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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs924181          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NT_019273.18:g.6587799G>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 ss1361347 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs924181 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
ss1361347TSC-CSHL|TSC0239374byFreqfwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag09/06/0004/07/0486Genomic95 %
ss16447154CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_019273.16_1676062rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt02/17/0403/04/04120Genomicunknown
ss20468276SSAHASNP|WGSA-200403-chr1.chr1.NT_019273.16_1676062rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt03/18/0403/18/04121Genomicunknown
ss24278562PERLEGEN|afd1087087byFreqrev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt08/10/0409/13/04123Genomicunknown
ss44100963ABI|hCV3193301byFreqrev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt07/18/0511/03/06126Genomicunknown
ss65720896ILLUMINA|Human1-rs924181fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag10/10/0610/10/06127Genomicunknown
ss66727017ILLUMINA|HumanHap300v1.1_rs924181fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag11/09/0611/09/06127Genomicunknown
ss67896206ILLUMINA|HumanHap550v1.1_rs924181fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag11/14/0611/14/06127Genomicunknown
ss68030493ILLUMINA|HumanHap650Yv1.0_rs924181fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag11/14/0611/15/06127Genomicunknown
ss71595142ILLUMINA|HumanHap650Yv3.0_rs924181fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag04/23/0704/23/07127Genomicunknown
ss75668150ILLUMINA|ILMN_Human_1M_rs924181fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag08/28/0708/29/07129Genomicunknown
ss77448202HGSV|Cor12156_SNV_20070510.chr1_110392156rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt10/09/0710/13/07129Genomicunknown
ss79289918ILLUMINA|HumanHap300v2.0_rs924181fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag04/18/0711/18/07130Genomicunknown
ss83090411HGSV|Cor18956_SNV_20070510.chr1_110392156rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt11/30/0712/04/07130Genomicunknown
ss83614234KRIBB_YJKIM|KHS502063fwd/BC/Taatatttagagagcagcaaggacattcctcagtttgtacatggggaaaagggtgaagaag12/04/0712/05/07130Genomicunknown
ss87710253BCMHGSC_JDW|JWB-0104329rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt02/26/0802/26/08129Genomicunknown
ss98237661ILLUMINA|HumanHap550v3.0__rs924181rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt04/20/0703/31/08130Genomicunknown
ss99239620HUMANGENOME_JCVI|1103675194035rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt04/03/0804/03/08130Genomicunknown
ss1085167171000GENOMES|CEU.trio.12.15.2008_142176_chr1_110481637rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt12/15/0812/16/08130Genomicunknown
ss1110022461000GENOMES|NA19240_2008_12_16_130149_chr1_110481637rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt12/16/0812/17/08130Genomicunknown
ss118966466ILLUMINA-UK|NA18507_000129005_NCBI36.1_chr1_110481637rev/TA/Gcttcttcacccttttccccatgtacaaactgaggaatgtccttgctgctctctaaatatt01/21/0901/21/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs924181|allelePos=515|totalLen=653|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TGTGCATGTG TTACCTGTTC ATTAAAATAA CAAAATGCAT TTCTCCCTGC TCCTCTAGAC
 TGCCCTTTCT TCGGCTCTGT CCTCAGCACC AGCCTTCCCT CCTGCCTCCT CCTTTTGAGC
 ACACTGTCTG CCACACTCCA TGGCCGGGCA CCTTGGGAAG AGCATGGACT TTAGGATTGG
 ATGACCCAGG TTCTCACACG GActctgagc gtcctcgtcc tcatctgtaa aatggggata
 aaagcagtat gttataggat gtggtgcgaa ttacatgaga taacttataa agtgAGTGCT
 CAAAAACAAC AGTTCCTGCT GGCTCGCTTT TCTGGAACAC GACTATCATA CCCATGAAGG
 GCAGAGGTGG CTGAACCTTT CTGTGGCTTG GACTCAGAAA TATCCTCCCT CCCTTTACCA
 GCAACCTCCA AACTCTTAAG GAAGAAACAA GTGGCAAAGT CTTTGAGGAA AGCAGTATCC
 CTCTAATATT TAGAGAGCAG CAAGGACATT CCTC
 Y
 AGTTTGTACA TGGGGAAAAG GGTGAAGAAG GGGTCCCAAA TTCCCAACAC ACCCAGCATC
 CTGGGGCCCC AAACTCCAGC CTGGAAGGAA GCATCGTTCA ATGTAAACAG AATAGGGGAG
 TCAGCTCTGG CAGGACCG

  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_019273 ABBA01068387 AC025865.3 AL160006.9 AL355990.1 AL360171.4
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 N
 T
ss1361347 TSC_42_AA 80 AF 0.738 0.262
TSC_42_C 80 AF 0.550 0.450
TSC_42_A 80 AF 0.725 0.275
HapMap-CEU European 120 IG 0.317 0.500 0.183 1.000 0.567 0.433
HapMap-HCB Asian 90 IG 0.578 0.356 0.067 1.000 0.756 0.244
HapMap-JPT Asian 88 IG 0.523 0.409 0.068 1.000 0.727 0.273
HapMap-YRI Sub-Saharan African 120 IG 0.600 0.350 0.050 1.000 0.775 0.225
CHMJ Asian 74 IG 0.568 0.014 0.419
ss24278562 AFD_EUR_PANEL European 48 IG 0.333 0.333 0.333 0.150 0.500 0.500
AFD_AFR_PANEL African American 46 IG 0.522 0.391 0.087 1.000 0.717 0.283
AFD_CHN_PANEL Asian 48 IG 0.500 0.417 0.083 1.000 0.708 0.292
ss44100963 AoD_African_American 90 AF 0.730 0.270
AoD_Caucasian 92 AF 0.510 0.490
AoD_Chinese 90 AF 0.810 0.190
AoD_Japanese 90 AF 0.640 0.360

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict		 Additional Freq. Data
0.431+/-0.172 1264 1052 15 0 ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: ILLUMINA, PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .