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LOC132089375 Neanderthal introgressed variant-containing enhancer experimental_91096 [ Homo sapiens (human) ]

Gene ID: 132089375, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089375
Gene description
Neanderthal introgressed variant-containing enhancer experimental_91096
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 the introgressed 6:155480813 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089375 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (155159594..155159763)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (156361552..156361721)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (155480728..155480897)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak6235 silencer Neighboring gene Sharpr-MPRA regulatory region 2718 Neighboring gene microRNA 1273c Neighboring gene ReSE screen-validated silencer GRCh37_chr6:155259719-155259894 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:155272494-155272994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155287362-155288008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155316343-155316950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155316951-155317556 Neighboring gene lysophosphatidylcholine acyltransferase 3 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155340532-155341032 Neighboring gene TIAM Rac1 associated GEF 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155434365-155434864 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:155440095-155440876 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:155440877-155441659 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:155448114-155449313 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155450845-155451460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25303 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:155499148-155499350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25304 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:155506493-155507300 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:155507301-155508106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155508589-155509092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155517063-155517562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155539515-155540016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155540017-155540516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155541579-155542078 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:155544888-155546087 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155568469-155569164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155574917-155575491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155575492-155576065 Neighboring gene transcription factor B1, mitochondrial Neighboring gene claudin 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25305 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155635711-155636701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155748671-155749628 Neighboring gene NADPH oxidase 3

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)

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_229934.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    155159594..155159763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    156361552..156361721
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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