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Reference SNP (refSNP) Cluster Report: rs2303428                 ** With Benign ,Uncertain significance allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/142
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G/T (FWD)
Allele Origin:C:germline
T:germline
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign ,Uncertain significance allele [ClinVar]
MAF/MinorAlleleCount:C=0.1320/661
MAF Source:1000 Genomes
HGVS Names
  • NC_000002.11:g.47703500T>A
  • NC_000002.11:g.47703500T>C
  • NC_000002.11:g.47703500T>G
  • NC_000002.12:g.47476361T>A
  • NC_000002.12:g.47476361T>C
  • NC_000002.12:g.47476361T>G
  • NG_007110.2:g.78238T>A
  • NG_007110.2:g.78238T>C
  • NG_007110.2:g.78238T>G
  • NM_000251.2:c.2006-6T>A
  • NM_000251.2:c.2006-6T>C
  • NM_000251.2:c.2006-6T>G
  • NM_001258281.1:c.1808-6T>A
  • NM_001258281.1:c.1808-6T>C
  • NM_001258281.1:c.1808-6T>G
  • XM_005264332.1:c.2006-6T>A
  • XM_005264332.1:c.2006-6T>C
  • XM_005264332.1:c.2006-6T>G
  • XM_005264333.1:c.1856-6T>A
  • XM_005264333.1:c.1856-6T>C
  • XM_005264333.1:c.1856-6T>G
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 ss276455355 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2303428 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
ss3250003YUSUKE|IMS-JST060088fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac09/05/0110/10/03100Genomicunknown
ss6903874SNP500CANCER|MSH2-03byFreqfwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac02/14/0304/07/04113Genomicunknown
ss16861693CSHL-HAPMAP|CSHL-HuAA-200402.chr2.NT_022184.13_26519432fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac02/17/0403/04/04120Genomicunknown
ss21643758SSAHASNP|WGSA-200403-chr2.chr2.NT_022184.13_26519432fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac03/20/0403/20/04121Genomicunknown
ss23141053EGP_SNPS|MSH2-074808byFreqfwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac04/22/0404/28/04126Genomicunknown
ss23856128PERLEGEN|afd1258476byFreqfwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac08/10/0409/13/04123Genomicunknown
ss44170260ABI|hCV11804019byFreqfwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac07/18/0511/03/06126Genomicunknown
ss65944951AFFY|SNP_A-1667880rev/TA/Gtttacctcccatattggggcctacaaacaaattatatcagaaagcaagat10/26/0610/26/06127Genomicunknown
ss66859545EGP_SNPS|MSH2_074808byFreqfwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac11/09/0612/16/06127Genomicunknown
ss68406375CSHL-HAPMAP|perlegen:assay:24707.1258476:1byFreqfwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac01/11/0701/16/07127NAunknown
ss76710922AFFY|AFFY_6_1M_SNP_A-8572414rev/TA/Gcatattggggcctacaaacaaattatatcaga08/28/0708/30/07130Genomicunknown
ss76863000CGM_KYOTO|3052fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac09/12/0709/12/07129cDNAunknown
ss96394523HUMANGENOME_JCVI|1103658090809fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac03/26/0803/26/08130Genomicunknown
ss103491169BGI|BGI_rs2303428fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac06/06/0806/17/09131Genomicunknown
ss104869142KRIBB_YJKIM|KHS1261460fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac07/10/0807/10/08130Genomicunknown
ss135861643ENSEMBL|ENSSNP1789271byFreqfwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac12/08/0803/07/10131Genomicunknown
ss166554591COMPLETE_GENOMICS|NA20431_36_chr2_47557004fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac09/30/0909/30/09132Genomicunknown
ss2311533011000GENOMES|pilot_1_CEU_757930_chr2_47557004fwd/C/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac05/01/1005/01/10132Genomicunknown
ss2387114451000GENOMES|pilot_1_CHB+JPT_596522_chr2_47557004fwd/C/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac05/01/1005/01/10132Genomicunknown
ss276455355GMI|GMI_AK_SNP_775524fwd/C/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac12/16/1012/16/10137Genomicunknown
ss292262662PJP|SNP_1769020_chr2_47557004fwd/C/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac01/21/1101/21/11134Genomicunknown
ss472343241CORRELAGEN|MSH2_2006-6T_C_092410fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac11/18/1111/22/11136Genomicunknown
ss4898152001000GENOMES|20110521_exome_341211_chr2_47703500fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac02/10/1202/21/12137Genomicunknown
ss491783017CLINSEQ_SNP|SNV-chr2-47557004byFreqfwd/BC/Tatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaa03/06/1209/05/14137Genomicunknown
ss535927098ILLUMINA|HumanOmni5-4v1_B__kgp6448645-0_T_R_1901936538rev/TA/Ggttgatttacctcccatattggggcctacaaacaaattatatcagaaagcaagattttaa06/22/1206/29/12138Genomicunknown
ss538293072MMR_WOODS|MSH2_complex_28fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac07/31/1210/24/12137Genomicunknown
ss538293073MMR_WOODS|MSH2_c.2006-6T>Gfwd/BG/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac07/31/1210/24/12137Genomicunknown
ss538293074MMR_WOODS|MSH2_complex_40fwd/A/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac07/31/1210/24/12137Genomicunknown
ss649123279SSMP|2_47703500fwd/BC/Tatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaa12/14/1202/10/15138Genomicunknown
ss712415896NHLBI-ESP|ESP6500SI-chr2-47703500fwd/BC/Tttaaaatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaatcaac02/20/1302/20/13138Genomicunknown
ss974442143JMKIDD_LAB|KhoeSan_Exomes_chr2_47703500fwd/BC/Tatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaa03/06/1403/06/14142Genomicunknown
ss976786324EVA-GONL|EVA-GONL_rs2303428fwd/BC/Tatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaa04/23/1404/23/14142Genomicunknown
ss1067437165JMKIDD_LAB|HGDP_exomes_chr2_47703500fwd/BC/Tatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaa07/09/1407/09/14142Genomicunknown
ss1069082455JMKIDD_LAB|HGDP_WGS_chr2_47703500fwd/BC/Tatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaa07/10/1407/10/14142Genomicunknown
ss12970539771000GENOMES|PHASE3_V1_8033690fwd/C/Tatcttgctttctgatataatttgtttgtaggccccaatatgggaggtaaa08/16/1408/16/14142Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2303428|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=142
 CAAATAAATT GCCTGTTTTT CAAAAGAAAG ATCATGTCTT CAGGTTTTTG TGTGGGGTTT
 AAATGATTCG AAAGATTTGA CCATACTGAT ACATTCACTA GTAACCTTAG TTACTAATGA
 GTAATGGTTT TGAGTTAATC AGTTAGGCCT GAACTACTTT TCTGGAAGTT AGTAAATTAT
 CTCACAGGCA GCCCTGTGAG CCATGGGAAA ATGTGTATAT GGTCTTTCTA GGCCACAGTC
 AAATTACAGG TATATTTGTC ATGGCTTCTC TTGATGAAAG GCCCAGTATC GGTTTGTCTG
 AAGATATATA ATAGCATTGC TTTTGGGGGT AATATGGGCA GTAACTCTGT CCACATCTTT
 GGGCAGGCTG TGGTTCTGCC TTTATATGCT ATGTCAGTGT AAACCTACGC GATTAATCAT
 CAGTGTACAG TTTAGGACTA ACAATCCATT TATTAGTAGC AGAAAGAAGT TTAAAATCTT
 GCTTTCTGAT ATAATTTGTT
 N
 TGTAGGCCCC AATATGGGAG GTAAATCAAC ATATATTCGA CAAACTGGGG TGATAGTACT
 CATGGCCCAA ATTGGGTGTT TTGTGCCATG TGAGTCAGCA GAAGTGTCCA TTGTGGACTG
 CATCTTAGCC CGAGTAGGGG CTGGTGACAG TCAATTGAAA GGAGTCTCCA CGTTCATGGC
 TGAAATGTTG GAAACTGCTT CTATCCTCAG GTAAGTGCAT CTCCTAGTCC CTTGAAGATA
 GAAATGTATG TCTCTGTCCT GTGAGAAGGA AAAGTATATT TGCAGATTCT CATGTAAAAA
 CATCTGAGAA TGTTTGTCTT AGTTTAATAG TTGTTTTCCT GTGGACTTTA TATACTTTGT
 ATTGTCTTAA AAGAGTGATT GATGGTAGCT ACGGAAAACT TTGATTTTTA AAATTGTCTC
 TTTAAGTAGA CAATTTATAA GCTACTGGTA CGAGTTCACC TTATAAATCT CCACTACCAT
 GTTTTTGCTT GGACTGTTCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_034483.2 ABBA01075164
dbSNP Blast Analysis

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss135861643ENSEMBL_Venter 2IG 1.000 1.000
ENSEMBL_celera 4IG 0.500 0.500 0.500 0.500
ss166554591PGP 2IG 1.000 0.500 0.500
ss231153301pilot_1_CEU_low_coverage_panel 120AF 0.100 0.900
ss23141053PDR90Global 176IG 0.034 0.159 0.807 0.050 0.114 0.886
ss23856128AFD_EUR_PANELEuropean 48IG 0.167 0.833 1.000 0.083 0.917
AFD_AFR_PANELAfrican American 46IG 0.043 0.957 1.000 0.022 0.978
AFD_CHN_PANELAsian 44IG 0.182 0.409 0.409 0.527 0.386 0.614
ss238711445pilot_1_CHB+JPT_low_coverage_panel 120AF 0.325 0.675
ss44170260HapMap-CEUEuropean 226IG 0.195 0.805 0.655 0.097 0.903
HapMap-HCBAsian 86IG 0.093 0.419 0.488 1.000 0.302 0.698
HapMap-JPTAsian 172IG 0.128 0.465 0.407 1.000 0.360 0.640
HapMap-YRISub-Saharan African 120IG 1.000 1.000
AoD_African_American 90AF 0.020 0.980
AoD_Caucasian 92AF 0.110 0.890
HAPMAP-ASW 98IG 0.075 0.925 1.000 0.041 0.959
HAPMAP-CHBAsian 82IG 0.146 0.341 0.512 0.200 0.317 0.683
HAPMAP-CHD 170IG 0.094 0.471 0.435 0.584 0.329 0.671
HAPMAP-GIH 176IG 0.011 0.182 0.807 1.000 0.102 0.898
HAPMAP-LWK 180IG 0.033 0.967 1.000 0.017 0.983
HAPMAP-MKK 286IG 0.070 0.930 1.000 0.035 0.965
HAPMAP-TSI 176IG 0.023 0.148 0.830 0.150 0.097 0.903
AX-AM 20IG 0.500 0.500 0.527 0.250 0.750
AX-AT 20IG 0.300 0.300 0.400 0.251 0.450 0.550
AX-ME 10IG 0.200 0.800 0.100 0.900
CEU 120IG 0.217 0.783 0.752 0.108 0.892
CHB 90IG 0.089 0.400 0.511 1.000 0.289 0.711
CN-CC 52IG 0.038 0.615 0.346 0.100 0.346 0.654
CN-GA 60IG 0.167 0.500 0.333 1.000 0.417 0.583
CN-HM 52IG 0.077 0.423 0.500 1.000 0.288 0.712
CN-JI 62IG 0.226 0.516 0.258 1.000 0.484 0.516
CN-JN 56IG 0.214 0.464 0.321 0.752 0.446 0.554
CN-SH 36IG 0.111 0.389 0.500 0.752 0.306 0.694
CN-UG 52IG 0.077 0.192 0.731 0.100 0.173 0.827
CN-WA 112IG 0.196 0.554 0.250 0.439 0.473 0.527
ID-AL 38IG 0.053 0.368 0.579 1.000 0.237 0.763
ID-DY 24IG 0.167 0.417 0.417 0.752 0.375 0.625
ID-JA 68IG 0.235 0.382 0.382 0.251 0.426 0.574
ID-JV 38IG 0.158 0.632 0.211 0.251 0.474 0.526
ID-KR 34IG 0.294 0.353 0.353 0.251 0.471 0.529
ID-LA 40IG 0.050 0.350 0.600 1.000 0.225 0.775
ID-LE 38IG 0.474 0.526 0.403 0.237 0.763
ID-ML 24IG 0.167 0.500 0.333 1.000 0.417 0.583
ID-MT 30IG 0.133 0.400 0.467 0.752 0.333 0.667
ID-RA 34IG 0.176 0.353 0.471 0.371 0.353 0.647
ID-SB 40IG 0.250 0.500 0.250 0.500 0.500
ID-SO 38IG 0.158 0.474 0.368 1.000 0.395 0.605
ID-SU 50IG 0.240 0.520 0.240 1.000 0.500 0.500
ID-TB 40IG 0.450 0.300 0.250 0.100 0.600 0.400
ID-TR 40IG 0.250 0.350 0.400 0.251 0.425 0.575
IN-DR 48IG 0.208 0.792 1.000 0.104 0.896
IN-EL 32IG 0.062 0.188 0.750 0.251 0.156 0.844
IN-IL 30IG 0.267 0.733 1.000 0.133 0.867
IN-NI 40IG 0.050 0.350 0.600 1.000 0.225 0.775
IN-NL 30IG 0.067 0.933 1.000 0.033 0.967
IN-SP 46IG 0.043 0.478 0.478 0.403 0.283 0.717
IN-TB 46IG 0.261 0.739 0.752 0.130 0.870
IN-WI 50IG 0.040 0.320 0.640 1.000 0.200 0.800
IN-WL 28IG 0.286 0.714 0.752 0.143 0.857
JP-ML 142IG 0.099 0.408 0.493 1.000 0.303 0.697
JP-RK 98IG 0.102 0.449 0.449 1.000 0.327 0.673
JPT 88IG 0.114 0.386 0.500 0.584 0.307 0.693
KR-KR 180IG 0.111 0.456 0.433 1.000 0.339 0.661
MY-BD 100IG 0.180 0.640 0.180 0.050 0.500 0.500
MY-JH 98IG 0.408 0.490 0.102 0.584 0.653 0.347
MY-KN 34IG 0.059 0.353 0.588 1.000 0.235 0.765
MY-KS 60IG 0.267 0.567 0.167 0.439 0.550 0.450
MY-MN 38IG 0.263 0.579 0.158 0.479 0.553 0.447
MY-TM 98IG 0.143 0.551 0.306 0.371 0.418 0.582
PI-AE 16IG 0.375 0.625 0.188 0.812
PI-AG 16IG 0.125 0.375 0.500 0.312 0.688
PI-AT 44IG 0.182 0.818 1.000 0.091 0.909
PI-IR 18IG 0.111 0.444 0.444 0.333 0.667
PI-MA 36IG 0.111 0.333 0.556 0.479 0.278 0.722
PI-MW 36IG 0.222 0.389 0.389 0.403 0.417 0.583
PI-UB 40IG 0.150 0.650 0.200 0.200 0.475 0.525
PI-UI 40IG 0.150 0.450 0.400 1.000 0.375 0.625
PI-UN 38IG 0.211 0.526 0.263 1.000 0.474 0.526
SG-CH 60IG 0.233 0.533 0.233 0.752 0.500 0.500
SG-ID 60IG 0.033 0.200 0.767 0.479 0.133 0.867
SG-ML 60IG 0.100 0.467 0.433 1.000 0.333 0.667
TH-HM 40IG 0.150 0.350 0.500 0.371 0.325 0.675
TH-KA 38IG 0.684 0.316 0.100 0.342 0.658
TH-LW 38IG 0.053 0.474 0.474 0.527 0.289 0.711
TH-MA 36IG 0.333 0.667 0.655 0.167 0.833
TH-MO 38IG 0.105 0.526 0.368 0.584 0.368 0.632
TH-PL 36IG 0.278 0.722 0.752 0.139 0.861
TH-PP 36IG 0.222 0.556 0.222 0.655 0.500 0.500
TH-TK 36IG 0.056 0.611 0.333 0.200 0.361 0.639
TH-TL 40IG 0.100 0.600 0.300 0.273 0.400 0.600
TH-TN 36IG 0.222 0.667 0.111 0.150 0.556 0.444
TH-TU 40IG 0.150 0.550 0.300 0.584 0.425 0.575
TH-TY 30IG 0.133 0.533 0.333 0.752 0.400 0.600
TH-YA 38IG 0.263 0.737 0.752 0.132 0.868
TW-HA 96IG 0.188 0.521 0.292 0.752 0.448 0.552
TW-HB 64IG 0.156 0.469 0.375 1.000 0.391 0.609
YRI 120IG 1.000 1.000
ss491783017CSAgilent 1185GF 0.005 0.172 0.823 0.091 0.909
ss66859545HSP_GENO_PANEL 120IG 0.183 0.817 0.752 0.092 0.908
CEU_GENO_PANELEuropean 120IG 0.217 0.783 0.752 0.108 0.892
AAM_GENO_PANELAfrican American 124IG 0.065 0.935 1.000 0.032 0.968
CHB_GENO_PANELAsian 90IG 0.089 0.400 0.511 1.000 0.289 0.711
YRI_GENO_PANELSub-Saharan African 120IG 1.000 1.000
JPT_GENO_PANELAsian 90IG 0.111 0.400 0.489 0.655 0.311 0.689
ss6903874P1 202AF 0.248 0.752 0.527 0.124 0.876
CAUC1 62AF 0.290 0.710 0.655 0.145 0.855
AFR1 48AF 0.083 0.917 1.000 0.042 0.958
HISP1 46AF 0.130 0.870 1.000 0.065 0.935
PAC1 46AF 0.478 0.522 0.343 0.239 0.761
AfAmAfrican American 12IG 1.000 1.000
CaucasianEuropean 24IG 0.250 0.750 1.000 0.125 0.875
AsianAsian 12IG 0.167 0.667 0.167 0.500 0.500
CEPHEuropean 10IG 1.000 1.000
PDpanelGlobal 48IG 0.167 0.833 1.000 0.083 0.917
ss96394523J. Craig Venter 2IG 1.000 1.000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.229+/-0.249335631712540ALFRED: 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
UNKNOWNUNKNOWNYES

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