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LOC128635607 CRISPR perturbation-validated SMYD3 cis-regulatory element TAD4.SE2.HS10 [ Homo sapiens (human) ]

Gene ID: 128635607, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128635607
Gene description
CRISPR perturbation-validated SMYD3 cis-regulatory element TAD4.SE2.HS10
Gene type
biological region
Feature type(s)
regulatory: transcriptional_cis_regulatory_region
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 represents a DNase I hypersensitive site located in a super-enhancer in an intron of the SMYD3 (SET and MYND domain containing 3) gene on chromosome 1. It was validated as an SMYD3 cis-regulatory element by the Mosaic-seq CRISPR perturbation method in K562 erythroleukemia cells. [provided by RefSeq, Feb 2023]
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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 (246182248..246182403)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (245603390..245603545)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SET and MYND domain containing 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246273353-246273854 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246273855-246274354 Neighboring gene Sharpr-MPRA regulatory region 4643 Neighboring gene SMYD3 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:246302792-246303991 Neighboring gene CRISPRi-validated SMYD3 hub enhancer Neighboring gene CRISPRi-validated SMYD3 non-hub enhancer Neighboring gene CRISPR perturbation-validated SMYD3 cis-regulatory element TAD4.SE2.HS8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2030 Neighboring gene uncharacterized LOC124904573 Neighboring gene RNA, U6 small nuclear 1283, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:246383465-246384417 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4 pseudogene 5 Neighboring gene VISTA enhancer hs2070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246487577-246488097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2853 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:246518331-246518956 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:246533672-246533878 Neighboring gene MPRA-validated peak812 silencer Neighboring gene Sharpr-MPRA regulatory region 15017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246591613-246592114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246592115-246592614 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:246612672-246613232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246669532-246670032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246670033-246670533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2034 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:246671208-246671440 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:246679947-246680127 Neighboring gene long intergenic non-protein coding RNA 1743

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. Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells. Xie S, et al. Mol Cell, 2017 Apr 20. PMID 28416141

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_149621.1 

    Range
    101..256
    Download
    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
    246182248..246182403
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    245603390..245603545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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