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LOC123575662 Sharpr-MPRA regulatory region 12169 [ Homo sapiens (human) ]

Gene ID: 123575662, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575662
Gene description
Sharpr-MPRA regulatory region 12169
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123575662 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (7115456..7115750)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (6985078..6985372)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (7115689..7115983)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 554, pseudogene Neighboring gene Sharpr-MPRA regulatory region 4402 Neighboring gene uncharacterized LOC105374904 Neighboring gene Sharpr-MPRA regulatory region 13455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7042699-7043587 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7051539-7052040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16885 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7119221-7119796 Neighboring gene NANOG hESC enhancer GRCh37_chr6:7124594-7125112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7140608-7141135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23937 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7145752-7146422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23938 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:7151030-7151195 Neighboring gene ras responsive element binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7156680-7157346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7160729-7161690 Neighboring gene VISTA enhancer hs2061 Neighboring gene Sharpr-MPRA regulatory region 4659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7169201-7169702 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7169703-7170202 Neighboring gene skeletal muscle cis-regulatory module in RREB1 intron Neighboring gene Sharpr-MPRA regulatory region 2698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:7258615-7259114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7261311-7262102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7262103-7262894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:7267569-7268070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:7273665-7274166 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94357 Neighboring gene MPRA-validated peak5642 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7312596-7313464 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7313465-7314331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16890 Neighboring gene signal sequence receptor subunit 1 Neighboring gene cancer antigen 1 Neighboring gene ribosomal protein S3 pseudogene 4

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_077921.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    7115456..7115750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    6985078..6985372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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