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Reference SNP (refSNP) Cluster Report: rs1049724                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0405/4593 (ExAC)
T=0.0355/178 (1000 Genomes)
T=0.0552/6934 (TOPMED)
HGVS Names
  • CM000668.2:g.31269085C>T
  • NC_000006.11:g.31236862C>T
  • NC_000006.12:g.31269085C>T
  • NG_029422.2:g.8047G>A
  • NM_001243042.1:c.*84G>A
  • NM_002117.5:c.*84G>A
  • NT_113891.2:g.2750117C>T
  • NT_113891.3:g.2750011C>T
  • NT_167245.1:g.2532468C>T
  • NT_167245.2:g.2526883C>T
  • NT_167246.1:g.2583755C>T
  • NT_167246.2:g.2578135C>T
  • NT_167247.1:g.2617398C>T
  • NT_167247.2:g.2611813C>T
  • NT_167248.1:g.2530111C>T
  • NT_167248.2:g.2524515C>T
  • NT_167249.1:g.2570339C>T
  • NT_167249.2:g.2571041C>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 ss116389865 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1049724 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
ss1523699LEE|371984fwd/TA/Gtgacttcaagagcctctggcatctctttctcaaaggcatctgaatgtgtctgcgttcctg09/13/0010/10/0386cDNAunknown
ss4414768LEE|e371984fwd/TA/Gtgacttcaagagcctctggcatctctttctcaaaggcatctgaatgtgtctgcgttcctg04/26/0210/10/03106cDNAunknown
ss116389865ILLUMINA-UK|NA18507_000048142_NCBI36.1_chr6_31344841rev/BC/Tcaggaacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttgaagtca01/17/0901/17/09130Genomic99 %
ss201614006BUSHMAN|BUSHMAN-chr6-31344840rev/BC/Tcaggaacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttgaagtca02/16/1003/08/10135Genomicunknown
ss3331819491000GENOMES|20100804_snps_4825486_chr6_31236862rev/C/Tcaggaacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttgaagtca03/22/1103/22/11137Genomicunknown
ss491884631CLINSEQ_SNP|SNV-chr6-31344841byFreqrev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga03/06/1209/05/14137Genomicunknown
ss534215323ILLUMINA|HumanOmni5-4v1_B_kgp17059836-0_T_R_1842416428rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga06/22/1208/29/15146Genomicunknown
ss539004527DBMHC|NG_029422.2:g.8047G>Afwd/TA/Gtgacttcaagagcctctggcatctctttctcaaaggcacctgaatgtgtctgcgttcctg09/21/1209/21/12137Genomicunknown
ss559110090TISHKOFF|snp_chr6_31236862rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga11/22/1211/23/12138Genomicunknown
ss982758442EVA-GONL|EVA-GONL_rs1049724rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga04/23/1404/24/14142Genomicunknown
ss1073501642JMKIDD_LAB|HGDP_WGS_chr6_31236862rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga07/10/1407/11/14142Genomicunknown
ss13195454451000GENOMES|PHASE3_V1_31477048rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga08/16/1408/16/14142Genomicunknown
ss1581602559EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1049724rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga02/19/1502/20/15144Genomicunknown
ss1584045110EVA_FINRISK|EVA_FINRISK_rs1049724rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga02/27/1502/27/15144Genomicunknown
ss1615271097EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_31236862_17459875rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga03/04/1503/04/15144Genomicunknown
ss1658265130EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_31236862_17459875rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga03/04/1503/04/15144Genomicunknown
ss1688227522EVA_EXAC|EVA_EXAC_3248443rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga03/04/1503/04/15144Genomicunknown
ss1711120157EVA_MGP|EVA_XIMO_235917rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga03/09/1503/09/15144Genomicunknown
ss1804353744HAMMER_LAB|Hsieh_3363604rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga07/15/1507/15/15146Genomicunknown
ss1926009889WEILL_CORNELL_DGM|SNV:chr6:31236862rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga10/16/1510/17/15147Genomicunknown
ss1958885776ILLUMINA|JHU_6.31236861-1_T_R_2232771101rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga11/13/1511/13/15147Genomicunknown
ss2023635864JJLAB|SNP4138419rev/BC/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga08/29/1608/30/16149Genomicunknown
ss2151801506USC_VALOUEV|NC_000006.11:g.31236862C>Trev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga11/17/1611/17/16151Genomicunknown
ss2282932220HUMAN_LONGEVITY|HLI-6-31269085-C-Trev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga11/18/1611/18/16150Genomicunknown
ss2451303950TOPMED|6_31236862_C/Trev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga11/20/1611/20/16150Genomicunknown
ss2707394521GRF|rs1049724rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga02/13/1702/13/17151Genomicunknown
ss2711068493ILLUMINA|Consortium-OncoArray_15047405_A_rs1049724-131_T_F_2146682330rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga03/22/1703/22/17151Genomicunknown
ss2735644408GNOMAD|exomes_rs1049724rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga05/17/1705/17/17151Genomicunknown
ss2747580154GNOMAD|coding_rs1049724rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga05/17/1705/17/17151Genomicunknown
ss2837399963GNOMAD|rs1049724rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga05/18/1705/18/17151Genomicunknown
ss2998785470SWEGEN|NC_000006.11:g.31236862C>Trev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga05/30/1705/30/17151Genomicunknown
ss3022597182ILLUMINA|MEGA_Consortium_v2_15070954_A2_JHU_6.31236861-1_T_R_2232771101rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga06/28/1706/28/17151Genomicunknown
ss3493788541TOPMED|TOPMed_freeze_5?chr6:31,269,085rev/C/Tacgcagacacattcaggtgcctttgagaaagagatgccagaggctcttga10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1049724|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 GAGATTCTGG GGAGCTGAAG TGGTCGGGGG TGGGGCAGAG GGAAAAGGCC TGGGTAATGG
 GGATTCTTTG ATTGGGACGT TTCGAGTGTG TGGTGGGCCG TTCAGAGTGT CATCGCTTAC
 CATGACTGAC CTGAATTTGT TCATGACTAT TGTGTTCTGT AGCCTGAGAC AGCTGCCTGT
 GTGGGACTGA GATGCAGGAT TTCTTCACAC CTCTCCTTTG TGACTTCAAG AGCCTCTGGC
 ATCTCTTTCT
 R
 CAAAGGCACC TGAATGTGTC TGCGTTCCTG TTAGCATAAT GTGAGGAGGT GGAGAGACAG
 CCCACCCCCG TGTCCACCGT GACCCCTGTC CCCACACTGA CCTGTGTTCC CTCCCCGATC
 ATCTTTCCTG TTCCAGAGAG GTGGGGCTGG ATGTCTCCAT CTCTGTCTCA AATTCATGGT
 GCACTGAGCT GCAACTTCTT ACTTCCCTAA TGAAGTTAAG AACCTGAATA TAAATTTGTG
 TTCTCAAATA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000006 Hs.248038 Hs.277477
dbSNP Blast Analysis
UniGene Cluster ID
534125

dbMHC locus: HLA-C
  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1049724 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/G
G/G
HWPA
G
ss116389865YRI 2IG1.00000000 0.500000000.50000000
ss1319545445EAS 1008AF 0.001000000.99900001
EUR 1006AF 0.044700000.95529997
AFR 1322AF 0.080900000.91909999
AMR 694AF 0.027400000.97259998
SAS 978AF 0.006100000.99390000
ss1688227522ExAc_Aggregated_Populations118764AF 0.039591120.96040887
ss201614006BANTU 2IG1.00000000 0.500000000.50000000
ss491884631CSAgilent 593GF0.094000000.906000021.000000000.047000000.95300001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.078+/-0.1810000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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