U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC132090599 Neanderthal introgressed variant-containing enhancer experimental_61158 [ Homo sapiens (human) ]

    Gene ID: 132090599, updated on 12-Sep-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC132090599
    Gene description
    Neanderthal introgressed variant-containing enhancer experimental_61158
    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 20:62221766 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 LOC132090599 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 (63590328..63590497)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65403776..65403945)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62221681..62221850)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18228 Neighboring gene Sharpr-MPRA regulatory region 13995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13164 Neighboring gene fibronectin type III domain containing 11 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18230 Neighboring gene helicase with zinc finger 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18233 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62202570-62202926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62205701-62206428 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62207026-62207211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62213946-62214446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62214447-62214947 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61137 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61148 Neighboring gene glucocorticoid modulatory element binding protein 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61169 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61181 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61184 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18235 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62250681-62251180 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13168 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13169 Neighboring gene melanoma highly expressed competing endogenous lncRNA for miR-425 and miR-489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62269990-62270750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62272271-62273029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62273358-62274096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62275446-62276015 Neighboring gene Sharpr-MPRA regulatory region 12780 Neighboring gene stathmin 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62282910-62283480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62284757-62285436

    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_231157.1 

      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
      63590328..63590497
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      65403776..65403945
      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