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Aliases for HCG9 Gene

Subcategory (RNA class) for HCG9 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for HCG9 Gene

  • HLA Complex Group 9 2 3 5
  • HLA Complex Group 9 (Non-Protein Coding) 2 3
  • HCGIX4 3
  • HCGIX 3

External Ids for HCG9 Gene

Previous GeneCards Identifiers for HCG9 Gene

  • GC06P029713
  • GC06P030048
  • GC06P030050
  • GC06P029943
  • GC06P030094
  • GC06P030182
  • GC06P030172
  • GC06P030224
  • GC06P032249
  • GC06P030347
  • GC06P030496
  • GC06P030698
  • GC06P030859
  • GC06P031019
  • GC06P031175
  • GC06P031354
  • GC06P031618

Summaries for HCG9 Gene

Entrez Gene Summary for HCG9 Gene

  • This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined. [provided by RefSeq, Jul 2009]

GeneCards Summary for HCG9 Gene

HCG9 (HLA Complex Group 9) is an RNA Gene, and is affiliated with the non-coding RNA class.

Additional gene information for HCG9 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HCG9 Gene

Genomics for HCG9 Gene

GeneHancer (GH) Regulatory Elements for HCG9 Gene

Promoters and enhancers for HCG9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J029976 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 600.7 +1.3 1291 2.8 ELF3 ZFX ZKSCAN8 POLR2A MLLT1 ZNF121 CEBPG GTF2F1 ZSCAN21 TFE3 MICD HCG9 HLA-J ENSG00000237669 HLA-K HLA-A ZFP57 GABBR1 HLA-H ZNRD1
GH06J030942 Promoter/Enhancer 1.4 Ensembl ENCODE 6.4 +967.6 967555 0.5 SP1 CTCF MLLT1 ZSCAN21 SP7 KLF14 SP5 PRDM1 HMG20B IKZF1 HCG9 MUCL3 SFTA2
GH06J030857 Enhancer 1.1 Ensembl ENCODE dbSUPER 6.3 +882.3 882300 1.6 SP1 ZNF652 CREM PKNOX1 ZIC2 ARNT ZBTB44 TGIF2 OSR2 RUNX3 VARS2 HLA-C RNU6-1133P MUCL3 HCG21 HCG9 ENSG00000272501 HLA-J LINC02570 GC06P032557
GH06J029371 Enhancer 0.3 Ensembl 3.9 -603.0 -603011 1.8 ZNF133 TRIM27 ZFP57 OR2H2 OR5V1 SUMO2P1 GABBR1 MICD HCG9 OR12D3 GC06P029355
GH06J029963 Enhancer 1.6 FANTOM5 ENCODE dbSUPER 0.4 -8.9 -8863 4.8 ZNF652 SP1 ZFX CC2D1A ELF3 ZKSCAN8 CBFA2T2 ZNF148 NKRF MLLT1 HLA-A HLA-K ENSG00000237669 ZNRD1 HLA-W TRIM39 HLA-H PPP1R10 MDC1 DHX16
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HCG9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HCG9 gene promoter:
  • AML1a
  • AREB6
  • ARP-1
  • ATF
  • HTF
  • p300
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for HCG9 Gene

Genomic Locations for HCG9 Gene
3,299 bases
Plus strand
3,295 bases
Plus strand

Genomic View for HCG9 Gene

Genes around HCG9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HCG9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HCG9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for HCG9 Gene

Post-translational modifications for HCG9 Gene

No Post-translational modifications

No data available for DME Specific Peptides for HCG9 Gene

Domains & Families for HCG9 Gene

Suggested Antigen Peptide Sequences for HCG9 Gene

GenScript: Design optimal peptide antigens:
  • HcgIX protein (Q93065_HUMAN)

Graphical View of Domain Structure for InterPro Entry

No data available for Gene Families , Protein Domains and UniProtKB/Swiss-Prot for HCG9 Gene

Function for HCG9 Gene

Phenotypes From GWAS Catalog for HCG9 Gene

Phenotypes for HCG9 Gene

genes like me logo Genes that share phenotypes with HCG9: view

Animal Model Products

CRISPR Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HCG9 Gene

Localization for HCG9 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for HCG9 Gene

Pathways & Interactions for HCG9 Gene

PathCards logo

SuperPathways for HCG9 Gene

No Data Available

Interacting Proteins for HCG9 Gene

Gene Ontology (GO) - Biological Process for HCG9 Gene


No data available for Pathways by source and SIGNOR curated interactions for HCG9 Gene

Drugs & Compounds for HCG9 Gene

No Compound Related Data Available

Transcripts for HCG9 Gene

mRNA/cDNA for HCG9 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
(1) RNA Central transcripts :

Unigene Clusters for HCG9 Gene

HLA complex group 9 (non-protein coding):
Representative Sequences:

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for HCG9 Gene

No ASD Table

Relevant External Links for HCG9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HCG9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HCG9 Gene

NURSA nuclear receptor signaling pathways regulating expression of HCG9 Gene:


SOURCE GeneReport for Unigene cluster for HCG9 Gene:

genes like me logo Genes that share expression patterns with HCG9: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HCG9 Gene

Orthologs for HCG9 Gene

Evolution for HCG9 Gene

Gene Tree for HCG9 (if available)
Gene Tree for HCG9 (if available)

No data available for Orthologs for HCG9 Gene

Paralogs for HCG9 Gene

(1) SIMAP similar genes for HCG9 Gene using alignment to 1 proteins:

  • Q93065_HUMAN
genes like me logo Genes that share paralogs with HCG9: view

No data available for Paralogs for HCG9 Gene

Variants for HCG9 Gene

Sequence variations from dbSNP and Humsavar for HCG9 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000145133 -- 29,974,292(+) C/G/T upstream_transcript_variant
rs1000605110 -- 29,975,849(+) C/A intron_variant
rs1001119111 -- 29,975,083(+) T/G upstream_transcript_variant
rs1001500123 -- 29,977,413(+) C/A intron_variant
rs1002328252 -- 29,977,410(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HCG9 Gene

Variant ID Type Subtype PubMed ID
dgv1088e199 CNV deletion 23128226
dgv992e201 CNV deletion 23290073
dgv993e201 CNV deletion 23290073
esv2641340 CNV deletion 19546169
esv2670487 CNV deletion 23128226
esv2731775 CNV deletion 23290073
esv2731777 CNV deletion 23290073
esv2731778 CNV deletion 23290073
esv2759412 CNV gain+loss 17122850
esv32544 CNV gain+loss 17666407
esv3303415 CNV mobile element insertion 20981092
esv3310214 CNV mobile element insertion 20981092
esv3332677 CNV duplication 20981092
esv3342659 CNV insertion 20981092
esv3350882 CNV duplication 20981092
esv3360519 CNV insertion 20981092
esv3369212 CNV duplication 20981092
nsv1074389 CNV deletion 25765185
nsv10810 CNV gain+loss 18304495
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv508398 CNV deletion 20534489
nsv511863 CNV loss 21212237
nsv601264 CNV loss 21841781

Additional Variant Information for HCG9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for HCG9 Gene

Disorders for HCG9 Gene

Additional Disease Information for HCG9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HCG9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HCG9 Gene

Publications for HCG9 Gene

  1. A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy. (PMID: 22197929) Yu XQ … Liu JJ (Nature genetics 2011) 3 45 58
  2. Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo. (PMID: 20410501) Jin Y … Spritz RA (The New England journal of medicine 2010) 3 45 58
  3. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree BA … IMSGC (PloS one 2010) 3 45 58
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 45 58
  5. Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. (PMID: 10557312) Shiina T … Inoko H (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 58

Products for HCG9 Gene

Sources for HCG9 Gene

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