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LOC132090727 Neanderthal introgressed variant-containing enhancer experimental_84325 [ Homo sapiens (human) ]

Gene ID: 132090727, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090727
Gene description
Neanderthal introgressed variant-containing enhancer experimental_84325
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 5:30712747 or rs78116128 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090727 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (30712555..30712724)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (30826519..30826688)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (30712662..30712831)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene hypoxanthine phosphoribosyltransferase 1 pseudogene 2 Neighboring gene dynein cytoplasmic 1 light intermediate chain 1, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:30486983-30487719 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:30495215-30495716 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:30495717-30496216 Neighboring gene NANOG hESC enhancer GRCh37_chr5:30596572-30597073 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84285 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84289 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84311 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84391 Neighboring gene uncharacterized LOC124900952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:30823216-30823800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:30823801-30824385 Neighboring gene NANOG hESC enhancer GRCh37_chr5:30845424-30846002 Neighboring gene VISTA enhancer hs1312 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31018943-31019142 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:31053108-31054307 Neighboring gene ribosomal protein L19 pseudogene 11

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_84325

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_231286.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    30712555..30712724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    30826519..30826688
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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