U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC132088838 Neanderthal introgressed variant-containing enhancer experimental_58220 [ Homo sapiens (human) ]

Gene ID: 132088838, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC132088838
Gene description
Neanderthal introgressed variant-containing enhancer experimental_58220
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 2:25346848 variant alleles. [provided by RefSeq, Sep 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC132088838 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 (25123894..25124063)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (25158347..25158516)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (25346763..25346932)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene EFR3 homolog B Neighboring gene RNA, 7SL, cytoplasmic 856, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:25293144-25293286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25311273-25312272 Neighboring gene SUCLA2 pseudogene 3 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:25312273-25313271 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:25320574-25320751 Neighboring gene Sharpr-MPRA regulatory region 3202 Neighboring gene Sharpr-MPRA regulatory region 11705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25359725-25360226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25360227-25360726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25383210-25384066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11245 Neighboring gene POMC promoter region Neighboring gene POMC distal enhancer region Neighboring gene proopiomelanocortin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11246 Neighboring gene long intergenic non-protein coding RNA 1381

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_229397.1 

    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
    25123894..25124063
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    25158347..25158516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases