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LOC132089724 Neanderthal introgressed variant-containing enhancer experimental_110230 [ Homo sapiens (human) ]

Gene ID: 132089724, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089724
Gene description
Neanderthal introgressed variant-containing enhancer experimental_110230
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 genetic variant, and was validated as an enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 9:97250445 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089724 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 (94488078..94488247)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (106657735..106657904)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (97250360..97250529)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100132077 Neighboring gene prothymosin alpha pseudogene 12 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:97136619-97137120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:97137121-97137620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28631 Neighboring gene major facilitator superfamily domain containing 14B Neighboring gene yrdC N(6)-threonylcarbamoyltransferase domain containing pseudogene 1 Neighboring gene MPRA-validated peak7296 silencer Neighboring gene uncharacterized LOC107987100 Neighboring gene MPRA-validated peak7297 silencer Neighboring gene leishmanolysin like peptidase pseudogene Neighboring gene RNA, U6 small nuclear 669, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110244 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110264 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110288 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110294 Neighboring gene uncharacterized LOC124902218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:97315577-97316239 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:97316904-97317566 Neighboring gene prostate cancer associated transcript 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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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_230282.1 

    Range
    101..270
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    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
    94488078..94488247
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    106657735..106657904
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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