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LOC132088617 Neanderthal introgressed variant-containing enhancer experimental_1801 [ Homo sapiens (human) ]

Gene ID: 132088617, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088617
Gene description
Neanderthal introgressed variant-containing enhancer experimental_1801
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 1:208605807 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088617 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 (208432377..208432546)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (207679156..207679325)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (208605722..208605891)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene plexin A2 Neighboring gene uncharacterized LOC105372884 Neighboring gene Sharpr-MPRA regulatory region 12529 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:208416267-208416768 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:208416769-208417268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1777 Neighboring gene uncharacterized LOC105372889 Neighboring gene uncharacterized LOC124904501 Neighboring gene NANOG hESC enhancer GRCh37_chr1:208443936-208444517 Neighboring gene MPRA-validated peak670 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:208547462-208548227 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:208551780-208552116 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:208586461-208586653 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1772 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1780 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:208618537-208619736 Neighboring gene uncharacterized LOC107985460 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:208774147-208774647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2463 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1994 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_2023 and experimental_2030 Neighboring gene long intergenic non-protein coding RNA 1735

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_229176.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    208432377..208432546
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    207679156..207679325
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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