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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs390720          
refSNP ID: rs390720
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:80/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_014337.3:c.32+998A>C
NM_148175.2:c.32+998A>C
NM_148176.2:c.32+998A>C
NT_011520.11:g.1411987A>C
Links

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 ss1749338 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs390720 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
ss505251SC_JCM|AC009516.19_143979fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt07/12/0010/10/0380Genomicunknown
ss1269320KWOK|OVLP-000804-122811rev/BG/Taaaaaaatgaggactgaggattgaatactaatttagcaacaagaagtcgctgggaacctg09/02/0010/10/03123Genomic94 %
ss1749338KWOK|OVLP-000925-283149fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt10/05/0010/10/0394Genomic94 %
ss13384822SC_SNP|NT_011520.9_1411987fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt10/23/0310/31/03123Genomicunknown
ss24212044PERLEGEN|afd4337961byFreqfwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt08/10/0409/13/04123Genomicunknown
ss41516993ABI|hCV32364701fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt07/17/0507/17/05126Genomicunknown
ss78337212HGSV|Cor12878_SNV_20070510.chr22_20345972fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt10/17/0710/19/07129Genomicunknown
ss78953221HGSV|Cor18507_SNV_20070510.chr22_20345972fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt10/19/0710/21/07129Genomicunknown
ss83567431HGSV|Cor19240_SNV_20070510.chr22_20345972fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt11/30/0712/05/07130Genomicunknown
ss91882704BCMHGSC_JDW|JWB-1512293fwd/TA/Ccaggttcccagcgacttcttgttgctaaattagtattcaatcctcagtcctcattttttt02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs390720|allelePos=1108|totalLen=4003|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 CGGCTCCATG GTCTGAGTTG TCAGCCGTTG TTTTTTCGTG CTCGCTAGTC GCCGCCGCCG
 CTCCGCCATG GGGAAGCGAC AGCACCAAAA GGACAAAATG TAAGTTGAGC CGCAGTCGGG
 AGCGGCGCTC CACTCTGCCT CAGTGAACCG CCTGTCCCGC ACTGCGCGCC GCTCGCCTTC
 CCTCTCAGCT ACTCCCCAGA GCACAGCCCA AAGGTCACTT CCTCCCGGAA GCTGCCGCCC
 TGTCTCCAGT CAGGGTAATG ACCCTCGGGC CGCCGCGCTC TCCCGGGGCC GCGGCTCCGA
 TGACGTCAGC TGCGGGCTCG AGCGCAGCCC GGTTTTCCTT ACTCTGGTTC TGCCCGGACC
 GTCCCCCGTC TGCTCGCGAG TTTCGCCCTT GAATGAGTAG TCTCTACCTC TTCCGTACTT
 CACGTCTCGC TGTGTTCTGG TTCATGCCTA TCAGCCTGCA AACGTGCTGC AGAGCCTTCT
 AATTTAAAGC AAACCAggtc gggcgcagtg gctcacctgt aatcacagca ctttgggagg
 ccgaggcggg cggatcacct gaggtcagga gttcaagacc agcctggcta atacggtgaa
 accccgtctc tactaaaaat acaaaaatta gcggggcgtg gtgacgagcg cctgtaatcc
 tagctatttg ggaggctgag gcaggagaat cgcttgaacc cgggaggcgg aggttgcggt
 gagccgagat cgtgtcactg cactccagcc tgggcgacag agcgagacgc tgtctcaaaa
 ataataaata aaaTTTAAAA ATCCACCCGT GCCCCGTGCC CCACGTCCCA CGTTCCCCTC
 CCGCTGCCGC CGTGTTGTTT CTCTTAAGAA CAAGTGAGAG ACTAGTGGCT TCATGCTGTT
 TTCTGAGTCT CTTGAAACCA CTCAAGTCAG AATTTCGACC CCAGAACTGC CCCAGAACTG
 TTGggcttct caacagtatg tcacaccgtt gaccactccc tctttctgaa gccctccttt
 ggtatctggg atttcacctg ctctttgttt tctctcgact tcagcggcct ctcttttcag
 gttcccagcg acttcttgtt gctaaat
 M
 tagtattcaa tcctcagtcc tcattttttt tttttttttt ttttgagacg cagtttcgct
 cttgttgccc aagctagagt gcaatggtga gatcttggct caccgcaacc tccgcttccc
 ggcttcaaga gattttcctg cctcagcctc ccgagtagct gggattacag gcatacgcca
 ccatgcccag ctaattttgt atttttagta gagaaggggt ttctccatgt tggtcaggct
 ggtctcgaac tcctgacctc aggtgatcca cctgcctcgg cctcccaaag tcctgggatt
 acaggcgtga gccaccgcgt ctgggcagcc tcagtcctca ttttgttggg cttctcaaca
 gtatgtccca ctgttgacca ctccctcctt ctgaagccct tctttggtat ctgggatttc
 acatgctctt tgttttccat cgacttcagc ggtctttctt ttcccagtct cctttctgga
 ccctcctccc ttctctcaga tctcatacgt ttcttttcca taaacattct ctgtgggtga
 tataatttcc cagtcatcta taagctgctt tccccagtct tgtgtagtta gtggcttact
 taatatctcc actggaggac tgaaagacat ctcaaatttt tttttttttt tttttttttt
 ttttgagatg gagtcttgct ctgtcgccca ggctggagtg caatggtgcc gtcttggctc
 actgcaacct ctacttccca cattcaagca attctcccac ctcagcctcc ccagtagctg
 ggattatagg tgcctgccac catgcccatg ctaatttttg tatttttagt agagacaggt
 tttcactatg ttggtcaggc cggtctcgaa ctcctgacgt cgagtgatcg acctacctct
 gcctcccaaa gtgctgggat tacaggcgtg agccaccgtg ccgggccaga catctcgaat
 ttaatatgcc ttaaacagaa ctcttgattt tcagctcttg agcctgctcc tccctgtaaa
 ctaaaaataa aaccctaagt ccccccactg gctaagcaga cacccttgtg gccaagagaa
 ccccaggaaa accttaaaac tgagttcctg gccatgatgg gatagagatc agctgtgcct
 tgttatatcc ccctcccttt tgtggcttag acacaacaac tgaccagcat taatgttgaa
 atagagatca taaggggcca ggcacggtgg ctcacacctg taatcccagc actttgggag
 gctgaggcgg gtggatcacc aggtcaggag atcgagacca tcctggctaa cacggtgaaa
 ccccatctct actaaaaata cacaaaaaaa tcagctgggc gtggtggcag gcgcctgtag
 taccagctac tcgggaggct gaggcaggag aatggcgtga actcacgagg tggagcttgc
 agtgagccga cattgcacaa ctgcactcca gcctgggcag cgagcaagac tccgtctcaa
 aaaaaaaata aataaaataa ataaaaataa agaaatagaa atcataagat tgacaaaaca
 gactctttgt ggcaataaga taccattttt tttttttttt gagacggagt ctcgctctgt
 cgcccaggct ggagtgcggt ggcatggtct ccgctcactg caagctccgc ctcccgggtt
 catgccattc tcctgcctca gcctcccgag tagctgggac tacaggcgcc tgccaccacg
 cccggctaat tttttgtatt ttcagtagag acggggtttc actgtgttag ccaggatggt
 ctccatctcc tgacctggtg atccgcccgc ctcggcctcc caaaatgctg ggattacagg
 tgtgagccac cgtgcctggc cCTCTATTtt tttttttttt ttagtagaga ctggtttcac
 cgtgttagcc agaatggtct ccatctcctg acctcgtgat ctgcccgcct tggcctccca
 aagtgctggg attataggcg tgagccacct tgcccggccG Gttttttttg ttttttgttt
 tgtttgtttt tgagacagag tctcccccgt cccccaggct ggagtgtagt ggtgctgtca
 cagctcactg cagcctcaac ctgccttcct gccttagtct ttggagtagc tgggaccaca
 ggtgtgagct gtcacacctg gctaagtttt aaattttctt gtagagacag attctcgctt
 tgttgcccca gctgttctcc aacgcctgga ctcaagcaat cttcctgcct tggcctccca
 aactgttggg attataggtg tgagccactg tgcctggtcT CCATGTCTGT TGTGTTTATC
 ACTGTGTGGC TGACATATAG TAGGTGtttt tttgtttgtt tgtttttttg agacagagtc
 tcactctgtc acccaggctg gagtacagtg gtgtgatctt ggctgactgc aacctccgcc
 tcccgggatc aagcaattct ctgcttcagc ctcccgagta gctgggatta caggcaccca
 ccaccatgcc cagctaattt ttgtattttt agtagagacg tggtttcacc atgttggcca
 ggcttgtctt aaacttctga cctctagtga ttcgcctgcc tcgggctccc aaagtgttgg
 gattacaggc gttagccacc gtgcccgccc CATAGTAGGT ATTTAGTAAG CATTTGCTGA
 GTAAGCAAAG ATTACTCACT TCCAAAGACT TCGTCCTCTT TATAAAGGTG GTGGTGGTAG
 CATTATCTTC CTCTCTTCTT CAGGTACATT ACCTGTGCTG AATACACTCA CTTTTATGGT
 GGCAAGAAGC CAGGTAAGGC ATGCAGTCTT TCTGTTCCCC GTTGGGGGAG TGGTATTAAG
 GAACTGTGTC TTCAG

  GeneView back to top
GeneView via analysis of contig annotation: PPIL2 peptidylprolyl isomerase (cyclophilin)-like 2
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_011520->NM_014337
function
referenceNT_011520->NM_148175
function
referenceNT_011520->NM_148176
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011520->NM_014337->NP_0551521411987forwardintron
referenceNT_011520->NM_148175->NP_6804801411987forwardintron
referenceNT_011520->NM_148176->NP_6804811411987forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs390720 maps exactly once on NCBI human chromosome 22
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
22NW_001838745.11064474979314plusAalt_assembly_8HuRefHuRefview1107
22NW_927628.11051475838953plusCalt_assembly_1CeleraCeleraview1107
22NT_011520.11141198720351418plusAref_assemblyreferencereferenceview1107

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011520 AP000553 AP000553.1
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/C
C/C
HWPA
C
ss24212044AFD_EUR_PANELEuropean 48IG 1.000 1.000
AFD_AFR_PANELAfrican American 44IG 1.000 1.000
AFD_CHN_PANELAsian 46IG 0.304 0.696 0.403 0.152 0.848

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.096+/-0.197715000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .