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LOC132088820 Neanderthal introgressed variant-containing enhancer experimental_56992 [ Homo sapiens (human) ]

Gene ID: 132088820, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088820
Gene description
Neanderthal introgressed variant-containing enhancer experimental_56992
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 2:218290781 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088820 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (217425973..217426142)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (217909112..217909281)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (218290696..218290865)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:218156138-218156638 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:218156639-218157139 Neighboring gene DIRC3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 8768 Neighboring gene disrupted in renal carcinoma 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:218199087-218199799 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:218234719-218235918 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56988 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56989 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56990 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56991 Neighboring gene uncharacterized LOC124907981 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:218291011-218292210 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:218365243-218365794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12307 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:218416177-218416745 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:218419796-218420396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218474359-218475066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17105 Neighboring gene ATPase H+/K+ transporting non-gastric alpha2 subunit pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12308 Neighboring gene RPL7L1 pseudogene 9

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_229379.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    217425973..217426142
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    217909112..217909281
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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