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LOC132090482 Neanderthal introgressed variant-containing enhancer experimental_47575 [ Homo sapiens (human) ]

Gene ID: 132090482, updated on 14-Oct-2023

Summary

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Gene symbol
LOC132090482
Gene description
Neanderthal introgressed variant-containing enhancer experimental_47575
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 17:78004816 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090482 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80030932..80031101)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (80929590..80929759)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene TBC1 domain family member 16 Neighboring gene uncharacterized LOC124904073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77961646-77962517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9097 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77966696-77967895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77975818-77976678 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77987013-77987179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77996703-77997568 Neighboring gene uncharacterized LOC124904072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78003463-78004332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12927 Neighboring gene Sharpr-MPRA regulatory region 13982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78018463-78018964 Neighboring gene coiled-coil domain 40 molecular ruler complex subunit Neighboring gene uncharacterized LOC124904074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78039691-78040515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78056255-78056756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78064021-78064580 Neighboring gene microRNA 1268b

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

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_231040.1 

    Range
    101..270
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    80030932..80031101
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791802.1 Reference GRCh38.p14 PATCHES

    Range
    53843..54012
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    80929590..80929759
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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