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LOC128505377 MPRA functional variant 1:3691528:A:G red blood cell enhancer [ Homo sapiens (human) ]

Gene ID: 128505377, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128505377
Gene description
MPRA functional variant 1:3691528:A:G red blood cell enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 red blood cell enhancer that was functionally validated by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. It includes rs1175550, an MPRA functional variant (MFV) that affects enhancer activity. Deletions encompassing the MFV, which were obtained by CRISPR/Cas9 editing, indicate this region is a positively-acting cis-regulatory element for the CEP104 (centrosomal protein 104), LRRC47 (leucine rich repeat containing 47) and SMIM1 (small integral membrane protein 1 (Vel blood group)) genes in K562 cells. [provided by RefSeq, Feb 2023]
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Genomic context

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See LOC128505377 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3774868..3775012)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3286458..3286605)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tumor protein p73 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3661686-3662521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3662522-3663358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 123 Neighboring gene Gfo/Idh/MocA-like oxidoreductase domain containing 3, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3678785-3679286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3679287-3679786 Neighboring gene coiled-coil domain containing 27 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3687696-3688374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3689661-3690176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3690177-3690692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3691725-3692240 Neighboring gene RNA, 7SL, cytoplasmic 574, pseudogene Neighboring gene small integral membrane protein 1 (Vel blood group) Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:3709930-3710608 Neighboring gene leucine rich repeat containing 47 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 125 Neighboring gene Sharpr-MPRA regulatory region 1968 Neighboring gene centrosomal protein 104 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3745882-3747081 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3747165-3748364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3755401-3755900 Neighboring gene uncharacterized LOC124903829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3767162-3767662

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. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits. Ulirsch JC, et al. Cell, 2016 Jun 2. PMID 27259154, Free PMC Article
  2. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, 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

General gene information

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Other Names

  • CRISPRi-validated CEP104, LRRC47 and SMIM1 regulatory element

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_149606.1 

    Range
    101..245
    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
    3774868..3775012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    3286458..3286605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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