80741 |
| Symbol | LY6G5C |
| Synonyms | C6orf20|G5C|LY6G5CA|LY6G5CB|NG33 |
| Description | lymphocyte antigen 6 complex, locus G5C |
| Reference | MIM:610434|HGNC:HGNC:13932|Ensembl:ENSG00000204428|HPRD:14328|Vega:OTTHUMG00000031228 |
| Gene type | protein-coding |
| Map location | 6p21.33 |
| Pascal p-value | 1.442E-12 |
| Sherlock p-value | 0.082 |
| Fetal beta | 0.531 |
| eGene | Anterior cingulate cortex BA24 Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Hypothalamus Nucleus accumbens basal ganglia Putamen basal ganglia Myers' cis & trans Meta |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| PMID:cooccur | High-throughput literature-search | Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included. | |
| GSMA_I | Genome scan meta-analysis | Psr: 0.033 | |
| Literature | High-throughput literature-search | Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias | Click to show details |
Section I. Genetics and epigenetics annotation
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs7584986 | chr2 | 184111432 | LY6G5C | 80741 | 8.943E-4 | trans | ||
| rs1368303 | chr5 | 147672388 | LY6G5C | 80741 | 3.475E-5 | trans | ||
| rs16955618 | chr15 | 29937543 | LY6G5C | 80741 | 2.685E-4 | trans | ||
| snp_a-1830894 | 0 | LY6G5C | 80741 | 0 | trans | |||
| rs16990006 | chrX | 32014626 | LY6G5C | 80741 | 0.09 | trans | ||
| rs2242660 | 6 | 31597753 | LY6G5C | ENSG00000204428.8 | 4.034E-8 | 0 | 54064 | gtex_brain_ba24 |
| rs2844465 | 6 | 31601022 | LY6G5C | ENSG00000204428.8 | 4.034E-8 | 0 | 50795 | gtex_brain_ba24 |
| rs2242659 | 6 | 31601513 | LY6G5C | ENSG00000204428.8 | 4.034E-8 | 0 | 50304 | gtex_brain_ba24 |
| rs805303 | 6 | 31616366 | LY6G5C | ENSG00000204428.8 | 4.034E-8 | 0 | 35451 | gtex_brain_ba24 |
| rs805302 | 6 | 31617957 | LY6G5C | ENSG00000204428.8 | 3.153E-8 | 0 | 33860 | gtex_brain_ba24 |
| rs805301 | 6 | 31618121 | LY6G5C | ENSG00000204428.8 | 4.034E-8 | 0 | 33696 | gtex_brain_ba24 |
| rs813115 | 6 | 31620020 | LY6G5C | ENSG00000204428.8 | 9.141E-9 | 0 | 31797 | gtex_brain_ba24 |
| rs707920 | 6 | 31629096 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | 22721 | gtex_brain_ba24 |
| rs7029 | 6 | 31629953 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | 21864 | gtex_brain_ba24 |
| rs7992 | 6 | 31630241 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | 21576 | gtex_brain_ba24 |
| rs805257 | 6 | 31634193 | LY6G5C | ENSG00000204428.8 | 7.217E-8 | 0 | 17624 | gtex_brain_ba24 |
| rs4569 | 6 | 31637807 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | 14010 | gtex_brain_ba24 |
| rs1266076 | 6 | 31640518 | LY6G5C | ENSG00000204428.8 | 1.674E-8 | 0 | 11299 | gtex_brain_ba24 |
| rs805271 | 6 | 31643251 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | 8566 | gtex_brain_ba24 |
| rs805290 | 6 | 31648403 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | 3414 | gtex_brain_ba24 |
| rs9279386 | 6 | 31650592 | LY6G5C | ENSG00000204428.8 | 3.453E-10 | 0 | 1225 | gtex_brain_ba24 |
| rs1266075 | 6 | 31653120 | LY6G5C | ENSG00000204428.8 | 4.31E-9 | 0 | -1303 | gtex_brain_ba24 |
| rs9281553 | 6 | 31653579 | LY6G5C | ENSG00000204428.8 | 4.82E-10 | 0 | -1762 | gtex_brain_ba24 |
| rs707918 | 6 | 31654732 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | -2915 | gtex_brain_ba24 |
| rs707917 | 6 | 31657754 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | -5937 | gtex_brain_ba24 |
| rs805282 | 6 | 31659731 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | -7914 | gtex_brain_ba24 |
| rs805281 | 6 | 31661489 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | -9672 | gtex_brain_ba24 |
| rs805280 | 6 | 31662229 | LY6G5C | ENSG00000204428.8 | 1.861E-10 | 0 | -10412 | gtex_brain_ba24 |
| rs805277 | 6 | 31662957 | LY6G5C | ENSG00000204428.8 | 5.749E-9 | 0 | -11140 | gtex_brain_ba24 |
| rs805276 | 6 | 31664219 | LY6G5C | ENSG00000204428.8 | 4.11E-10 | 0 | -12402 | gtex_brain_ba24 |
| rs805274 | 6 | 31665194 | LY6G5C | ENSG00000204428.8 | 3.481E-10 | 0 | -13377 | gtex_brain_ba24 |
| rs1266073 | 6 | 31667028 | LY6G5C | ENSG00000204428.8 | 2.518E-9 | 0 | -15211 | gtex_brain_ba24 |
| rs2242660 | 6 | 31597753 | LY6G5C | ENSG00000204428.8 | 5.903E-7 | 0 | 54064 | gtex_brain_putamen_basal |
| rs2844465 | 6 | 31601022 | LY6G5C | ENSG00000204428.8 | 5.903E-7 | 0 | 50795 | gtex_brain_putamen_basal |
| rs2242659 | 6 | 31601513 | LY6G5C | ENSG00000204428.8 | 5.903E-7 | 0 | 50304 | gtex_brain_putamen_basal |
| rs805303 | 6 | 31616366 | LY6G5C | ENSG00000204428.8 | 5.903E-7 | 0 | 35451 | gtex_brain_putamen_basal |
| rs805302 | 6 | 31617957 | LY6G5C | ENSG00000204428.8 | 5.95E-7 | 0 | 33860 | gtex_brain_putamen_basal |
| rs805301 | 6 | 31618121 | LY6G5C | ENSG00000204428.8 | 5.903E-7 | 0 | 33696 | gtex_brain_putamen_basal |
| rs813115 | 6 | 31620020 | LY6G5C | ENSG00000204428.8 | 5.74E-7 | 0 | 31797 | gtex_brain_putamen_basal |
| rs707920 | 6 | 31629096 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | 22721 | gtex_brain_putamen_basal |
| rs7029 | 6 | 31629953 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | 21864 | gtex_brain_putamen_basal |
| rs7992 | 6 | 31630241 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | 21576 | gtex_brain_putamen_basal |
| rs805260 | 6 | 31630831 | LY6G5C | ENSG00000204428.8 | 2.428E-7 | 0 | 20986 | gtex_brain_putamen_basal |
| rs805257 | 6 | 31634193 | LY6G5C | ENSG00000204428.8 | 8.351E-8 | 0 | 17624 | gtex_brain_putamen_basal |
| rs14365 | 6 | 31635710 | LY6G5C | ENSG00000204428.8 | 9.693E-9 | 0 | 16107 | gtex_brain_putamen_basal |
| rs34561980 | 6 | 31635958 | LY6G5C | ENSG00000204428.8 | 6.854E-8 | 0 | 15859 | gtex_brain_putamen_basal |
| rs34161953 | 6 | 31635963 | LY6G5C | ENSG00000204428.8 | 6.808E-7 | 0 | 15854 | gtex_brain_putamen_basal |
| rs4569 | 6 | 31637807 | LY6G5C | ENSG00000204428.8 | 2.402E-15 | 0 | 14010 | gtex_brain_putamen_basal |
| rs1266076 | 6 | 31640518 | LY6G5C | ENSG00000204428.8 | 7.783E-8 | 0 | 11299 | gtex_brain_putamen_basal |
| rs805271 | 6 | 31643251 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | 8566 | gtex_brain_putamen_basal |
| rs805290 | 6 | 31648403 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | 3414 | gtex_brain_putamen_basal |
| rs9279386 | 6 | 31650592 | LY6G5C | ENSG00000204428.8 | 1.308E-16 | 0 | 1225 | gtex_brain_putamen_basal |
| rs1266075 | 6 | 31653120 | LY6G5C | ENSG00000204428.8 | 8.214E-16 | 0 | -1303 | gtex_brain_putamen_basal |
| rs9281553 | 6 | 31653579 | LY6G5C | ENSG00000204428.8 | 7.09E-16 | 0 | -1762 | gtex_brain_putamen_basal |
| rs707918 | 6 | 31654732 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | -2915 | gtex_brain_putamen_basal |
| rs707917 | 6 | 31657754 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | -5937 | gtex_brain_putamen_basal |
| rs805282 | 6 | 31659731 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | -7914 | gtex_brain_putamen_basal |
| rs805281 | 6 | 31661489 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | -9672 | gtex_brain_putamen_basal |
| rs805280 | 6 | 31662229 | LY6G5C | ENSG00000204428.8 | 2.781E-13 | 0 | -10412 | gtex_brain_putamen_basal |
| rs805277 | 6 | 31662957 | LY6G5C | ENSG00000204428.8 | 3.925E-16 | 0 | -11140 | gtex_brain_putamen_basal |
| rs805276 | 6 | 31664219 | LY6G5C | ENSG00000204428.8 | 7.488E-17 | 0 | -12402 | gtex_brain_putamen_basal |
| rs805274 | 6 | 31665194 | LY6G5C | ENSG00000204428.8 | 1.646E-16 | 0 | -13377 | gtex_brain_putamen_basal |
| rs1266073 | 6 | 31667028 | LY6G5C | ENSG00000204428.8 | 1.917E-13 | 0 | -15211 | gtex_brain_putamen_basal |
| rs805288 | 6 | 31678028 | LY6G5C | ENSG00000204428.8 | 3.894E-12 | 0 | -26211 | gtex_brain_putamen_basal |
| rs805287 | 6 | 31678730 | LY6G5C | ENSG00000204428.8 | 7.668E-11 | 0 | -26913 | gtex_brain_putamen_basal |
| rs805286 | 6 | 31679307 | LY6G5C | ENSG00000204428.8 | 1.177E-7 | 0 | -27490 | gtex_brain_putamen_basal |
| rs805285 | 6 | 31679465 | LY6G5C | ENSG00000204428.8 | 6.019E-8 | 0 | -27648 | gtex_brain_putamen_basal |
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 III. Gene Ontology annotation
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005576 | extracellular region | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| ODONNELL TFRC TARGETS UP | 456 | 228 | All SZGR 2.0 genes in this pathway |
| XU HGF TARGETS REPRESSED BY AKT1 DN | 95 | 58 | All SZGR 2.0 genes in this pathway |
| RIZKI TUMOR INVASIVENESS 3D DN | 270 | 181 | All SZGR 2.0 genes in this pathway |
| PURBEY TARGETS OF CTBP1 NOT SATB1 UP | 344 | 215 | All SZGR 2.0 genes in this pathway |