U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC132090798 Neanderthal introgressed variant-containing enhancer experimental_104606 [ Homo sapiens (human) ]

Gene ID: 132090798, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC132090798
Gene description
Neanderthal introgressed variant-containing enhancer experimental_104606
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region contains a Neanderthal adaptively introgressed expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 9:112790036 or rs7024673 variant alleles. [provided by RefSeq, Sep 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC132090798 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (110027671..110027840)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (122197204..122197373)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (112789951..112790120)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene PALM2 and AKAP2 fusion Neighboring gene putative uncharacterized protein DDB_G0287265 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104519 Neighboring gene Sharpr-MPRA regulatory region 11524 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:112578478-112579677 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28781 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104594 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:112767573-112768074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:112809348-112809922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:112810496-112811069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20171 Neighboring gene ribosomal protein L21 pseudogene 87 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:112831420-112832619 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_104629 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:112868296-112868903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:112887224-112887786 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:112893707-112894550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28782 Neighboring gene uncharacterized LOC124902244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28783 Neighboring gene uncharacterized LOC105376217

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • emVar-containing allelic enhancer experimental_104606

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_231357.1 

    Range
    101..270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    110027671..110027840
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    122197204..122197373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases