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Reference SNP (refSNP) Cluster Report: rs1377638                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.2192/1098 (1000 Genomes)
T=0.1538/19310 (TOPMED)
HGVS Names
  • CM000664.2:g.5153392C>T
  • NC_000002.11:g.5293525C>T
Links , Linkout
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 ss21704062 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1377638 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
ss2166685TSC-CSHL|TSC0535874fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg10/19/0010/25/0688Genomic95 %
ss21704062SSAHASNP|WGSA-200403-chr2.chr2.NT_005334.14_127660byFreqfwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg03/20/0410/26/06121Genomicunknown
ss23911309PERLEGEN|afd1219830byFreqfwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg08/10/0409/13/04123Genomicunknown
ss44282034ABI|hCV9015033fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg07/18/0507/18/05126Genomicunknown
ss66671334ILLUMINA|HumanHap300v1.1_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg11/09/0611/09/06127Genomicunknown
ss67090159ILLUMINA|HumanHap550v1.1_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg11/14/0611/14/06127Genomicunknown
ss67423987ILLUMINA|HumanHap650Yv1.0_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg11/14/0611/14/06127Genomicunknown
ss68395946CSHL-HAPMAP|perlegen:assay:24708.1219830:1byFreqfwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg01/11/0701/16/07127NAunknown
ss70427611ILLUMINA|HumanHap300v2.0_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg04/18/0711/18/07127Genomicunknown
ss70610835ILLUMINA|HumanHap550v3.0__rs1377638rev/TA/Gcaggcagctttaggaatcggagcaaaaccagtgtgtggtggactagaaaccaagacaaca04/20/0703/30/08130Genomicunknown
ss71158222ILLUMINA|HumanHap650Yv3.0_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg04/23/0704/23/07127Genomicunknown
ss75603925ILLUMINA|ILMN_Human_1M_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg08/28/0708/29/07129Genomicunknown
ss83745462KRIBB_YJKIM|KHS533254fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg12/04/0712/05/07130Genomicunknown
ss97008992HUMANGENOME_JCVI|1103658011216fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg03/28/0803/28/08130Genomicunknown
ss103453670BGI|BGI_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg06/06/0806/17/09131Genomicunknown
ss1091857971000GENOMES|CEU.trio.12.15.2008_305329_chr2_5210976fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg12/16/0812/16/08130Genomicunknown
ss1122092921000GENOMES|NA19240_2008_12_16_277698_chr2_5210976fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg12/17/0812/17/08130Genomicunknown
ss121668360ILLUMINA|HumanCNV370v1_C_rs1377638fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg04/14/0904/14/09131Genomicunknown
ss135853330ENSEMBL|ENSSNP1795358byFreqfwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg12/08/0803/07/10131Genomicunknown
ss153400532ILLUMINA|Human610_Quadv1_B_rs1377638-128_T_R_1501660986rev/TA/Gcaggcagctttaggaatcggagcaaaaccagtgtgtggtggactagaaaccaagacaaca06/18/0906/19/09131Genomicunknown
ss159262439ILLUMINA|Human660W-Quad_v1_A_rs1377638-128_T_R_1501660986rev/TA/Gcaggcagctttaggaatcggagcaaaaccagtgtgtggtggactagaaaccaagacaaca07/06/0907/06/09131Genomicunknown
ss163034466COMPLETE_GENOMICS|NA19240_36_chr2_5210976fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg09/29/0909/29/09132Genomicunknown
ss170434906ILLUMINA|HumanCNV370-Quadv3_C_rs1377638-128_T_R_1501660986rev/TA/Gcaggcagctttaggaatcggagcaaaaccagtgtgtggtggactagaaaccaagacaaca10/01/0910/03/09132Genomicunknown
ss172455225ILLUMINA|Human1M-Duov3_B_rs1377638-128_T_R_1501660986rev/TA/Gcaggcagctttaggaatcggagcaaaaccagtgtgtggtggactagaaaccaagacaaca10/01/0910/02/09132Genomicunknown
ss199983504BUSHMAN|BUSHMAN-chr2-5210975byFreqfwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg02/16/1009/05/14132Genomicunknown
ss205793211BCM-HGSC-SUB|BCM_CMT_1011-382473fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg03/15/1003/16/10132Genomicunknown
ss2190402881000GENOMES|pilot_1_YRI_849971_chr2_5210976fwd/C/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg04/22/1004/22/10132Genomicunknown
ss2310200451000GENOMES|pilot_1_CEU_624674_chr2_5210976fwd/C/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg05/01/1005/01/10132Genomicunknown
ss2386093331000GENOMES|pilot_1_CHB+JPT_494410_chr2_5210976fwd/C/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg05/01/1005/01/10132Genomicunknown
ss276334757GMI|GMI_AK_SNP_654924fwd/C/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg12/16/1012/16/10137Genomicunknown
ss292317907PJP|SNP_1824265_chr2_5210976fwd/C/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg01/21/1101/21/11134Genomicunknown
ss491314898EXOME_CHIP|.GWAS._31125_chr_2_5293525fwd/BC/Ttgttgtcttggtttctagtccaccacacactggttttgctccgattcctaaagctgcctg03/05/1203/05/12137Genomicunknown
ss536860936ILLUMINA|HumanOmni5-4v1_B_rs1377638-131_T_R_1885472072fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct06/22/1208/28/15146Genomicunknown
ss555325677TISHKOFF|snp_chr2_5293525fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct11/22/1211/23/12138Genomicunknown
ss648904106SSMP|2_5293525fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct12/14/1202/10/15138Genomicunknown
ss780681871ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs1377638-131_T_R_1990488604fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct05/30/1307/09/15146Genomicunknown
ss783355202ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs1377638-131_T_R_1990488604fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct05/31/1306/19/15146Genomicunknown
ss825396885ILLUMINA|HumanCNV370v1_C_rs1377638-126_T_R_IFB1135736998:0fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct06/24/1311/21/14144Genomicunknown
ss976443562EVA-GONL|EVA-GONL_rs1377638fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct04/23/1404/23/14142Genomicunknown
ss1068825362JMKIDD_LAB|HGDP_WGS_chr2_5293525fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct07/10/1407/10/14142Genomicunknown
ss12957410521000GENOMES|PHASE3_V1_6670245fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct08/16/1408/16/14142Genomicunknown
ss1428465465DDI|DDI_rs1377638fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct11/04/1411/04/14144Genomicunknown
ss1578720829EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1377638fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct02/19/1502/20/15144Genomicunknown
ss1585842503EVA_DECODE|EVA_DECODE_2_5210976_44389_rs1377638fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct03/02/1503/02/15144Genomicunknown
ss1602715187EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_5293525_3673440fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct03/04/1503/04/15144Genomicunknown
ss1645709220EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_5293525_3673440fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct03/04/1503/04/15144Genomicunknown
ss1712427675EVA_SVP|EVA_SVP_122227fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct03/12/1503/12/15144Genomicunknown
ss1752361239ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs1377638-131_T_R_1990488604fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct05/27/1506/09/15146Genomicunknown
ss1796197137HAMMER_LAB|Hsieh_713084fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct07/15/1507/15/15146Genomicunknown
ss1917745638ILLUMINA|HumanExome-12v1-1_B_exm-rs1377638-131_T_R_1990488604fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct10/16/1510/16/15147Genomicunknown
ss1919673264WEILL_CORNELL_DGM|SNV:chr2:5293525fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct10/16/1510/16/15147Genomicunknown
ss1946031271ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs1377638-131_T_R_1990488604fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct10/29/1510/29/15147Genomicunknown
ss1958384520ILLUMINA|exm-rs1377638-131_T_R_1990488604fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct11/13/1511/13/15147Genomicunknown
ss1968683349GENOMED|rs1377638fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct02/16/1602/16/16147Genomicunknown
ss2020363356JJLAB|SNP865911fwd/BC/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct08/29/1608/30/16149Genomicunknown
ss2148405821USC_VALOUEV|NC_000002.11:g.5293525C>Tfwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct11/17/1611/17/16150Genomicunknown
ss2227169141HUMAN_LONGEVITY|HLI-2-5153392-C-Tfwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct11/18/1611/18/16150Genomicunknown
ss2393072644TOPMED|2_5293525_C/Tfwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct11/19/1611/19/16150Genomicunknown
ss2624697139SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV551916fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct01/06/1701/06/17151Genomicunknown
ss2633565867ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs1377638-131_T_R_2130fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct02/02/1702/02/17151Genomicunknown
ss2635085952ILLUMINA|Cancer_BeadChip_11459870_A_rs1377638-128_T_R_1775074424fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct02/02/1702/02/17151Genomicunknown
ss2702961549GRF|rs1377638fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct02/13/1702/13/17151Genomicunknown
ss2769276290GNOMAD|rs1377638fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct05/17/1705/17/17151Genomicunknown
ss2985157961AFFY|Axiom_PsorMich_Affx-20202379fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct05/24/1705/24/17151Genomicunknown
ss2988912009SWEGEN|NC_000002.11:g.5293525C>Tfwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct05/30/1705/30/17151Genomicunknown
ss3021935837ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs1377638-131_T_R_1990488604fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct06/28/1706/28/17151Genomicunknown
ss3023946542BIOINF_KMB_FNS_UNIBA|2.5153392C>Tfwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct07/05/1707/05/17151Genomicunknown
ss3298249990TOPMED|TOPMed_freeze_5?chr2:5,153,392fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct10/02/1710/02/17151Genomicunknown
ss3344054767CSHL|rs1377638fwd/C/Ttcttggtttctagtccaccacacactggttttgctccgattcctaaagct10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1377638|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 ACACTGTCCT TACTCAACTT ACAGTAGTTC TTATGAATAA ATGATTTGTT TCTGTTGTGT
 ACCATTGGTG CATTACCAGA GGACCGAAAT AGTTTTTTGT CAGTTTCAGT AGTTTGCTTT
 GTGAGAGTAG GATTTGTCAA CCTCTTCAAT CTGTAATGCC AAAAGTTAGG AGTTCTCACA
 CATCGTTTTT TTGGATTCTG TATCTACTGC AAACTCTATG TTTCTGTCTT TCCTTTCTCT
 TCACACCCAG ACTTCTTAAT TATTATCTCT ACTTCATGTT TCCATTTTCG TATTTCCCAT
 TCACTTTTTG GATTTTAAAA TCTGACTTCC AGGTTAATCA TGACATACAA GCATATCCTG
 TGAATATCCC TGGTGACAGT CCTATTGATA CATTCAGTAG AACATTTTGA TACATAGTTT
 TTCTTGTATC ACCTCCCACT TTTGAATAGG GCCCCATCCT AGAAACACTC TGTTGTCTTG
 GTTTCTAGTC CACCACACAC
 Y
 TGGTTTTGCT CCGATTCCTA AAGCTGCCTG TTTCAGACTC TGGTATGGGC TGAGGAGTCC
 TCACCTGCTA GTCCTCCCCC GACTGTGCTC CAGCCACGTC ATTCTGGTTG CATTACCCCT
 GCCTCCTCCT GTGGATCTCC AAAGACTGtt tttacctctg atctagatcc tttacctgag
 cttcagaatt tatcttcagt tgctttctgg actctccatt tgattcctca tcccacagac
 atgcaaaatt cttaatgtcc aaaactgaac ctatgatttt ccataacaag tccatatctc
 ctgtcatacc cccattttaa tgaataacac ttccatcaac caagttctgc tctgggtcca
 tggatgccat tcttcacttc actACATTGA AGTACACTTA AAATTTAATG ACCATGAATC
 ATTTCATTTC CCTACTCCCC AGCCACTTCC TCCAGTCCCC ATTGCCACAT CCCTGGGTGG
 ACCACAGTCA GTGCTAGCAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005334 ABBA01023881
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1295741052EAS 1008AF 0.610099970.38990000
EUR 1006AF 0.850899990.14910001
AFR 1322AF 0.885800000.11420000
AMR 694AF 0.770899950.22910000
SAS 978AF 0.749499980.25049999
ss135853330ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ENSEMBL_celera 6IG0.66666669 0.33333334 0.666666690.33333334
ss163034466YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss199983504BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss21704062HapMap-CEUEuropean 226IG0.769911530.194690270.035398230.150222000.867256640.13274336
HapMap-HCBAsian 86IG0.325581400.465116290.209302320.751830000.558139560.44186047
HapMap-JPTAsian 172IG0.372093020.511627910.116279070.402784000.627906980.37209302
HapMap-YRISub-Saharan African 226IG0.752212410.221238940.026548670.527089000.862831830.13716814
HAPMAP-ASW 98IG0.836734710.16326530 1.000000000.918367330.08163265
HAPMAP-CHBAsian 82IG0.292682920.585365830.121951220.200325000.585365830.41463414
HAPMAP-CHD 170IG0.400000010.447058830.152941180.751830000.623529430.37647060
HAPMAP-GIH 176IG0.636363630.306818190.056818180.479500000.789772750.21022727
HAPMAP-LWK 180IG0.788888870.200000000.011111111.000000000.888888900.11111111
HAPMAP-MEX 100IG0.699999990.259999990.040000000.583882000.829999980.17000000
HAPMAP-MKK 286IG0.615384640.363636370.020979020.150222000.797202830.20279720
HAPMAP-TSI 176IG0.715909060.261363630.022727271.000000000.846590940.15340909
ss219040288pilot_1_YRI_low_coverage_panel 118AF 0.864406760.13559322
ss231020045pilot_1_CEU_low_coverage_panel 120AF 0.858333350.14166667
ss238609333pilot_1_CHB+JPT_low_coverage_panel 120AF 0.600000020.40000001
ss23911309AFD_EUR_PANELEuropean 48IG0.583333310.41666666 0.438578000.791666690.20833333
AFD_AFR_PANELAfrican American 46IG0.956521750.04347826 1.000000000.978260870.02173913
AFD_CHN_PANELAsian 48IG0.250000000.541666690.208333330.751830000.520833310.47916666
ss97008992J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.342+/-0.2320000ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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