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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1799990          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:89/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_000311.3:c.385A>G
NM_001080121.1:c.385A>G
NM_001080122.1:c.385A>G
NM_001080123.1:c.385A>G
NM_183079.2:c.385A>G
NP_000302.1:p.Met129Val
NP_001073590.1:p.Met129Val
NP_001073591.1:p.Met129Val
NP_001073592.1:p.Met129Val
NP_898902.1:p.Met129Val
XM_001717568.1:c.402T>C
XM_001717946.1:c.402T>C
XM_001718208.1:c.402T>C
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 ss76885314 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1799990 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
ss2420046HGBASE|SNP000002608fwd/TA/Gagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcc11/07/0010/10/0389Genomicunknown
ss12495190WI_SSAHASNP|chr20.NT_011387.8_4620251byFreqfwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca07/04/0305/16/04116Genomicunknown
ss28505273MGC_GENOME_DIFF|BC012844x27501067-A4620251Gfwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca08/25/0408/25/04126cDNAunknown
ss28512950MGC_GENOME_DIFF|BC022532x27501067-A4620251Gfwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca08/25/0408/25/04126cDNAunknown
ss44197730ABI|hCV2969398byFreqfwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca07/18/0511/03/06126Genomicunknown
ss65725862ILLUMINA|Human1-rs1799990fwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca10/10/0610/10/06127Genomicunknown
ss69234107PERLEGEN|PGP04694321byFreqfwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca01/30/0708/14/07127Genomicunknown
ss74806003AFFY|SNP_M-173918fwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca08/09/0708/09/07128Genomicunknown
ss74866749ILLUMINA|ILMN_Human_1M_rs1799990fwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca08/28/0708/29/07129Genomicunknown
ss76885314SI_EXO|NT_011387.8_4620251fwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca09/20/0709/20/07129Genomicunknown
ss91622784BCMHGSC_JDW|JWB-1413032fwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca02/26/0803/02/08129Genomicunknown
ss96210496HUMANGENOME_JCVI|1103643146185fwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca03/25/0803/25/08130Genomicunknown
ss1116449121000GENOMES|CEU.trio.12.15.2008_3650615_chr20_4628251fwd/TA/Gggggcagtggtggggggccttggcggctactgctgggaagtgccatgagcaggcccatca12/15/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1799990|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TTGCAGAGCA GTCATTATGG CGAACCTTGG CTGCTGGATG CTGGTTCTCT TTGTGGCCAC
 ATGGAGTGAC CTGGGCCTCT GCAAGAAGCG CCCGAAGCCT GGAGGATGGA ACACTGGGGG
 CAGCCGATAC CCGGGGCAGG GCAGCCCTGG AGGCAACCGC TACCCACCTC AGGGCGGTGG
 TGGCTGGGGG CAGCCTCATG GTGGTGGCTG GGGGCAGCCT CATGGTGGTG GCTGGGGGCA
 GCCCCATGGT GGTGGCTGGG GACAGCCTCA TGGTGGTGGC TGGGGTCAAG GAGGTGGCAC
 CCACAGTCAG TGGAACAAGC CGAGTAAGCC AAAAACCAAC ATGAAGCACA TGGCTGGTGC
 TGCAGCAGCT GGGGCAGTGG TGGGGGGCCT TGGCGGCTAC
 R
 TGCTGGGAAG TGCCATGAGC AGGCCCATCA TACATTTCGG CAGTGACTAT GAGGACCGTT
 ACTATCGTGA AAACATGCAC CGTTACCCCA ACCAAGTGTA CTACAGGCCC ATGGATGAGT
 ACAGCAACCA GAACAACTTT GTGCACGACT GCGTCAATAT CACAATCAAG CAGCACACGG
 TCACCACAAC CACCAAGGGG GAGAACTTCA CCGAGACCGA CGTTAAGATG ATGGAGCGCG
 TGGTTGAGCA GATGTGTATC ACCCAGTACG AGAGGGAATC TCAGGCCTAT TACCAGAGAG
 GATCGAGCAT GGTCCTCTTC TCCTCTCCAC CTGTGATCCT CCTGATCTCT TTCCTCATCT
 TCCTGATAGT GGGATGAGGA AGGTCTTCCT GTTTTCACCA

  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_011387.8 ABBA01053856 BC012844 BC022532
dbSNP Blast Analysis
UniGene Cluster ID
472010

  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
ss12495190 CEPH 184 AF 0.560 0.440
ss44197730 HapMap-CEU European 120 IG 0.433 0.433 0.133 0.752 0.650 0.350
HapMap-HCB Asian 90 IG 0.933 0.067 1.000 0.967 0.033
HapMap-JPT Asian 88 IG 0.977 0.023 1.000 0.989 0.011
HapMap-YRI Sub-Saharan African 120 IG 0.400 0.517 0.083 0.251 0.658 0.342
AoD_African_American 90 AF 0.600 0.400
AoD_Caucasian 92 AF 0.760 0.240
AoD_Chinese 90 AF 0.990 0.010
AoD_Japanese 90 AF 0.990 0.010
ss69234107 HapMap-CEU European 120 GF 0.433 0.433 0.133 0.650 0.350
HapMap-HCB Asian 90 GF 0.933 0.067 0.967 0.033
HapMap-JPT Asian 90 GF 0.956 0.044 0.978 0.022
HapMap-YRI Sub-Saharan African 120 GF 0.400 0.517 0.083 0.658 0.342

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.330+/-0.237 1208 1002 270 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 .