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LOC132205957 Neanderthal introgressed variant-containing enhancers experimental_67549, experimental_67550 and experimental_67551 [ Homo sapiens (human) ]

Gene ID: 132205957, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132205957
Gene description
Neanderthal introgressed variant-containing enhancers experimental_67549, experimental_67550 and experimental_67551
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 includes three overlapping subregions containing Neanderthal adaptively introgressed genetic variants. All three subregions were validated as enhancers by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 3:195553184 variant alleles for one subregion, and for the non-introgressed 3:195553199 and 3:195553259 variant alleles for the other two subregions. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132205957 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (195826228..195826472)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (198531317..198531562, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (195553099..195553343)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr3:195474413-195474579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195489021-195489522 Neighboring gene mucin 4, cell surface associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195495435-195495936 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:195505212-195506411 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:195508163-195508662 Neighboring gene Sharpr-MPRA regulatory region 430 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195533677-195534240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195535933-195536496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195536497-195537060 Neighboring gene vegetative cell wall protein gp1-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195543301-195544106 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:195547535-195548734 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr3:195550530-195551217 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_67540 and experimental_67545 Neighboring gene MPRA-validated peak4987 silencer Neighboring gene uncharacterized LOC107984010 Neighboring gene long intergenic non-protein coding RNA 1983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195577694-195578194 Neighboring gene kinesin family member 3A pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195586662-195587186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195587187-195587709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195604399-195604953 Neighboring gene tyrosine kinase non receptor 2 Neighboring gene microRNA 6829

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)

General gene information

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Other Names

  • Neanderthal introgressed variant-containing enhancer experimental_67549
  • Neanderthal introgressed variant-containing enhancer experimental_67550
  • Neanderthal introgressed variant-containing enhancer experimental_67551

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_231490.1 

    Range
    101..345
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    195826228..195826472
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187532.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    204048..204292
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_187689.1 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    196087..196331
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    198531317..198531562 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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