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LOC132090605 Neanderthal introgressed variant-containing enhancer experimental_61295 [ Homo sapiens (human) ]

Gene ID: 132090605, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090605
Gene description
Neanderthal introgressed variant-containing enhancer experimental_61295
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 20:62512368 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090605 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63880930..63881099)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65700775..65700944)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62512283..62512452)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62475261-62475938 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62477766-62477915 Neighboring gene chromosome 20 putative open reading frame 181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62484853-62485706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13189 Neighboring gene uncharacterized LOC112268269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18254 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:62495674-62496873 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62497355-62498074 Neighboring gene abhydrolase domain containing 16B Neighboring gene TPD52 like 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61287 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61302 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62517585-62517755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62525794-62526321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13191 Neighboring gene DnaJ heat shock protein family (Hsp40) member C5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62541709-62542208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62543630-62544130 Neighboring gene RNA, U1 small nuclear 134, pseudogene Neighboring gene uncharacterized LOC124904951 Neighboring gene microRNA 941-1 Neighboring gene microRNA 941-2

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_231163.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63880930..63881099
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65700775..65700944
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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