NCBI
dbSNP
dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
Re-designed RefSNP Report page!
Clean, modern design that makes it easy to find the information that you are looking for. Report any problems by sending us an email.
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP (refSNP) Cluster Report: rs6430538                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.1891/947 (1000 Genomes)
C=0.3565/44763 (TOPMED)
HGVS Names
  • CM000664.2:g.134782397C>T
  • NC_000002.11:g.135539967C>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 ss276691451 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6430538 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
ss9957515BCM_SSAHASNP|chr2.NT_005058.13_4148866byFreqfwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg06/27/0305/17/04116Genomicunknown
ss11479007WI_SSAHASNP|chr2.NT_005058.13_4148866fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg07/03/0310/10/03116Genomicunknown
ss19454490CSHL-HAPMAP|CSHL-HuDD-200402.chr2.NT_005058.14_4148976fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg02/20/0403/04/04120Genomicunknown
ss44262209ABI|hCV2688714fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg07/18/0507/18/05126Genomicunknown
ss66182665AFFY|SNP_A-2229014byFreqrev/TA/Gctagcactgtaagatataagagtgtgttgttc10/27/0603/31/08127Genomicunknown
ss75241996ILLUMINA|ILMN_Human_1M_rs6430538fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg08/28/0708/29/07129Genomicunknown
ss76249389AFFY|AFFY_6_1M_SNP_A-2229014byFreqrev/TA/Gctagcactgtaagatataagagtgtgttgttc08/28/0703/07/10130Genomicunknown
ss82226962KRIBB_YJKIM|KHS210649fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg11/30/0712/02/07130Genomicunknown
ss85104449HGSV|Cor18517_SNV_20070510.chr2_135373699fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg12/06/0712/08/07130Genomicunknown
ss91357089BCMHGSC_JDW|JWB-1310709fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg02/26/0803/01/08129Genomicunknown
ss106120954BGI|BGI_rs6430538fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg09/13/0806/18/09130Genomicunknown
ss1109600691000GENOMES|NA19240_2008_12_16_432106_chr2_135256437fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg12/17/0812/17/08130Genomicunknown
ss117886225ILLUMINA-UK|NA18507_000169336_NCBI36.1_chr2_135256437fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg01/19/0901/20/09130Genomic99 %
ss138536685ENSEMBL|ENSSNP6737165fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg05/15/0905/18/09131Genomicunknown
ss157713975GMI|GMI_SNP_76247163fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg06/24/0906/25/09131Genomicunknown
ss160772421ILLUMINA|HumanOmni1-Quad_v1-0_B_rs6430538-128_T_R_1514220875rev/TA/Gcagagttccaacctctagcactgtaagatataagagtgtgttgttcgaagccaccaggct08/04/0910/04/09131Genomicunknown
ss161184979ENSEMBL|ENSSNP1614760fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg09/24/0909/24/09131Genomicunknown
ss164284966COMPLETE_GENOMICS|NA19240_36_chr2_135256437fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg09/29/0909/29/09132Genomicunknown
ss165271610COMPLETE_GENOMICS|NA07022_36_chr2_135256437fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg09/29/0909/30/09132Genomicunknown
ss172970779AFFY|GenomeWideSNP_5_SNP_A-2229014rev/TA/Gctagcactgtaagatataagagtgtgttgttc10/01/0910/02/09132Genomicunknown
ss173998570ILLUMINA|Human1M-Duov3_B_rs6430538-128_T_R_1514220875rev/TA/Gcagagttccaacctctagcactgtaagatataagagtgtgttgttcgaagccaccaggct10/01/0910/04/09132Genomicunknown
ss201091303BUSHMAN|BUSHMAN-chr2-135256436fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg02/16/1003/07/10132Genomicunknown
ss205845937BCM-HGSC-SUB|BCM_CMT_1011-426121fwd/BC/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg03/15/1003/16/10132Genomicunknown
ss2195255811000GENOMES|pilot_1_YRI_1335264_chr2_135256437fwd/C/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg04/22/1004/22/10132Genomicunknown
ss2313723671000GENOMES|pilot_1_CEU_976996_chr2_135256437fwd/C/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg05/01/1005/01/10132Genomicunknown
ss2388787471000GENOMES|pilot_1_CHB+JPT_763824_chr2_135256437fwd/C/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg05/01/1005/01/10132Genomicunknown
ss276691451GMI|GMI_AK_SNP_1011660fwd/C/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg12/16/1012/16/10137Genomicunknown
ss292373260PJP|SNP_1879618_chr2_135256437fwd/C/Tagcctggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaactctg01/21/1101/21/11134Genomicunknown
ss481237672ILLUMINA|HumanOmni2.5-4v1_B_rs6430538-128_T_R_1780690137fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa01/30/1210/28/16137Genomicunknown
ss481261305ILLUMINA|HumanOmniExpress-12v1_C_rs6430538-131_T_R_1856959735fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa01/30/1210/27/16137Genomicunknown
ss482247204ILLUMINA|HumanOmni1-Quad_v1-0_C_rs6430538-131_T_R_1865236565fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa01/30/1208/28/15146Genomicunknown
ss485414179ILLUMINA|HumanOmni2.5-4v1_D_rs6430538-131_T_R_1856959735fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa01/30/1210/28/16137Genomicunknown
ss537347410ILLUMINA|HumanOmni5-4v1_B_rs6430538-131_T_R_1894951122fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa06/22/1208/28/15146Genomicunknown
ss555893333TISHKOFF|snp_chr2_135539967fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa11/22/1211/23/12138Genomicunknown
ss649520597SSMP|2_135539967fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa12/14/1202/10/15138Genomicunknown
ss778939352ILLUMINA|HumanOmni25Exome-8v1_A_rs6430538-131_T_R_1865236565fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa05/30/1307/09/15146Genomicunknown
ss783152526ILLUMINA|HumanOmni2.5-4v1_H_rs6430538-131_T_R_1856959735fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa05/30/1307/28/15146Genomicunknown
ss784108457ILLUMINA|HumanOmniExpressExome-8v1_A_rs6430538-131_T_R_1894951122fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa05/31/1306/19/15146Genomicunknown
ss832411750ILLUMINA|HumanOmniExpress-12v1_H_rs6430538-131_T_R_1856959735fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa09/17/1306/18/15146Genomicunknown
ss834401040ILLUMINA|HumanOmni2.5-8v1_A_rs6430538-131_T_R_1865236565fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa09/18/1307/28/15146Genomicunknown
ss977385433EVA-GONL|EVA-GONL_rs6430538fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa04/23/1404/23/14142Genomicunknown
ss1069515948JMKIDD_LAB|HGDP_WGS_chr2_135539967fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa07/10/1407/10/14142Genomicunknown
ss12994336471000GENOMES|PHASE3_V1_10506736fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa08/16/1408/16/14142Genomicunknown
ss1428748822DDI|DDI_rs6430538fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa11/04/1411/04/14144Genomicunknown
ss1579097431EVA_GENOME_DK|EVA_GENOME_DK_snv_rs6430538fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa02/19/1502/20/15144Genomicunknown
ss1586813872EVA_DECODE|EVA_DECODE_2_135256437_1015783_rs6430538fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa03/02/1503/02/15144Genomicunknown
ss1604620154EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_135539967_5757675fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa03/04/1503/04/15144Genomicunknown
ss1647614187EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_135539967_5757675fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa03/04/1503/04/15144Genomicunknown
ss1712491938EVA_SVP|EVA_SVP_186490fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa03/12/1503/12/15144Genomicunknown
ss1752312195ILLUMINA|OmniExpressExome-8v1-1_B_rs6430538-131_T_R_1894951122fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa05/27/1506/09/15146Genomicunknown
ss1797572173HAMMER_LAB|Hsieh_1111580fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa07/15/1507/15/15146Genomicunknown
ss1920643823WEILL_CORNELL_DGM|SNV:chr2:135539967fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa10/16/1510/16/15147Genomicunknown
ss1946052476ILLUMINA|HumanCoreExome-12v1-0_C_rs6430538-131_T_R_1894951122fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa10/29/1510/29/15147Genomicunknown
ss1958460764ILLUMINA|rs6430538-131_T_R_1894951122fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa11/13/1511/13/15147Genomicunknown
ss1968894970GENOMED|rs6430538fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa02/16/1602/16/16147Genomicunknown
ss2020845930JJLAB|SNP1348485fwd/BC/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa08/29/1608/30/16149Genomicunknown
ss2148911805USC_VALOUEV|NC_000002.11:g.135539967C>Tfwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa11/17/1611/17/16150Genomicunknown
ss2234491436HUMAN_LONGEVITY|HLI-2-134782397-C-Tfwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa11/18/1611/18/16150Genomicunknown
ss2400850500TOPMED|2_135539967_C/Tfwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa11/19/1611/19/16150Genomicunknown
ss2624929608SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV849956fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa01/06/1701/06/17151Genomicunknown
ss2633676200ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs6430538-131_T_R_18949511fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa02/02/1702/02/17151Genomicunknown
ss2703536125GRF|rs6430538fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa02/13/1702/13/17151Genomicunknown
ss2710912429ILLUMINA|Consortium-OncoArray_15047405_A_rs6430538-131_T_R_1894951122fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa03/22/1703/22/17151Genomicunknown
ss2779962038GNOMAD|rs6430538fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa05/17/1705/17/17151Genomicunknown
ss2990472031SWEGEN|NC_000002.11:g.135539967C>Tfwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa05/30/1705/30/17151Genomicunknown
ss3024186350BIOINF_KMB_FNS_UNIBA|2.134782397C>Tfwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa07/05/1707/05/17151Genomicunknown
ss3323671302TOPMED|TOPMed_freeze_5?chr2:134,782,397fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa10/02/1710/02/17151Genomicunknown
ss3344493812CSHL|rs6430538fwd/C/Tggtggcttcgaacaacacactcttatatcttacagtgctagaggttggaa10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6430538|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 AAAACTGGTT AGAAGAAAAA TGCTGCATTA GTGGTTCCCC AAGTGGTGGA GTTATGGGTG
 ATTTTTATTC TCTGTTTTCC TATATTTTCT AATTTTCTAG AGTGCACATG TAACATATAT
 CTATTGCCTA AGGAAAAAAG TGTTTATTTC AAAAAAAGAT CCCCCTCCCT AGGACAGTTA
 GGTGTATTCT CATCAGTCAG GTAACTGTCA TCATTTACTT TTGCAAGGAT GCCACCTTGG
 TTGGCTCTCT GTTGGGCCAG AGAGAGTAAA ATTTCTCTTC CTGTAAATGC ATTTTCACAG
 TGTCATGACT TTCAAGGATT TGGTTCACGT TCTTCCTGGG TGATTAACAC AAAAGCAACA
 GCACCAGGGT CAGGGTTTTA GGTCTCCTGG CAGCGTGCCC CATAGCGGCT TTCTCTTTTC
 TCAAAAACTA GTCTATTCGT TTCCTATGGC CGCTGTAACT AATCACCAGT AGCCTGGTGG
 CTTCGAACAA CACACTCTTA
 Y
 TATCTTACAG TGCTAGAGGT TGGAACTCTG AAATGGGTCT CACTGGGCTA AAATTAAGGT
 GTCACCAATC CTGGGTTCCT ATCGGAGGCT CTAGGGGAGA ATCTGTTCCC TTGCTTTTTC
 TAGCTTTATG AAGCTGCCTG TGTTCCTTGG ATCATGGTCT CCTCCTCCAT CTTCAGAGAC
 AGCATCAAAG CATTTTCAGC TCTCACTCTG CTTCTGTTCT ATCTCCTTGT CTCACTCTGG
 CCTTCCTGCC TCTTTCTTGA TGGCACCTTC TGATTACATT GGGCCCACCT GGATAATCCA
 GGGTAACTGC CCATCTCAAT GTCCTTAACT TAATGACATC TGCAAAGTCC TTTTGGCCAT
 GTATGGTAAC ATATTCACAG GTTCTGGGGA TTAAGACACA GACGTCTTTG ATTGGGGGTG
 GGTGGGAAAG AATGTTCTGT CTACCACAGC CAGGTTTGAC AGAACAGCTT GAAACTGGGA
 AGTTTCATCC CGCTTGCATA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005058
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/T
HWPC
T
ss117886225YRI 2IG 1.00000000 1.00000000
ss1299433647EAS 1008AF 0.015900000.98409998
EUR 1006AF 0.503000020.49700001
AFR 1322AF 0.019700000.98029995
AMR 694AF 0.295399990.70459998
SAS 978AF 0.198400010.80159998
ss138536685ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss161184979ENSEMBL_celera 2IG 1.00000000 1.00000000
ss164284966YRISub-Saharan African 2IG 1.00000000 1.00000000
ss165271610CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss201091303BANTU 1IG 1.00000000 1.00000000
ss219525581pilot_1_YRI_low_coverage_panel 118AF 1.00000000
ss231372367pilot_1_CEU_low_coverage_panel 120AF 0.591666640.40833333
ss238878747pilot_1_CHB+JPT_low_coverage_panel 120AF 0.025000000.97500002
ss66182665HapMap-CEUEuropean 118IG0.355932210.49152541 0.152542371.000000000.601694940.39830509
HapMap-HCBAsian 90IG 0.04444445 0.955555561.000000000.022222220.97777778
HapMap-JPTAsian 90IG 0.06666667 0.933333341.000000000.033333340.96666664
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss76249389ICMHP 6IG0.333333340.33333334 0.33333334 0.500000000.50000000
ss9957515HapMap-CEUEuropean 226IG0.389380540.46902654 0.141592921.000000000.623893800.37610620
HapMap-HCBAsian 86IG 0.02325581 0.976744171.000000000.011627910.98837209
HapMap-JPTAsian 172IG 0.09302326 0.906976761.000000000.046511630.95348835
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 96IG0.020833330.10416666 0.875000000.150222000.072916660.92708331
HAPMAP-CHBAsian 82IG 0.02439024 0.975609781.000000000.012195120.98780489
HAPMAP-CHD 170IG 0.01176471 0.988235291.000000000.005882350.99411762
HAPMAP-GIH 176IG0.034090910.26136363 0.704545440.654721000.164772730.83522725
HAPMAP-MEX 98IG0.102040820.36734694 0.530612230.527089000.285714300.71428573
HAPMAP-MKK 286IG 0.02097902 0.979020951.000000000.010489510.98951048
HAPMAP-TSI 172IG0.023255810.40697673 0.569767420.150222000.226744190.77325583
ENSEMBL_Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.307+/-0.2430000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement