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Reference SNP (refSNP) Cluster Report: rs1042571                 ** With Likely benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Likely benign allele [ClinVar]
MAF/MinorAlleleCount:A=0.1156/579 (1000 Genomes)
A=0.1536/19283 (TOPMED)
HGVS Names
  • CM000664.2:g.25161018G>A
  • NC_000002.11:g.25383887G>A
  • NC_000002.12:g.25161018G>A
  • NG_008997.1:g.12673C>T
  • NM_000939.3:c.*63C>T
  • NM_001035256.2:c.*63C>T
  • NM_001319204.1:c.*63C>T
  • NM_001319205.1:c.*63C>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss38339122 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1042571 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
ss1509903LEE|25580fwd/BC/Tcaggaggtcgaccccaaagccccttgctctccctgccctgctgccgcctcccagcctggg09/13/0010/10/0386cDNAunknown
ss4403954LEE|e25580fwd/BC/Tcaggaggtcgaccccaaagccccttgctctccctgccctgctgccgcctcccagcctggg04/26/0210/10/03106cDNAunknown
ss12586976HG_BONN_CNS_SNPS|pomc_x3:911byFreqfwd/BC/Tcaggaggtcgaccccaaagccccttgctctccctgccctgctgccgcctcccagcctggg08/05/0310/25/06117Genomicunknown
ss16264502CGAP-GAI|1529292rev/TA/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg11/18/0311/22/03120cDNAunknown
ss38339122CEPH|G4-SN-E3S10fwd/BC/Tcaggaggtcgaccccaaagccncttgctctccctgccctgctgccgcctcccagcctggg05/11/0505/11/05125GenomicC100 %
ss48296390SNP500CANCER|POMC-02byFreqfwd/BC/Tcaggaggtcgaccccaaarccccttgctctccctgcyctgctgccgcctcccagcctggg08/19/0511/03/06126Genomicunknown
ss69365676PHARMGKB_PHAT|PS205137_PA141936837_101byFreqrev/TA/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg03/22/0708/14/07127Genomicunknown
ss91092135BCMHGSC_JDW|JWB-1214261rev/TA/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg02/26/0803/01/08129Genomicunknown
ss1093256521000GENOMES|CEU.trio.12.15.2008_335974_chr2_25237391rev/TA/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg12/16/0812/16/08130Genomicunknown
ss164026442COMPLETE_GENOMICS|NA07022_36_chr2_25237391rev/TA/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg09/29/0909/29/09132Genomicunknown
ss2191272041000GENOMES|pilot_1_YRI_936887_chr2_25237391rev/A/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg04/22/1004/22/10132Genomicunknown
ss2310816301000GENOMES|pilot_1_CEU_686259_chr2_25237391rev/A/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg05/01/1005/01/10132Genomicunknown
ss252981000BL|SNP29448_2_25237391rev/TA/Gcccaggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacctcctg08/18/1008/18/10134Genomicunknown
ss555424862TISHKOFF|snp_chr2_25383887rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc11/22/1211/23/12138Genomicunknown
ss649004835SSMP|2_25383887rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc12/14/1202/10/15138Genomicunknown
ss976600578EVA-GONL|EVA-GONL_rs1042571rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc04/23/1404/23/14142Genomicunknown
ss1068943315JMKIDD_LAB|HGDP_WGS_chr2_25383887rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc07/10/1407/10/14142Genomicunknown
ss12963352371000GENOMES|PHASE3_V1_7288153rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc08/16/1408/16/14142Genomicunknown
ss1428510862DDI|DDI_rs1042571rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc11/04/1411/04/14144Genomicunknown
ss1586004427EVA_DECODE|EVA_DECODE_2_25237391_206315_rs1042571rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc03/02/1503/02/15144Genomicunknown
ss1603037763EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_25383887_4026249rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc03/04/1503/04/15144Genomicunknown
ss1646031796EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_25383887_4026249rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc03/04/1503/04/15144Genomicunknown
ss1710956377EVA_MGP|EVA_XIMO_73129rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc03/09/1503/09/15144Genomicunknown
ss1796435656HAMMER_LAB|Hsieh_782363rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc07/15/1507/15/15146Genomicunknown
ss1919832614WEILL_CORNELL_DGM|SNV:chr2:25383887rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc10/16/1510/16/15147Genomicunknown
ss1958398087ILLUMINA|2:25383887-G-A-0_T_F_2304232611rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc11/13/1511/13/15147Genomicunknown
ss2020444955JJLAB|SNP947510rev/TA/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc08/29/1608/30/16149Genomicunknown
ss2148488986USC_VALOUEV|NC_000002.11:g.25383887G>Arev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc11/17/1611/17/16150Genomicunknown
ss2228396256HUMAN_LONGEVITY|HLI-2-25161018-G-Arev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc11/18/1611/18/16150Genomicunknown
ss2394312475TOPMED|2_25383887_G/Arev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc11/19/1611/19/16150Genomicunknown
ss2703049897GRF|rs1042571rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc02/13/1702/13/17151Genomicunknown
ss2770920090GNOMAD|rs1042571rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc05/17/1705/17/17151Genomicunknown
ss2985786624AFFY|Axiom_Smokesc1_Affx-19829666rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc05/24/1705/24/17151Genomicunknown
ss2989148357SWEGEN|NC_000002.11:g.25383887G>Arev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc05/30/1705/30/17151Genomicunknown
ss3021950409ILLUMINA|MEGA_Consortium_v2_15070954_A2_2:25383887-G-A-0_T_F_2304232611rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc06/28/1706/28/17151Genomicunknown
ss3023989215BIOINF_KMB_FNS_UNIBA|2.25161018G>Arev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc07/05/1707/05/17151Genomicunknown
ss3302029497TOPMED|TOPMed_freeze_5?chr2:25,161,018rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc10/02/1710/02/17151Genomicunknown
ss3344124619CSHL|rs1042571rev/A/Ggctgggaggcggcagcagggcagggagagcaaggggctttggggtcgacc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1042571|allelePos=935|totalLen=1486|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TTTGAGTGCC AAGAAAAGCA GTGGGCAGAC CTGCTCTGTA GGGAGGCCTC GACGCTTGAC
 ACGCCCGACA CTGTGCCCTG TGTCCTCGGC ACGTGGCGAG GGCGGCCNGG GCCTAGGCGC
 AGTGACGGGC GCGGCAGCCG GGCCGGGGTG CGGGGCACGG GCTGCCCTCA TGCCCTCGCG
 TCTTCCCCCA GGAGTGCATC CGGGCCTGCA AGCCCGNCCT CTCGGCCGAG ACTCCCATGT
 TCCNGGGAAA TGGCGACGAG CAGCCTCTGA CCGAGAACCC CCGGAAGTAC GTCATGGGCC
 ACTTCCGCTG GGACCGATTC GGCCGCCGCA ACAGCAGCAG NAGCGGCAGC AGCGGCNGCA
 GCGGCGCAGG GCAGAAGCGC GAGGACGTCT CAGCGGGCGA AGACTGCGGC CCGCTGCCTG
 AGGGCGGCCC CGAGCCCCGC AGCGATGGTG CCAAGCCGGG CNCGCGCGAG GGCAAGCGCT
 CCTACTCCAT GGAGCACTTC CGCTGGGGCA AGCCGGTGGG CAAGAAGCGG CGCCCAGTGA
 AGGTGTACCC TAACGGCGCC GAGGACGAGT CGGCCGAGGC CTTCCCCCTG GAGTTCAAGA
 GGGAGCTGAC TGGCCAGCGA CTCCGGGAGG GAGATGGCCC CGACGGCCCT GCNGATGACG
 GCGCAGGGGC CCAGGCCGAC CTGGAGCACA GCCTGCTGGT GGCGGCCGAG AAGAAGGACG
 AGGGCCCCTA CAGGATGGAG CACTTCCGCT GGGGCAGCCC GCCCAAGGAC AAGNGCTACG
 GCGGTTTCAT GACCTCCGAG AAGAGCCAGA CGCCCCTGGT GACGCTGTTC AAAAACGCCA
 TCATCAAGAA CGCCTACAAG AAGGGCGAGT GAGGGCACAG CGGGGCCCCA GGGCTACCCT
 CCCCCAGGAG GTCGACCCCA AAGCCNCTTG CTCT
 Y
 CCCTGCCCTG CTGCCGCCTC CCAGCCTGGG GGGGTCGTGG CAGATAATCA GCCTCTTAAA
 GCTGCCTGTA GTTAGGAAAT AAAACCTTTC AAATTTCACA TCCACCTCTG ACTTTGAATG
 TAAACTGTGT GAATAAAGTA AAAATACGTA GCCGTCAAAT AACAGCAGCA TGGATCGGAG
 GAGCACAGTG GTTTCCATGC GGTAGGATAT TTCACAGGAC TTANTGAGCG TGAAAGGAAA
 ATGTGCTTCC TGCCCCCACC CCCAAATGGA TCTTCGAGGG ATCAGATAGT TTGGGTGAAG
 GCACAGGGTG GCTCCAGCAC CTCTAGGATG GCCGTATTTT CCACACACTC CACTGAGTGG
 GAGACTGCTC AGCTAGCACA CGTGTAAAGG CAGGATTCCT GCAAGAGTGA CCCCGGGCGC
 TCAGGGGCTC CCCGGCTCCG GTCCCACCTC CAAAAAAAAA AAAAAAAAAC GTGCTGCGCG
 ACGCAGCCAC CTACACCACC CCGCCTCCAC CCCGCCTCCA GCCATTCTAA TGGGACCACC
 CCGCGTGACG T

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022184 AI828843 Hs.1897
dbSNP Blast Analysis
UniGene Cluster ID
1897
OMIM
605552
176830

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1042571 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss12586976CEPH 184AF 0.699999990.30000001
COHORT_CONSORTIUM_B 76AF 0.837840020.16215999
COHORT_CONSORTIUM_C 76AF 0.736840010.26315999
COHORT_CONSORTIUM_H 76AF 0.828570010.17143001
COHORT_CONSORTIUM_J 76AF 0.973680020.02632000
COHORT_CONSORTIUM_L 76AF 0.945949970.05405000
CEPH-TRIOS 606AF 0.789770010.21022999
ss1296335237EAS 1008AF 0.965300020.03470000
EUR 1006AF 0.796199980.20379999
AFR 1322AF 0.887300010.11269999
AMR 694AF 0.831399980.16859999
SAS 978AF 0.925400020.07460000
ss164026442CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss219127204pilot_1_YRI_low_coverage_panel 118AF 0.915254240.08474576
ss231081630pilot_1_CEU_low_coverage_panel 120AF 0.758333330.24166666
ss38339122ENSEMBL_Venter 2IG1.00000000 1.00000000
ss48296390P1 202AF0.692999960.276999980.030000001.000000000.832000020.16800000
CAUC1 62AF0.484000000.419000000.097000001.000000000.694000010.30599999
AFR1 48AF0.750000000.25000000 0.527089000.875000000.12500000
HISP1 44AF0.591000020.40900001 0.250592000.795000020.20500001
PAC1 48AF1.00000000 1.00000000
ss69365676PA141936838 906AF 0.820088330.17991170

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.204+/-0.2460000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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