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LOC132088704 Neanderthal introgressed variant-containing enhancer experimental_7120 [ Homo sapiens (human) ]

Gene ID: 132088704, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088704
Gene description
Neanderthal introgressed variant-containing enhancer experimental_7120
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 1:3375181 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088704 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 (3458532..3458701)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2963298..2963467)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3375096..3375265)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene PR/SET domain 16 Neighboring gene collagen alpha-5(IV) chain-like Neighboring gene VISTA enhancer hs705 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3191818-3193017 Neighboring gene Sharpr-MPRA regulatory region 1987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3212462-3212962 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3215870-3217069 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3220731-3221288 Neighboring gene uncharacterized LOC105378604 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3229262-3230461 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:3231799-3232358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3235695-3236196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3236197-3236696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3237397-3238015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3246879-3247556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3255514-3256329 Neighboring gene VISTA enhancer hs1912 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3268668-3269642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3269643-3270616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3272921-3273812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3273813-3274702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3277409-3277908 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:3285513-3286094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3303704-3304204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3304205-3304705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3307961-3308462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3311898-3312581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3312582-3313264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3320127-3320627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3325025-3325602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3332377-3333072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3331680-3332376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3337228-3337728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3350015-3350524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3357159-3357921 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3369311-3370063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3373825-3374576 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3388131-3388756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3399659-3400494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3400495-3401329 Neighboring gene Rho guanine nucleotide exchange factor 16 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3408710-3409234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3408184-3408709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 119 Neighboring gene MEGF6 intron CAGE-defined mid-level expression enhancer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3439723-3440262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3445841-3446528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3447217-3447902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3449965-3450651 Neighboring gene multiple EGF like domains 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3459643-3460294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3460295-3460948 Neighboring gene MPRA-validated peak19 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3463961-3464599 Neighboring gene uncharacterized LOC105378608 Neighboring gene microRNA 551a

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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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_229263.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    3458532..3458701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    2963298..2963467
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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