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LOC110121223 VISTA enhancer hs1912 [ Homo sapiens (human) ]

Gene ID: 110121223, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121223
Gene description
VISTA enhancer hs1912
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 locus represents a conserved genomic element that can function as an enhancer. It can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic heart of transgenic mice. Three subregions marked by the H3K4me1 histone modification were also shown to be active enhancers by the ChIP-STARR-seq massively parallel reporter assay in naive and/or primed human embryonic stem cells. [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3345529..3349801)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2849698..2853970)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3262093..3266365)

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 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_chr1:3331680-3332376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3332377-3333072 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 Neanderthal introgressed variant-containing enhancer experimental_7120 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 119 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 120 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

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. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, Free PMC Article
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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)

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr1:3262617-3263116
  • H3K4me1 hESC enhancer GRCh37_chr1:3263472-3264272
  • H3K4me1 hESC enhancer GRCh37_chr1:3264273-3265072

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_053838.1 

    Range
    101..4373
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    3345529..3349801
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    2849698..2853970
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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