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LOC132090086 Neanderthal introgressed variant-containing enhancer experimental_27027 [ Homo sapiens (human) ]

Gene ID: 132090086, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090086
Gene description
Neanderthal introgressed variant-containing enhancer experimental_27027
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 12:27257033 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090086 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (27104015..27104184)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (26976079..26976248)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (27256948..27257117)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6131 Neighboring gene mediator complex subunit 21 Neighboring gene MPRA-validated peak1625 silencer Neighboring gene nontranscribed chromatin-defined enhancer upstream of C12orf71 Neighboring gene chromosome 12 open reading frame 71 Neighboring gene liprin-beta-1-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:27366569-27367070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4309 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6143 Neighboring gene serine/threonine kinase 38 like Neighboring gene Sharpr-MPRA regulatory region 14756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6144 Neighboring gene MPRA-validated peak1626 silencer Neighboring gene uncharacterized LOC124902905 Neighboring gene uncharacterized LOC124902906 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4310

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_230644.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    27104015..27104184
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    26976079..26976248
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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