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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1042391          
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:A/T
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_006877.3:c.766T>A
NP_006868.3:p.Phe256Ile
NT_007592.14:g.7149012T>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 ss71645711 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1042391 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
ss1509579LEE|18120fwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct09/13/0010/10/0386cDNAunknown
ss2420536HGBASE|SNP000003188fwd/BA/Ttcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaa11/07/0010/10/0389Genomicunknown
ss4403718LEE|e18120fwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct04/26/0210/10/03106cDNAunknown
ss10319972BCM_SSAHASNP|chr6.NT_007592.13_7149012byFreqfwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct06/29/0304/07/04116Genomicunknown
ss11815751WI_SSAHASNP|chr6.NT_007592.13_7149012fwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct07/04/0310/10/03116Genomicunknown
ss16225312CGAP-GAI|1458238fwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct11/18/0311/22/03120cDNAunknown
ss22461815SSAHASNP|WGSA-200403-chr6.chr6.NT_007592.13_7149012fwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct03/21/0403/21/04121Genomicunknown
ss24374803PERLEGEN|afd0267259byFreqfwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct08/10/0409/13/04123Genomicunknown
ss28497541MGC_GENOME_DIFF|29804415-T7149012Afwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct08/20/0408/20/04126cDNAunknown
ss28512263MGC_GENOME_DIFF|BC008281x29804415-T7149012Afwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct08/25/0408/25/04126cDNAunknown
ss44735226ABI|hCV3123794byFreqfwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct07/19/0511/03/06126Genomicunknown
ss48428096APPLERA_GI|hCV3123794byFreqfwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct09/28/0511/03/06126Genomicunknown
ss65724631ILLUMINA|Human1-rs1042391fwd/BA/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct10/10/0610/10/06127Genomicunknown
ss68966502PERLEGEN|PGP00267259byFreqfwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct01/30/0708/14/07127Genomicunknown
ss71645711SI_EXO|NT_007592.14_7149012byFreqfwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct05/07/0703/31/08127Genomicunknown
ss74907103ILLUMINA|ILMN_Human_1M_rs1042391fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct08/28/0708/29/07129Genomicunknown
ss78041529HGSV|Cor12878_SNV_20070510.chr6_16398740fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct10/17/0710/17/07129Genomicunknown
ss78516355HGSV|Cor18507_SNV_20070510.chr6_16398740fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct10/19/0710/19/07129Genomicunknown
ss81641046HGSV|Cor18956_SNV_20070510.chr6_16398740fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct11/30/0712/01/07130Genomicunknown
ss98476397HUMANGENOME_JCVI|1103652792765fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct04/01/0804/01/08130Genomicunknown
ss105982651BGI|BGI_rs1042391fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct09/12/0806/18/09130Genomicunknown
ss1097844541000GENOMES|CEU.trio.12.15.2008_1457220_chr6_16398740fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct12/15/0812/16/08130Genomicunknown
ss1139551671000GENOMES|NA19240_2008_12_16_1311444_chr6_16398740fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct12/18/0812/18/08130Genomicunknown
ss116324930ILLUMINA-UK|NA18507_000024245_NCBI36.1_chr6_16398740fwd/A/Ttcgggtcatacggagtgtgctggagaagtgttgagaggaacggacggaagctcaagctct01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1042391|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 AATCTTAATG TTTCTGTGAT TCTAAGAGAG TTAGATCTGA GGAAGGTGGT CGTAGTTAGC
 CATTAAAAGC CATTCAGCAT GGTCCAGTAT ATGGGACACT AGCCTTCAGT AGGCTGCATT
 TGTTTCTCGC AGTGTCCCAT GGCCCTTTCT CCCTGCATGG AAGCCTTCTC CCTTTTTCCA
 GGAGGAGACA GGCGAGAGAG GTCCAGCCTT TCTCTTGACT ATAGCTGGGC GGGGAGGGAG
 GTGAACTGGG CAAGCACTGG GATTTTTTGA GAGCCTTTTC CCCTGAGCTG TTTTCTCTGC
 TACTCGCTTT CATCCCCACC GTTGGCATTT AGGAGCTGGA GCAGATTTTG TCATGCTGGG
 AGGAATGTTT TCGGGTCATA CGGAGTGTGC TGGAGAAGTG
 W
 TTGAGAGGAA CGGACGGAAG CTCAAGCTCT TCTACGGGAT GAGCTCTGAC ACCGCCATGA
 ACAAGCACGC AGGAGGAGTT GCTGAGTACA GGTGAGGAGG TGACCCCGGG GCGCACCCTC
 GAGGCCTGGC CTTGCTTTTC TTACGGAGAT GGGATGGAAG CAGGTCTGAA TAGCAGCTCT
 GTGTATATTA AAGTACCGTG GGAAGGGGTT CTTTTTAAAG ACCCCTAATT TGTATCCAGT
 TAGCATTTGC AGTGTTTGGG GTTCCCAAAA GCAAGTACAG AGCAGCAGTG TTTGGTGATG
 GGTTGGAAGT GTGACCAGGG TTATATGTGA GTGGGTGCCA GTCCTGAAGG GAATACTTCA
 GACCTCTGGG GGTAGGTGGA ATTATTGTCT TGTCCTTCCA

  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
S73066 ABBA01022186 BC008281 BG034306 Hs.1435
dbSNP Blast Analysis
UniGene Cluster ID
484741

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/T
 T/T
 HWP A
 N
 T
ss10319972 CEPH 184 AF 0.430 0.570
CHMJ Asian 74 IG 0.932 0.014 0.054
ss24374803 AFD_EUR_PANEL European 48 IG 0.083 0.500 0.417 0.584 0.333 0.667
AFD_AFR_PANEL African American 46 IG 0.696 0.217 0.087 0.150 0.804 0.196
AFD_CHN_PANEL Asian 48 IG 0.750 0.208 0.042 0.439 0.854 0.146
ss44735226 HapMap-CEU European 112 IG 0.107 0.518 0.375 0.403 0.366 0.634
HapMap-HCB Asian 90 IG 0.822 0.156 0.022 0.371 0.900 0.100
HapMap-JPT Asian 88 IG 0.818 0.182 0.527 0.909 0.091
HapMap-YRI Sub-Saharan African 120 IG 0.817 0.183 0.439 0.908 0.092
AoD_African_American 90 AF 0.820 0.180
AoD_Caucasian 92 AF 0.400 0.600
AoD_Chinese 90 AF 0.890 0.110
AoD_Japanese 90 AF 0.840 0.160
ss48428096 AGI_ASP population multiple 56 IG 0.393 0.393 0.214 0.343 0.589 0.411
ss68966502 HapMap-CEU European 120 GF 0.100 0.500 0.400 0.350 0.650
HapMap-HCB Asian 90 GF 0.822 0.156 0.022 0.900 0.100
HapMap-JPT Asian 90 GF 0.822 0.178 0.911 0.089
HapMap-YRI Sub-Saharan African 120 GF 0.817 0.183 0.908 0.092
ss71645711 HapMap-CEU European 112 IG 0.107 0.518 0.375 0.366 0.634
HapMap-HCB Asian 90 IG 0.822 0.156 0.022 0.900 0.100
HapMap-JPT Asian 88 IG 0.818 0.182 0.909 0.091
HapMap-YRI Sub-Saharan African 120 IG 0.817 0.183 0.908 0.092

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.386+/-0.210 611 488 276 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 .