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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2031530          
refSNP ID: rs2031530
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:94/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_152719.1:c.156+3764A>G
NT_024524.13:g.27260755A>G
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss2940388 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2031530 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss2940388TSC-CSHL|TSC1102666byFreqfwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag01/26/0110/25/0694Genomicunknown
ss12248578WI_SSAHASNP|chr13.NT_024524.12_14855246fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag07/04/0310/10/03116Genomicunknown
ss13284377SC_SNP|NT_024524.12_14855246fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag10/22/0310/31/03119Genomicunknown
ss14531083WUGSC_SSAHASNP|chr13.NT_024524.13_27260755fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag11/05/0311/22/03119Genomicunknown
ss19962002CSHL-HAPMAP|CSHL-HuFF-200402.chr13.NT_024524.13_27260755fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag02/21/0403/04/04120Genomicunknown
ss21137208SSAHASNP|WGSA-200403-chr13.chr13.NT_024524.13_27260755fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag03/19/0403/19/04121Genomicunknown
ss24425619PERLEGEN|afd2118981byFreqfwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag08/10/0409/13/04123Genomicunknown
ss43454534ABI|hCV9230839fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag07/18/0507/18/05126Genomicunknown
ss78940316HGSV|Cor18507_SNV_20070510.chr13_45178755fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag10/19/0710/21/07129Genomicunknown
ss89644194BCMHGSC_JDW|JWB-0666157fwd/TA/Gctctatgtgagggcatttcctagagaccagaaagagacaatcttttattttcatggtcag02/26/0802/28/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2031530|allelePos=189|totalLen=1209|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=129
 TGAGCACATT TCCCCTGAGG ACAGAGTCTC TTGGCACCTT TCTAGCACCC GACAGGAAGG
 CATGATGAGC CCATGACCAA CTTATTCCCC TTCTGCATCA GCTTCATATC TCATTCCTCC
 ATGAAGAAGC CAACCTTTTT CTTTCCTACC TACTGGATCT CTATGTGAGG GCATTTCCTA
 GAGACCAG
 R
 AAAGAGACAA TCTTTTATTT TCATGGTCAG TTGCACCATG CTACACAGGC TGTACCTCCC
 AGGCTTAGGA GAACATTACT GGGGTGTTCT TGGGGCTTTG TATTGGCATA GACCTCTTGT
 CAAGGGCTAA AGGATATCAG GGCAGGTTAG CTTGGCCCAT GAAACCAATC CAGTGATACC
 ACTGGTCGAG GAGTCCTACT GAGAAGGAAC TGGCTTCTAA CATAGGCCAA GGAGGTCTGG
 AATCCTGGAA CTGCATATGT TCGCTGAGCT CAGATGCTTA GTTTTTGGGT AGCCCTTTTG
 TAAAGAAATA TACTCCACGT TGCATAGCGC TTTAGGCTGG GTATGTTTAA ACCTTACCAG
 TAGAACTGAC CATCTGTTTA GTCTTTATGA CAGCTTGGCT ACCACTTTCT TGTCCTCTGG
 CAACCCCAGG AAGTAGGCAG AGCAGCCATG TTTAGGCTTA TTTTAGAGGT GACATTCTGA
 GAGGCAAAAT GACTTTCTCA AGAGCAGTCA AAGGAAGGAC TTTTGAGCCC AAAGTTACTG
 GAAATTTAGG GCGTTTACCC TCGTTGGATT ATATATTCAA GATGATGAAA GGGACCACTA
 GCGTGCTTGT GTGCAGGGGG TGGTGGGAGC TTCCTCTAAG GGAGTACATG GATGAACCTA
 GGGGTTTGTG GAATTCACGT GAGGAAAACT CCATGCTTAT AGATTTTACA TCATACCATA
 ACAGCTTTGC CCTGGGACTA TTTTAAAGTC TTAAAATATG AATGGAAATG AGGATATAGC
 TTATCAAATA CACTAACTAT ATTAAGGCAA AAgaaatggc catttttgta ggccaaaaat
 ggtaaaatgt taacagtttc ttatggttca acctaGTATT TCCTCCCAAT CTTTCAGTGT
 ATTTTGGTTG ATTCAGTTAT TGCCAAGGAC TCATTAAGCC TCCACCACAT GTGAAATTTG
 CTTTCTAATT CCCAAGACTT GGGATGTCAC AAAAACAAGG GATAGGTCAC TGTGCTTAGA

  GeneView back to top
GeneView via analysis of contig annotation: SPERT spermatid associated
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_024524->NM_152719
svfunction
HuRefNW_001838074->NM_152719
svfunction
CeleraNW_925473->NM_152719
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_024524->NM_152719->NP_68993227260755forwardintron
HuRefNW_001838074->NM_152719->NP_689932280444forwardintron
CeleraNW_925473->NM_152719->NP_68993227070642forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2031530 maps exactly once on NCBI human chromosome 13
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
13NW_001838074.128044427077435plusGalt_assembly_8HuRefHuRefview188
13NW_925473.12707064227335418plusGalt_assembly_1CeleraCeleraview188
13NT_024524.132726075545178755plusAref_assemblyreferencereferenceview188

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_024524
dbSNP Blast Analysis
GenBank HTGS Finished:
AL139320.18 NC_000013.9

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss24425619AFD_EUR_PANELEuropean 46IG 0.304 0.391 0.304 0.317 0.500 0.500
AFD_AFR_PANELAfrican American 46IG 0.130 0.217 0.652 0.100 0.239 0.761
AFD_CHN_PANELAsian 48IG 0.667 0.250 0.083 0.251 0.792 0.208
ss2940388HapMap-CEUEuropean 118IG 0.220 0.542 0.237 0.527 0.492 0.508
HapMap-HCBAsian 90IG 0.556 0.422 0.022 0.251 0.767 0.233
HapMap-JPTAsian 88IG 0.341 0.432 0.227 0.439 0.557 0.443
HapMap-YRISub-Saharan African 120IG 0.317 0.683 0.150 0.158 0.842

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.499+/-0.02033226090

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .