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LOC123956266 Sharpr-MPRA regulatory region 4172 [ Homo sapiens (human) ]

Gene ID: 123956266, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956266
Gene description
Sharpr-MPRA regulatory region 4172
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956266 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (149787501..149787795)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (150969408..150969702)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (149484589..149484883)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149438995-149439524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149463303-149463978 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18768 Neighboring gene zinc finger protein 467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149479128-149479704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149480282-149480858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149480859-149481434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149482621-149483120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149484857-149485446 Neighboring gene SCO-spondin, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149487626-149488414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149496913-149497414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149497415-149497914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18769 Neighboring gene zinc finger protein 862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149552405-149552958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149552959-149553510 Neighboring gene ATP6V0E2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149570857-149571825 Neighboring gene ATPase H+ transporting V0 subunit e2

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_078457.1 

    Range
    101..395
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    149787501..149787795
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    150969408..150969702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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