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LOC132090668 Neanderthal introgressed variant-containing enhancer experimental_558 [ Homo sapiens (human) ]

Gene ID: 132090668, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090668
Gene description
Neanderthal introgressed variant-containing enhancer experimental_558
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 the non-introgressed 1:161941092 or rs61809500 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090668 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 (161971217..161971386)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (161315499..161315668)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (161941007..161941176)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2008 Neighboring gene activating transcription factor 6 Neighboring gene proteasome activator subunit 3 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:161972665-161973166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1489 Neighboring gene Sharpr-MPRA regulatory region 11962 Neighboring gene olfactomedin like 2B Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:162025767-162026281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1491 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:162061183-162061778 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:162061779-162062373 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_577 Neighboring gene uncharacterized LOC105371475 Neighboring gene nitric oxide synthase 1 adaptor protein Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:162106088-162107287 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:162114645-162115359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:162121700-162122200 Neighboring gene microRNA 4654

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_558

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_231227.1 

    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
    161971217..161971386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    161315499..161315668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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