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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1868024          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:92/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_058165.2:c.487T>C
NP_477513.2:p.Ser163Pro
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 ss44167345 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1868024 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
ss2743545TSC-CSHL|TSC0865553byFreqfwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg01/02/0104/07/0492Genomicunknown
ss11522863WI_SSAHASNP|chr2.NT_005403.13_73718422fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg07/03/0310/10/03116Genomicunknown
ss24362385PERLEGEN|afd1424944byFreqfwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg08/10/0409/13/04123Genomicunknown
ss24784986SEQUENOM|sqnm49919fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg06/18/0406/18/04123cDNAunknown
ss44167345ABI|hCV11471470byFreqfwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg07/18/0511/03/06126Genomicunknown
ss48418875APPLERA_GI|hCV11471470byFreqfwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg09/28/0511/03/06126Genomicunknown
ss66739367ILLUMINA|HumanHap300v1.1_rs1868024fwd/TC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg11/09/0611/09/06127Genomicunknown
ss67201086ILLUMINA|HumanHap550v1.1_rs1868024fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg11/14/0611/14/06127Genomicunknown
ss67592951ILLUMINA|HumanHap650Yv1.0_rs1868024fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg11/14/0611/14/06127Genomicunknown
ss68844327PERLEGEN|PGP01424944byFreqfwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg01/30/0708/14/07127Genomicunknown
ss70679315ILLUMINA|HumanHap550v3.0__rs1868024rev/TA/Gccatgtaggacacacttttcttggaaactgaaccagcccttagtgaataaaacaaaaagt04/20/0703/30/08130Genomicunknown
ss71242799ILLUMINA|HumanHap650Yv3.0_rs1868024fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg04/23/0704/23/07127Genomicunknown
ss74810750AFFY|SNP_M-184353fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg08/09/0708/09/07128Genomicunknown
ss75721907ILLUMINA|ILMN_Human_1M_rs1868024fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg08/28/0708/29/07129Genomicunknown
ss77142416HGSV|Cor12156_SNV_20070510.chr2_223384594fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg10/09/0710/11/07129Genomicunknown
ss79097172ILLUMINA|HumanHap300v2.0_rs1868024fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg04/18/0711/18/07130Genomicunknown
ss80732026KRIBB_YJKIM|KHS1004901fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg11/26/0711/26/07130Genomicunknown
ss83893427KRIBB_YJKIM|KHS566718fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg12/04/0712/06/07130Genomicunknown
ss1108285961000GENOMES|CEU.trio.12.15.2008_591418_chr2_223267333fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg12/15/0812/17/08130Genomicunknown
ss1117123021000GENOMES|NA19240_2008_12_16_529306_chr2_223267333fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg12/16/0812/17/08130Genomicunknown
ss118093884ILLUMINA-UK|NA18507_000270648_NCBI36.1_chr2_223267333fwd/BC/Tactttttgttttattcactaagggctggttcagtttccaagaaaagtgtgtcctacatgg01/19/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1868024|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GTCCTCTAGA GTTCAGTAGT GCACAACCTA CCTAAACAAA CAAGTGGTAG ACCTAGTAAT
 GACTGAATGA CATTTTAAAG ACCTAGCCCA TTACCTGCCA AGATGTTAAC TTATTAATAG
 AATACATTAC TAAAGATTTG GCTATGAAAA ATTACAAACT TACAAAGTGC TCCAAAGGTA
 AGCAGTGTAG GAAATTTTGT TAAATGTTTA CTATTGTCAT GGAATATTAT GATAAAACAT
 TGTAATATTG TTAGAAAAGG ATAACTAGTT ACTTTTTGTT TTATTCACTA AGGGCTGGTT
 Y
 CAGTTTCCAA GAAAAGTGTG TCCTACATGG TAAGCAAGGA GGGAGGTGGA AACATCTCTG
 TCATTGTCCT TGGGGGTGCA AAAGAATCAC TGGATGCTCA TCCTGGAAAG TTCACTCTGT
 TCATCCGCCA GCGGAAAGGA TTTGTTAAAA TTGCTTTGAC CCATGGGTAA GTGGCTTTTT
 GTATAAAGTA GGGGGTCAGA AAAGTTAAGA CATTATTAAA CAAACCACGA AGAAGTAAGG
 TGATTTTCTA GCCCTTAAAG ACCTCCTCCA AATCGATCTG ACAGTAAAAG CAGGTGTGGA

  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
dbSTS GenBank
sqnm49919 NT_005403
dbSNP Blast Analysis
UniGene Cluster ID
344090

  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
ss24362385 AFD_EUR_PANEL European 48 IG 0.125 0.417 0.458 1.000 0.333 0.667
AFD_AFR_PANEL African American 46 IG 0.043 0.217 0.739 0.479 0.152 0.848
AFD_CHN_PANEL Asian 48 IG 0.250 0.750 0.527 0.125 0.875
ss2743545 CHMJ Asian 74 IG 0.041 0.054 0.905
ss44167345 HapMap-CEU European 120 IG 0.067 0.317 0.617 0.479 0.225 0.775
HapMap-HCB Asian 90 IG 0.044 0.244 0.711 0.439 0.167 0.833
HapMap-JPT Asian 88 IG 0.114 0.886 0.752 0.057 0.943
HapMap-YRI Sub-Saharan African 120 IG 0.133 0.400 0.467 0.439 0.333 0.667
ss48418875 AGI_ASP population multiple 62 IG 0.194 0.194 0.613 0.005 0.290 0.710
ss68844327 HapMap-CEU European 120 GF 0.067 0.333 0.600 0.233 0.767
HapMap-HCB Asian 90 GF 0.044 0.244 0.711 0.167 0.833
HapMap-JPT Asian 90 GF 0.133 0.867 0.067 0.933
HapMap-YRI Sub-Saharan African 120 GF 0.117 0.433 0.450 0.333 0.667
ss80732026 KHP1 180 AF 0.089 0.911
Concordant Genotype Total Sample C/C C/T T/T
ss24362385 71 4 21 46
ss44167345 1202 91 432 656
ss48418875 38 6 6 19
ss68844327 265 17 86 162
ss80732026 90 16 74
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs1868024 1391 101 478 800
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
252 ss44167345 T/T CSHL-HAPMAP HapMap-CEU NA11839 CEPH1349.13 r27_ch2_CEU_illumina:human_1m_beadchip 289191
252 ss68844327 C/T CSHL-HAPMAP HapMap-CEU NA11839 CEPH1349.13 chr2-HapMap-CEU
5141 ss44167345 C/C CSHL-HAPMAP HapMap-YRI NA19098 YOR105.03 r27_ch2_YRI_illumina:human_1m_beadchip 289191
5141 ss68844327 C/T CSHL-HAPMAP HapMap-YRI NA19098 YOR105.03 chr2-HapMap-YRI
5234 ss44167345 T/T CSHL-HAPMAP HapMap-JPT NA18999 JA18999 r27_ch2_JPT_illumina:human_1m_beadchip 289191
5234 ss68844327 C/T CSHL-HAPMAP HapMap-JPT NA18999 JA18999 chr2-HapMap-JPT
5280 ss44167345 T/T CSHL-HAPMAP HapMap-YRI NA19173 YOR047.01 r27_ch2_YRI_illumina:human_1m_beadchip 289191
5280 ss68844327 C/T CSHL-HAPMAP HapMap-YRI NA19173 YOR047.01 chr2-HapMap-YRI
5293 ss44167345 T/T CSHL-HAPMAP HapMap-YRI NA19159 YOR056.02 r27_ch2_YRI_illumina:human_1m_beadchip 289191
5293 ss68844327 C/T CSHL-HAPMAP HapMap-YRI NA19159 YOR056.02 chr2-HapMap-YRI
Genotype data submitted for1406 samples from1391 individualsIndividual with multiple genotypes submission:276

  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: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .