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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1028484          
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:T
Clinical Association:unknown
HGVS Names
NT_007299.12:g.2825315C>T
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 ss1493627 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1028484 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
ss1493627TSC-CSHL|TSC0253002byFreqfwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa09/07/0004/07/0486Genomic95 %
ss12805757SC_SNP|NT_007299.12_2825315fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa10/21/0310/31/03119Genomicunknown
ss14686205WI_SSAHASNP|chr6.NT_007299.12_2825315fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa11/05/0311/22/03119Genomicunknown
ss22513185SSAHASNP|WGSA-200403-chr6.chr6.NT_007299.12_2825315fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa03/21/0403/21/04121Genomicunknown
ss44730751ABI|hCV11429415byFreqfwd/BC/Ttgataataaaattcttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa07/19/0511/03/06126Genomicunknown
ss66340478AFFY|SNP_A-1944804byFreqfwd/BC/Tttgtgcctgaggtatagctacctaattattaa10/29/0608/14/07127Genomicunknown
ss76044423AFFY|AFFY_6_1M_SNP_A-1944804fwd/BC/Tttgtgcctgaggtatagctacctaattattaa08/28/0708/29/07129Genomicunknown
ss81451774KRIBB_YJKIM|KHS77959fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa11/30/0711/30/07130Genomicunknown
ss84831084HGSV|Cor19240_SNV_20070510.chr6_65061863fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa11/30/0712/08/07130Genomicunknown
ss85787889HGSV|Cor19129_SNV_20070510.chr6_65061863fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa12/06/0712/10/07130Genomicunknown
ss93477972BCMHGSC_JDW|JWB-2153599fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa02/26/0803/04/08129Genomicunknown
ss98502857HUMANGENOME_JCVI|1103652884119fwd/BC/Ttgataataaaattcttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa04/01/0804/01/08130Genomicunknown
ss106005975BGI|BGI_rs1028484fwd/BC/Ttgataataaaattmttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa09/12/0806/19/09130Genomicunknown
ss1102217261000GENOMES|CEU.trio.12.15.2008_1533189_chr6_65061863fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa12/15/0812/17/08130Genomicunknown
ss1144629671000GENOMES|NA19240_2008_12_16_1375360_chr6_65061863fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa12/18/0812/18/08130Genomicunknown
ss116507202ILLUMINA-UK|NA18507_000092035_NCBI36.1_chr6_65061863fwd/BC/Ttgataataaaatttttgtgcctgaggtatagctacctaattattaagaacacaggtgaaa01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1028484|allelePos=307|totalLen=1187|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CATAGAGATG TATTTTATTC TTTTCTCTGA CTTATAAGTA TTACTATTCC ATTTTATTTA
 TTACATTTTT AAACGTCCAT TTCTCTGCTT TGCAATGTTC CTACTATTTC TAATAAGGCT
 ATTCAGAGAG TCATTAGATT ACATGTGAGT GCTTCTGTAG GGAAGAAACT AGAGGTAGAA
 TAACTGATTT AGCTGTTCTT AATATCGTAC CTGTCTACTC TGCCTGAATG AGAAATCAAT
 CTTTCATATT TTAGGCATAA GACATAAGCA AATATGTGAT AATAAAATTT TTGTGCCTGA
 GGTATA
 Y
 GCTACCTAAT TATTAAGAAC ACAGGTGAAA CAAATGTAGG TGACTATAAA ATAGAGATAG
 AAAATGCTAT ACGAGTTAAT CCAAAGTTTG ACATATACAC AGATATCATT AGTATCAACT
 TTACTGGTGG AAAAAACCTT GGTAAAATGA TTCAAGCAAA CATAAAACCA AATAACAATC
 CCCATCACCA AATAAAAACC AAAATACCAA ACTGGTGAAT CAGTTTCTCT GTCAATGCTA
 TGTTAAGAAC TATTGCTAGA TTTTCTTATA TCAGCATAAA GCTGACTGCA AAGAAGAGGT
 GAGGAAATAG ATCATGCTAT TCtaaaaatt taaatatttt gataaattta aaaaatGTGT
 CACTGAGCAT CAGGCAAGAG ATTTATAATT TGTGGTGATA GTCACCTTAC TTCCTTCATG
 TGAGTAGGAC TTTTAGCTTC TCAATAACAG AACCTCAGTG ATATAATTAA TATAAAATAG
 TAAGGTAAGA CTACATTCCC TGTAATAAAA TCCTGCATCA CATGTCGTCT TCCAAGGACC
 ATCTGTCCAG ATGAGCCTTG CTGTAATAAT CAAGTAAACG GAGCCACCAG ACAAATTAGT
 GGAGAGCTTC AATTCTCATA GTGTCATCTG GGGGTtattt aaatgttatt tgactttttc
 actgtggtta tacttgcact gatagtcaaa gataatagtg gataaaacta ctgatggctt
 agtatgatac aaatagtggc accacctgta ctagATAAGA GTATTATCAC TTTAATTTAA
 AAAATTAAGA TTATACTTGA AACAGTGGTA ACACTAACTT TATTCAAATA TAAGTTATGA
 ATTACATGCC TTTTTAATAA AGTGTATGAT GAAAAGGGGG

  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_007299 ABBA01023948
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
 T
ss1493627 TSC_42_AA 82 AF 0.256 0.744
TSC_42_C 80 AF 0.288 0.712
TSC_42_A 80 AF 0.463 0.537
CEPH 184 AF 0.210 0.790
HapMap-CEU European 120 IG 0.083 0.367 0.550 0.267 0.733
HapMap-HCB Asian 90 IG 0.422 0.511 0.067 0.678 0.322
HapMap-JPT Asian 88 IG 0.091 0.523 0.386 0.352 0.648
HapMap-YRI Sub-Saharan African 120 IG 0.017 0.183 0.800 0.108 0.892
ss44730751 AoD_African_American 90 AF 0.250 0.750
AoD_Caucasian 92 AF 0.250 0.750
AoD_Chinese 90 AF 0.530 0.470
AoD_Japanese 90 AF 0.510 0.490
ss66340478 HapMap-CEU European 118 GF 0.085 0.356 0.559 0.263 0.737
HapMap-HCB Asian 90 GF 0.422 0.511 0.067 0.678 0.322
HapMap-JPT Asian 90 GF 0.111 0.511 0.378 0.367 0.633
HapMap-YRI Sub-Saharan African 120 GF 0.017 0.183 0.800 0.108 0.892
ss76044423 ICMHP 6 IG 0.333 0.667 0.333 0.667

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.442+/-0.161 1211 1002 269 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
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .