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LOC132090626 Neanderthal introgressed variant-containing enhancer experimental_62431 [ Homo sapiens (human) ]

Gene ID: 132090626, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090626
Gene description
Neanderthal introgressed variant-containing enhancer experimental_62431
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 22:17859856 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090626 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (17379826..17379995)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (18047549..18047718)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (17859771..17859940)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17741695-17742280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17744419-17745245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17745246-17746072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17750393-17751381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13436 Neighboring gene NANOG hESC enhancer GRCh37_chr22:17764354-17764855 Neighboring gene cat eye syndrome chromosome region, candidate 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:17768852-17769352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17787810-17788548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17788549-17789287 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62410 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:17811413-17811590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:17812630-17813130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:17813131-17813631 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62420 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:17822020-17822264 Neighboring gene Sharpr-MPRA regulatory region 13223 Neighboring gene RNA, 7SL, cytoplasmic 843, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17855418-17856368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17856369-17857317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:17859097-17859774 Neighboring gene NANOG hESC enhancer GRCh37_chr22:17860543-17861103 Neighboring gene CECR2 histone acetyl-lysine reader Neighboring gene TERF2 interacting protein pseudogene 1 Neighboring gene Charcot-Leyden crystal protein 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_231184.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    17379826..17379995
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    18047549..18047718
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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