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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs4878199          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_000692.3:c.757G>A
NP_000683.3:p.Val253Met
NT_008413.17:g.38386502G>A
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 ss76892923 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4878199 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
ss6740188WI_SSAHASNP|NT_023974.13_11350438fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt02/12/0310/25/06111Genomicunknown
ss15542437SC_SNP|NT_008413.16_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt11/14/0311/22/03120Genomicunknown
ss18021795CSHL-HAPMAP|CSHL-HuCC-200402.chr9.NT_008413.16_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt02/19/0403/04/04120Genomicunknown
ss22823601SSAHASNP|WGSA-200403-chr9.chr9.NT_008413.16_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt03/21/0403/21/04121Genomicunknown
ss24555214PERLEGEN|afd4420527byFreqfwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt08/10/0409/13/04123Genomicunknown
ss28497301MGC_GENOME_DIFF|37540361-G38386502Afwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt08/20/0408/20/04126cDNAunknown
ss28511942MGC_GENOME_DIFF|BC001619x37540361-G38386502Afwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt08/25/0408/25/04126cDNAunknown
ss48407629APPLERA_GI|hCV25471773byFreqrev/BC/Taaccggtgaaggcaactttgtcaacatccagtgctgggcgatggccgcacctgctgttgg09/28/0511/03/06126Genomicunknown
ss66812995ILLUMINA|HumanHap300v1.1_rs4878199fwd/BA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt11/09/0611/09/06127Genomicunknown
ss67392024ILLUMINA|HumanHap550v1.1_rs4878199fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt11/14/0611/14/06127Genomicunknown
ss67765261ILLUMINA|HumanHap650Yv1.0_rs4878199fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt11/14/0611/14/06127Genomicunknown
ss68363339CSHL-HAPMAP|sanger:assay:4247956:1byFreqrev/BC/Taaccggtgaaggcaactttgtcaacatccagtgctgggcgatggccgcacctgctgttgg01/11/0701/16/07127NAunknown
ss69290100PERLEGEN|PGP04420527fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt01/30/0701/30/07127Genomicunknown
ss70832684ILLUMINA|HumanHap550v3.0__rs4878199fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt04/20/0703/31/08130Genomicunknown
ss71415522ILLUMINA|HumanHap650Yv3.0_rs4878199fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt04/23/0704/23/07127Genomicunknown
ss75823150ILLUMINA|ILMN_Human_1M_rs4878199fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt08/28/0708/29/07129Genomicunknown
ss76600588AFFY|AFFY_6_1M_SNP_A-8461710rev/BC/Tactttgtcaacatccagtgctgggcgatggcc08/28/0708/30/07130Genomicunknown
ss76892923SI_EXO|NT_008413.17_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt09/20/0709/20/07129Genomicunknown
ss77762695HGSV|Cor12156_SNV_20070510.chr9_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt10/09/0710/14/07129Genomicunknown
ss78708723HGSV|Cor12878_SNV_20070510.chr9_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt10/17/0710/20/07129Genomicunknown
ss79200353ILLUMINA|HumanHap300v2.0_rs4878199fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt04/18/0711/18/07130Genomicunknown
ss84160466PHARMGKB_AB_DME|PS206163_PA149403926_301fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt12/06/0712/10/07130Genomicunknown
ss84384905KRIBB_YJKIM|KHS698595fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt12/04/0712/07/07130Genomicunknown
ss94051084BCMHGSC_JDW|JWB-2590452fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt02/26/0803/05/08129Genomicunknown
ss97723109HUMANGENOME_JCVI|1103652078190fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt03/30/0803/30/08130Genomicunknown
ss105439691SNP500CANCER|ALDH1B1-05fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt09/05/0809/05/08130Genomicunknown
ss105678253BGI|BGI_rs4878199fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt09/10/0806/18/09130Genomicunknown
ss1087695561000GENOMES|CEU.trio.12.15.2008_2177095_chr9_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt12/15/0812/16/08130Genomicunknown
ss1144802261000GENOMES|NA19240_2008_12_16_1967530_chr9_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt12/18/0812/18/08130Genomicunknown
ss115729685ILLUMINA-UK|NA18507_000060098_NCBI36.1_chr9_38386502fwd/TA/Gccaacagcaggtgcggccatcgcccagcactggatgttgacaaagttgccttcaccggtt01/15/0901/16/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4878199|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GGCCTCACTC GAGACCTTGG ACAATGGGAA GCCTTTCCAA GAGTCTTACG CCTTGGACTT
 GGATGAGGTC ATCAAGGTGT ATCGGTACTT TGCTGGCTGG GCTGACAAGT GGCATGGCAA
 GACCATCCCC ATGGATGGCC AGCATTTCTG CTTCACCCGG CATGAGCCCG TTGGTGTCTG
 TGGCCAGATC ATCCCGTGGA ACTTCCCCTT GGTCATGCAG GGTTGGAAAC TTGCCCCGGC
 ACTCGCCACA GGCAACACTG TGGTTATGAA GGTGGCAGAG CAGACCCCCC TCTCTGCCCT
 GTATTTGGCC TCCCTCATCA AGGAGGCAGG CTTTCCCCCT GGGGTGGTGA ACATCATCAC
 GGGGTATGGC CCAACAGCAG GTGCGGCCAT CGCCCAGCAC
 R
 TGGATGTTGA CAAAGTTGCC TTCACCGGTT CCACCGAGGT GGGCCACCTG ATCCAGAAAG
 CAGCTGGCGA TTCCAACCTC AAGAGAGTCA CCCTGGAGCT GGGTGGTAAG AGCCCCAGCA
 TCGTGCTGGC CGATGCTGAC ATGGAGCATG CCGTGGAGCA GTGCCACGAA GCCCTGTTCT
 TCAACATGGG CCAGTGCTGC TGTGCTGGCT CCCGGACCTT CGTGGAAGAA TCCATCTACA
 ATGAGTTTCT CGAGAGAACC GTGGAGAAAG CAAAGCAGAG GAAAGTGGGG AACCCCTTTG
 AGCTGGACAC CCAGCAGGGG CCTCAGGTGG ACAAGGAGCA GTTTGAACGA GTCCTAGGCT
 ACATCCAGCT TGGCCAGAAG GAGGGCGCAA AACTCCTCTG

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_008413.17 ABBA01050381 BC001619
dbSNP Blast Analysis
UniGene Cluster ID
436219

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss105439691 P1 204 GF 0.882 0.118 0.941 0.059
CAUC1 62 GF 0.871 0.129 0.935 0.065
AFR1 48 GF 0.792 0.208 0.896 0.104
HISP1 46 GF 0.870 0.130 0.935 0.065
PAC1 48 GF 1.000 1.000
P2 418 GF 0.876 0.124 0.938 0.062
CAUC2 120 GF 0.900 0.100 0.950 0.050
AFR2 120 GF 0.667 0.333 0.833 0.167
P3 550 GF 0.920 0.069 0.011 0.955 0.045
CAUC3 130 GF 0.938 0.046 0.015 0.962 0.038
AFR3 148 GF 0.784 0.189 0.027 0.878 0.122
HISP3 98 GF 1.000 1.000
PAC3 174 GF 0.977 0.023 0.989 0.011
ASI2 178 GF 1.000 1.000
ss24555214 AFD_EUR_PANEL European 48 IG 0.917 0.083 1.000 0.958 0.042
AFD_AFR_PANEL African American 42 IG 0.952 0.048 1.000 0.976 0.024
AFD_CHN_PANEL Asian 44 IG 1.000 1.000
ss48407629 HapMap-CEU European 120 IG 0.900 0.100 0.752 0.950 0.050
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 118 IG 0.661 0.339 0.150 0.831 0.169
AGI_ASP population multiple 78 IG 0.872 0.103 0.026 0.100 0.923 0.077
ss84160466 PA149403927 356 AF 0.975 0.025

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.102+/-0.202 1218 1006 15 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .