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LOC132090664 Neanderthal introgressed variant-containing enhancer experimental_8792 [ Homo sapiens (human) ]

Gene ID: 132090664, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090664
Gene description
Neanderthal introgressed variant-containing enhancer experimental_8792
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 1:59880094 or rs11582325 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090664 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (59414337..59414506)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (59292714..59292883)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (59880009..59880178)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:59604949-59605450 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:59605451-59605950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 939 Neighboring gene uncharacterized LOC729467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:59672311-59672933 Neighboring gene Sharpr-MPRA regulatory region 10857 Neighboring gene Sharpr-MPRA regulatory region 13133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 941 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:59764225-59765424 Neighboring gene FGGY divergent transcript Neighboring gene FGGY carbohydrate kinase domain containing Neighboring gene MPRA-validated peak254 silencer Neighboring gene MPRA-validated peak255 silencer Neighboring gene uncharacterized LOC124904192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1110 Neighboring gene MPRA-validated peak256 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:60134970-60135524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:60139185-60139712 Neighboring gene Sharpr-MPRA regulatory region 6224 Neighboring gene microRNA 4711

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)

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_8792

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_231223.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    59414337..59414506
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    59292714..59292883
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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