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LOC132088759 Neanderthal introgressed variant-containing enhancer experimental_53210 [ Homo sapiens (human) ]

Gene ID: 132088759, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088759
Gene description
Neanderthal introgressed variant-containing enhancer experimental_53210
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 2:149521861 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088759 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 (148764207..148764376)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (149214596..149214765)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (149521776..149521945)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907896 Neighboring gene OCT4 hESC enhancer GRCh37_chr2:149280763-149281300 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:149300377-149300570 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:149311371-149312328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:149317839-149318790 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149335391-149336105 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149336106-149336819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16618 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149371380-149371985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16619 Neighboring gene ribosomal protein S29 pseudogene 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:149402393-149402897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149435593-149436192 Neighboring gene enhancer of polycomb homolog 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:149596595-149596791 Neighboring gene RNA, U2 small nuclear 9, pseudogene Neighboring gene uncharacterized LOC101928526

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

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_229318.1 

    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
    148764207..148764376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    149214596..149214765
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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