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LOC132089723 Neanderthal introgressed variant-containing enhancer experimental_110085 [ Homo sapiens (human) ]

Gene ID: 132089723, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089723
Gene description
Neanderthal introgressed variant-containing enhancer experimental_110085
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 the non-introgressed 9:96916536 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089723 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 (94154169..94154338)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (106322228..106322397)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (96916451..96916620)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96717631-96718162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96718163-96718693 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96730989-96731521 Neighboring gene BARX1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96741809-96742308 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:96748340-96749539 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:96767229-96768428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20051 Neighboring gene protein tyrosine phosphatase domain containing 1 Neighboring gene CYCS pseudogene 24 Neighboring gene Sharpr-MPRA regulatory region 768 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96856496-96857248 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96880956-96881652 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110048 Neighboring gene tripartite motif-containing protein 54-like Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110072 Neighboring gene PTPDC1-MIRLET7DHG intergenic CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20053 Neighboring gene miRlet-7a-1/let-7f-1/let-7d cluster host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20054 Neighboring gene microRNA let-7a-1 Neighboring gene microRNA let-7f-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_230281.1 

    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
    94154169..94154338
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    106322228..106322397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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