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LOC132088761 Neanderthal introgressed variant-containing enhancer experimental_53336 [ Homo sapiens (human) ]

Gene ID: 132088761, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088761
Gene description
Neanderthal introgressed variant-containing enhancer experimental_53336
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 the non-introgressed 2:157095635 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088761 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (156239038..156239207)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (156691695..156691864)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (157095550..157095719)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373703 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:156697781-156698549 Neighboring gene VISTA enhancer hs411 Neighboring gene MPRA-validated peak3904 silencer Neighboring gene long intergenic non-protein coding RNA 1876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:156903772-156904272 Neighboring gene MPRA-validated peak3905 silencer Neighboring gene MPRA-validated peak3906 silencer Neighboring gene HEBP2 pseudogene 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:156939984-156941183 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:157031916-157032139 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:157149084-157149974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:157190964-157191836 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:157197537-157198092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:157198093-157198646 Neighboring gene uncharacterized LOC440918 Neighboring gene nuclear receptor subfamily 4 group A member 2

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_229320.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    156239038..156239207
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    156691695..156691864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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