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LOC132089734 Neanderthal introgressed variant-containing enhancer experimental_110687 [ Homo sapiens (human) ]

Gene ID: 132089734, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089734
Gene description
Neanderthal introgressed variant-containing enhancer experimental_110687
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 9:98309740 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089734 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (95547373..95547542)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (107717013..107717182)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (98309655..98309824)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98196113-98196685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98196686-98197257 Neighboring gene metallothionein 1 pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98209829-98210813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98224469-98225332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98225569-98226070 Neighboring gene uncharacterized LOC100507346 Neighboring gene patched 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98255961-98256702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98256703-98257442 Neighboring gene VISTA enhancer hs1258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20068 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:98269229-98269862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20071 Neighboring gene NANOG hESC enhancer GRCh37_chr9:98271448-98271997 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:98272951-98273714 Neighboring gene VISTA enhancer hs1417 Neighboring gene uncharacterized LOC105376157 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:98314166-98315130 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:98315131-98316095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98326699-98327200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98327201-98327700 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110694 Neighboring gene uncharacterized LOC105376158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98362911-98363412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98363413-98363912 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:98389397-98390596 Neighboring gene proteasome subunit alpha 7 pseudogene 1

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_230292.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    95547373..95547542
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    107717013..107717182
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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