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LOC132088689 Neanderthal introgressed variant-containing enhancer experimental_6552 [ Homo sapiens (human) ]

Gene ID: 132088689, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088689
Gene description
Neanderthal introgressed variant-containing enhancer experimental_6552
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 1:2940998 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088689 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3024349..3024518)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2525969..2526138)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2940913..2941082)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903826 Neighboring gene uncharacterized LOC124903825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2766741-2767242 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:2824551-2825750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2837727-2838286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 57 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2931349-2932112 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6546 Neighboring gene translation initiation factor IF-2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2976872-2977417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2984086-2984660 Neighboring gene opioid growth factor receptor pseudogene Neighboring gene actin related protein T2 Neighboring gene PRDM16 divergent transcript Neighboring gene PR/SET domain 16

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_229248.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    3024349..3024518
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    2525969..2526138
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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