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LOC132088597 Neanderthal introgressed variant-containing enhancer experimental_1250 [ Homo sapiens (human) ]

Gene ID: 132088597, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088597
Gene description
Neanderthal introgressed variant-containing enhancer experimental_1250
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 1:169500929 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088597 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 (169531606..169531775)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (168886850..168887019)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (169500844..169501013)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene basic leucine zipper nuclear factor 1 Neighboring gene coiled-coil domain containing 181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1546 Neighboring gene solute carrier family 19 member 2 Neighboring gene Sharpr-MPRA regulatory region 5964 Neighboring gene MPRA-validated peak447 silencer Neighboring gene MPRA-validated peak448 silencer Neighboring gene MPRA-validated peak449 silencer Neighboring gene coagulation factor V Neighboring gene Sharpr-MPRA regulatory region 2803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:169555193-169555694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:169555695-169556194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2075 Neighboring gene selectin P Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2076 Neighboring gene uncharacterized LOC107985745 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:169636965-169637470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2077

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 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_229156.1 

    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
    169531606..169531775
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    168886850..168887019
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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