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LOC132089092 Neanderthal introgressed variant-containing enhancer experimental_76272 [ Homo sapiens (human) ]

Gene ID: 132089092, updated on 27-Aug-2024

Summary

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Gene symbol
LOC132089092
Gene description
Neanderthal introgressed variant-containing enhancer experimental_76272
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 4:177142488 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (176221252..176221421)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (179560344..179560513)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900182 Neighboring gene WD repeat domain 17 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:177077413-177078612 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76278 Neighboring gene spermatogenesis associated 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76283 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76286 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76293 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76294 Neighboring gene ankyrin repeat and SOCS box containing 5 Neighboring gene CRISPRi-validated cis-regulatory element chr4.3423 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:177240928-177241428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15817 Neighboring gene SPCS3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22166 Neighboring gene NANOG hESC enhancer GRCh37_chr4:177278841-177279359 Neighboring gene signal peptidase complex subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22168 Neighboring gene uncharacterized LOC124900817

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 variants in ClinVar

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_229651.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    176221252..176221421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    179560344..179560513
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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