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LOC132088690 Neanderthal introgressed variant-containing enhancer experimental_6604 [ Homo sapiens (human) ]

Gene ID: 132088690, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088690
Gene description
Neanderthal introgressed variant-containing enhancer experimental_6604
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 1:3062228 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088690 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 (3145579..3145748)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2647689..2647858)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3062143..3062312)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene translation initiation factor IF-2 Neighboring gene opioid growth factor receptor pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2989243-2990091 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:3008649-3008795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3011815-3012660 Neighboring gene PR/SET domain 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3023590-3024149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3030215-3030791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3030792-3031367 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3041525-3042136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3042749-3043359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3044803-3045728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3052001-3052522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3052523-3053044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3054481-3054980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3062305-3063167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3066095-3066595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3070263-3070764 Neighboring gene microRNA 4251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3070765-3071264 Neighboring gene uncharacterized LOC105378606 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3080396-3081595 Neighboring gene uncharacterized LOC107984909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3105417-3105918

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_229249.1 

    Range
    101..270
    Download
    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
    3145579..3145748
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    2647689..2647858
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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