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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs12474441          
refSNP ID: rs12474441
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_000463.2:c.1304+1583T>G
NM_001072.3:c.1301+1583T>G
NM_007120.2:c.1307+1583T>G
NM_019075.2:c.1295+1583T>G
NM_019076.4:c.1295+1583T>G
NM_019077.2:c.1295+1583T>G
NM_019078.1:c.1307+1583T>G
NM_019093.2:c.1307+1583T>G
NM_021027.2:c.1295+1583T>G
NM_205862.1:c.500+1583T>G
NT_005120.15:g.611422T>G
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 ss52070496 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12474441 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
ss19450047CSHL-HAPMAP|CSHL-HuDD-200402.chr2.NT_005120.14_609202fwd/BG/Ttcaataccattaaaacctgacttctttcccgcactgttgaagctccttcttgaggctcac02/20/0410/26/06120Genomicunknown
ss28520086BROAD|BI139378fwd/BG/Ttcaataccattaaaacctgacttctttcccgcactgttgaagctccttcttgaggctcac08/20/0410/04/04124Genomicunknown
ss44228349ABI|hCV2669341byFreqfwd/BG/Ttcaataccattaaaacctgacttctttcccgcactgttgaagctccttcttgaggctcac07/18/0511/03/06126Genomicunknown
ss50393283EGP_SNPS|UGT1A1-011748byFreqfwd/BG/Ttcaataccattaaaacctgacttctttcccgcactgttgaagctccttcttgaggctcac01/27/0611/03/06126Genomicunknown
ss52070496SI_EXO|NT_005120.15_611422byFreqfwd/BG/Ttcaataccattaaaacctgacttctttcccgcactgttgaagctccttcttgaggctcac03/29/0603/31/08127Genomicunknown
ss65835234KRIBB_YJKIM|KHS11026fwd/BG/Ttcaataccattaaaacctgacttctttcccgcactgttgaagctccttcttgaggctcac10/17/0611/15/06127Genomicunknown
ss75254662ILLUMINA|ILMN_Human_1M_rs12474441fwd/BG/Ttcaataccattaaaacctgacttctttcccgcactgttgaagctccttcttgaggctcac08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12474441|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=129
 GGGACAACAG GGGAGGACTG ATGACTGACT TCCCACCTTT GAGGTGCTAA TGTGTGTGTG
 GTGGCACTGG ATAAAAGATC AATGTTGGCT AGGCACCATG GCACACGCCT GTAGTCCCAG
 CCACTCTGGA GGCTAAGGCG GGAGGATTGC TTGAGCCCAG AAGTTGGAGG CTGCTATGAG
 CCGTGATCAT GCCACTGCAC TCCAGCAACC TGGGCAACAG AGTGAGACCC TGTCTCAAAA
 AAAAAAAAAA AAATGAAAAG TCCACATAAC CTGAGCATCA TGTGCCCAGA GCGTTGGGTG
 GTGTGGTCCC ATTCCTTCCT TCCAGCGGCT TCTTCTGGCC ACCTCAATGT CAGGATGTCC
 TGCTCACATA TCAATACCAT TAAAACCTGA CTTCTTTCCC
 K
 GCACTGTTGA AGCTCCTTCT TGAGGCTCAC ATTATGGATA TAATTTTGAT TCTTTCTTCA
 GTGGTATAGA TAACTACTTG TAACCTAAGA ACAACTTGGT GAAAGTCCTC TAATACATTA
 TTTTTTAAAA AAACACAAAT CAATGAGCTC AACTTATTAA CTAACTTTCA TCTATTCATT
 TTTGAGCCAT CCCTGTCTGA TTGTGAATCT CCATGATTCC AACACTCTGA GCTGGGGATA
 GTGCCTACAC AAAATAAAAA GAAGTGGAAA ATTTTCAAAC ATCAGTTTAT GCTGACAACC
 AGGCCATAAT AGGTGCTCAA TTACTATTGA ATGAATGAAT GAAAGTTCTG GCCAGGTACG
 GTGGCTCATG CCTGTAGTCC CAACACTTTG GGAGGCCGAG

  GeneView back to top
GeneView via analysis of contig annotation: UGT1A1 UDP glucuronosyltransferase 1 family, polypeptide A1
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A4 UDP glucuronosyltransferase 1 family, polypeptide A4
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A9 UDP glucuronosyltransferase 1 family, polypeptide A9
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A10 UDP glucuronosyltransferase 1 family, polypeptide A10
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A6 UDP glucuronosyltransferase 1 family, polypeptide A6
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A8 UDP glucuronosyltransferase 1 family, polypeptide A8
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A7 UDP glucuronosyltransferase 1 family, polypeptide A7
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A5 UDP glucuronosyltransferase 1 family, polypeptide A5
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: UGT1A3 UDP glucuronosyltransferase 1 family, polypeptide A3
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_005120->NM_000463
function
referenceNT_005120->NM_007120
function
referenceNT_005120->NM_021027
function
referenceNT_005120->NM_019075
function
referenceNT_005120->NM_001072
function
referenceNT_005120->NM_205862
function
referenceNT_005120->NM_019076
function
referenceNT_005120->NM_019077
function
referenceNT_005120->NM_019078
function
referenceNT_005120->NM_019093
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_005120->NM_000463->NP_000454611422forwardintron
referenceNT_005120->NM_007120->NP_009051611422forwardintron
referenceNT_005120->NM_021027->NP_066307611422forwardintron
referenceNT_005120->NM_019075->NP_061948611422forwardintron
referenceNT_005120->NM_001072->NP_001063611422forwardintron
referenceNT_005120->NM_205862->NP_995584611422forwardintron
referenceNT_005120->NM_019076->NP_061949611422forwardintron
referenceNT_005120->NM_019077->NP_061950611422forwardintron
referenceNT_005120->NM_019078->NP_061951611422forwardintron
referenceNT_005120->NM_019093->NP_061966611422forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs12474441 maps exactly once on NCBI human chromosome 2
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
2NW_001838868.1624044226478502plusTalt_assembly_8HuRefHuRefview400
2NW_921618.139313830228399300plusTalt_assembly_1CeleraCeleraview400
2NT_005120.15611422234343407plusTref_assemblyreferencereferenceview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005120.15
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/T
T/T
HWPG
T
ss50393283EGP_YORUB-PANELSub-Saharan African 24IG 1.000 1.000
EGP_HISP-PANELHispanic 42IG 0.095 0.905 1.000 0.048 0.952
EGP_CEPH-PANELEuropean 44IG 1.000 1.000
EGP_AD-PANELAfrican American 28IG 0.071 0.929 1.000 0.036 0.964
EGP_ASIAN-PANELAsian 44IG 1.000 1.000
ss52070496HapMap-CEUEuropean 120IG 0.033 0.967 0.017 0.983
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 1.000 1.000
ss65835234KHP1 180AF 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.013+/-0.079307247580

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNYES

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Revised: May 25, 2006 1:38 PM .