rs117064827 Rat Genome Database

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Variant: rs117064827 -  Homo sapiens

RGD ID: 13526768
RS ID: rs117064827
ClinVar ID: CV497307
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: S1PR2  
Reference Nucleotide: A
Variant Nucleotide: G
Position
Assembly Chr Position
GRCh37 19 10,334,725
GRCh38 19 10,224,049
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Trait Synonyms
NG_046802.1:g.12759T>C
NP_004221.3:p.Val286Ala
NC_000019.10:g.10224049A>G
NC_000019.9:g.10334725A>G
More... 		12/18/2018 missense variant benign|likely benign AllHighlyPenetrant; none provided
GWAS Catalog Data
GWAS Catalog Study Disease Trait Study Size Risk Allele Risk Allele Frequency P Value P Value MLOG SNP Passing QC Reported Odds Ratio or Beta-coefficient Ontology Accession PubMed
GCST90002385 High light scatter reticulocyte count 408,112 British individuals G 0.00965199999999999 2E-20 19.69897000433602 Affymetrix [93095623] (imputed) 0.10578037 reticulocyte count (EFO:0007986)
 PMID:32888494
GCST90002340 Monocyte count 521,594 European ancestry individuals G 0.009659 4E-19 18.397940008672037 Affymetrix, Illumina [50262088] (imputed) 0.089062 monocyte count (EFO:0005091)
 PMID:32888493
GCST90002344 Monocyte count 639,696 African American or Afro-Caribbean, African ancestry, European ancestry, East Asian ancestry, Hispanic or Latin American and South Asian ancestry individuals G 0.00813241 2E-16 15.698970004336019 Affymetrix, Illumina [23467995] (imputed) N/A monocyte count (EFO:0005091)
 PMID:32888493
GCST90002387 Immature fraction of reticulocytes 408,112 British individuals G 0.00966699999999998 1E-12 12.0 Affymetrix [93095623] (imputed) 0.08099172 reticulocyte measurement (EFO:0010700)
 PMID:32888494
GCST90002407 White blood cell count 408,112 British individuals G 0.00967200000000001 5E-9 8.301029995663981 Affymetrix [93095623] (imputed) 0.065826274 leukocyte count (EFO:0004308)
 PMID:32888494
GCST90002405 Reticulocyte count 408,112 British individuals G 0.00966400000000001 1E-18 18.0 Affymetrix [93095623] (imputed) 0.1011308 reticulocyte count (EFO:0007986)
 PMID:32888494
GCST90002406 Reticulocyte fraction of red cells 408,112 British individuals G 0.00966500000000003 4E-20 19.397940008672037 Affymetrix [93095623] (imputed) 0.10543739 reticulocyte measurement (EFO:0010700)
 PMID:32888494
GCST004611 High light scatter reticulocyte count 170,761 European ancestry individuals G 0.0085 4E-9 8.397940008672037 Affymetrix [~ 2500000] (imputed) 0.1210407 reticulocyte count (EFO:0007986)
 PMID:27863252
GCST004612 High light scatter reticulocyte percentage of red cells 170,763 European ancestry individuals G 0.0085 2E-9 8.698970004336019 Affymetrix [~ 2500000] (imputed) 0.1239822 reticulocyte count (EFO:0007986)
 PMID:27863252
GCST90002386 High light scatter reticulocyte percentage of red cells 408,112 British individuals G 0.00965099999999996 9E-21 20.045757490560675 Affymetrix [93095623] (imputed) 0.1066247 reticulocyte measurement (EFO:0010700)
 PMID:32888494
GCST90025972 Reticulocyte count 437,291 European ancestry individuals ? NR 2E-23 22.69897000433602 NR [9800000] (imputed) 0.100609 reticulocyte count (EFO:0007986)
 PMID:34226706
GCST90025971 Immature fraction of reticulocytes 438,154 European ancestry individuals ? NR 1E-10 10.0 NR [9800000] (imputed) 0.0669511 Immature Reticulocyte Fraction Measurement (EFO:0009253)
 PMID:34226706
GCST90025970 High light scatter reticulocyte count 437,723 European ancestry individuals ? NR 3E-26 25.522878745280337 NR [9800000] (imputed) 0.105046 reticulocyte count (EFO:0007986)
 PMID:34226706
GCST90025950 Monocyte count 443,529 European ancestry individuals ? NR 2E-18 17.69897000433602 NR [9800000] (imputed) 0.0888359 monocyte count (EFO:0005091)
 PMID:34226706
GCST90025985 White blood cell count 444,734 European ancestry individuals ? NR 5E-18 17.30102999566398 NR [9800000] (imputed) 0.086649 leukocyte count (EFO:0004308)
 PMID:34226706
GCST90025984 Lymphocyte count 443,762 European ancestry individuals ? NR 7E-13 12.154901959985743 NR [9800000] (imputed) 0.0700205 lymphocyte count (EFO:0004587)
 PMID:34226706
GCST90018967 Monocyte count 349,856 European ancestry individuals, 95,119 East Asian ancestry individuals G NR 2E-11 10.698970004336019 Affymetrix, Illumina [20531031] (imputed) 0.0779 monocyte count (EFO:0005091)
 PMID:34594039

Variant Details
Variant Transcripts
Gene Symbol:S1PR2
Accession:NM_004230
Location:EXON
Amino Acid Prediction: V to A (nonsynonymous)
Amino Acid Position: 286
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MGSLYSEYLNPNKVQEHYNYTKETLETQETTSRQVASAFIVILCCAIVVENLLVLIAVARNSKFHSAMYLFLGNLAASDL
LAGVAFVANTLLSGSVTLRLTPVQWFAREGSAFITLSASVFSLLAIAIERHVAIAKVKLYGSDKSCRMLLLIGASWLISL
VLGGLPILGWNCLGHLEACSTVLPLYAKHYVLCVVTIFSIILLAIVALYVRIYCVVRSSHADMAAPQTLALLKTVTIVLG
VFIVCWLPAFSILLLDYACPVHSCPILYKAHYFFAVSTLNSLLNPAIYTWRSRDLRREVLRPLQCWRPGVGVQGRRRGGT
PGHHLLPLRSSSSLERGMHMPTSPTFLEGNTVV*
Variant Samples
Additional References at PubMed
PMID:24033266   PMID:26467025   PMID:28492532  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000604582 CLINVAR
  RCV000843700 CLINVAR
dbSNP (RS) rs117064827 CLINVAR
GWAS Catalog GCST004611 GWAS Catalog
  GCST004612 GWAS Catalog
  GCST90002340 GWAS Catalog
  GCST90002344 GWAS Catalog
  GCST90002385 GWAS Catalog
  GCST90002386 GWAS Catalog
  GCST90002387 GWAS Catalog
  GCST90002405 GWAS Catalog
  GCST90002406 GWAS Catalog
  GCST90002407 GWAS Catalog
MedGen C3661900 CLINVAR
  CN169374 CLINVAR
NCBI Gene S1PR2 CLINVAR
OMIM 605111 CLINVAR