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Reference SNP (refSNP) Cluster Report: rs4987188                 ** With Benign ,Uncertain significance allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:113/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G/T (FWD)
Allele Origin:A:germline
G:germline
T:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign ,Uncertain significance allele [ClinVar]
MAF/MinorAlleleCount:A=0.0141/1709 (ExAC)
A=0.0062/31 (1000 Genomes)
A=0.0114/148 (GO-ESP)
A=0.0095/1188 (TOPMED)
HGVS Names
  • CM000664.2:g.47416318G>A
  • CM000664.2:g.47416318G>T
  • NC_000002.11:g.47643457G>A
  • NC_000002.11:g.47643457G>T
  • NC_000002.12:g.47416318G>A
  • NC_000002.12:g.47416318G>T
  • NG_007110.2:g.18195G>A
  • NG_007110.2:g.18195G>T
  • NM_000251.2:c.965G>A
  • NM_000251.2:c.965G>T
  • NM_001258281.1:c.767G>A
  • NM_001258281.1:c.767G>T
  • NP_000242.1:p.Gly322Asp
  • NP_000242.1:p.Gly322Val
  • NP_001245210.1:p.Gly256Asp
  • NP_001245210.1:p.Gly256Val
  • XP_005264389.1:p.Gly322Asp
  • XP_005264389.1:p.Gly322Val
  • XP_005264389.2:p.Gly322Asp
  • XP_005264389.2:p.Gly322Val
  • XP_005264390.1:p.Gly272Asp
  • XP_005264390.1:p.Gly272Val
  • XP_011531169.1:p.Gly322Asp
  • XP_011531169.1:p.Gly322Val
  • XR_001738747.1:n.1037G>A
  • XR_001738747.1:n.1037G>T
  • XR_939685.1:n.1037G>A
  • XR_939685.1:n.1037G>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 ss23140883 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4987188 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
ss6903873SNP500CANCER|MSH2-02byFreqfwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa02/14/0304/07/04113Genomicunknown
ss23140883EGP_SNPS|MSH2-014756byFreqfwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa04/22/0410/26/06126Genomicunknown
ss38347354ADLCLAB|MSH2-NT_022184.14-26459390fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa07/07/0507/07/05126Genomicunknown
ss68408351CSHL-HAPMAP|perlegen:assay:24708.4427703:1fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa01/11/0701/11/07127NAunknown
ss68813053PERLEGEN|PGP04427703byFreqfwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa01/30/0703/31/08127Genomicunknown
ss74817440AFFY|SNP_M-315174fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa08/09/0708/09/07128Genomicunknown
ss74910857ILLUMINA|ILMN_Human_1M_rs4987188fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa08/28/0708/29/07129Genomicunknown
ss86344842CANCER-GENOME|27311fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa01/25/0801/25/08129Genomicunknown
ss160735810ILLUMINA|HumanOmni1-Quad_v1-0_B_rs4987188-128_B_R_1513943022rev/BC/Tttattcagcaaggcagccagagactgagagcagtggtatcttcaacagaaccctagtaaa08/04/0910/04/09131Genomicunknown
ss166553971COMPLETE_GENOMICS|NA20431_36_chr2_47496961fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa09/30/0909/30/09132Genomicunknown
ss173903543ILLUMINA|Human1M-Duov3_B_rs4987188-128_B_R_1513943022rev/BC/Tttattcagcaaggcagccagagactgagagcagtggtatcttcaacagaaccctagtaaa10/01/0910/04/09132Genomicunknown
ss2311531071000GENOMES|pilot_1_CEU_757736_chr2_47496961fwd/A/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa05/01/1005/01/10132Genomicunknown
ss244238090OMICIA|2010_April_001_088_MSH2_609309_0010fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa05/27/1005/28/10132Genomicunknown
ss256301847OMIM-CURATED-RECORDS|16259fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa08/25/1008/25/10132Genomicunknown
ss342059036NHLBI-ESP|ESP2500-chr2-47643457byFreqfwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa03/25/1109/05/14134Genomicunknown
ss472343251CORRELAGEN|MSH2_965G_A_082510fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa11/18/1111/22/11136Genomicunknown
ss481126015ILLUMINA|HumanOmni2.5-4v1_B_rs4987188-128_B_R_1616887810fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg01/30/1210/28/16137Genomicunknown
ss481148168ILLUMINA|HumanOmniExpress-12v1_C_rs4987188-131_B_R_1853527113fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg01/30/1210/27/16137Genomicunknown
ss482137103ILLUMINA|HumanOmni1-Quad_v1-0_C_rs4987188-131_B_R_1865486741fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg01/30/1208/28/15146Genomicunknown
ss485358081ILLUMINA|HumanOmni2.5-4v1_D_rs4987188-131_B_R_1853527113fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg01/30/1210/28/16137Genomicunknown
ss4898151581000GENOMES|20110521_exome_341190_chr2_47643457fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa02/10/1202/21/12137Genomicunknown
ss491318683EXOME_CHIP|nonsyn_34910_chr_2_47643457fwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa03/05/1203/05/12137Genomicunknown
ss491782996CLINSEQ_SNP|SNV-chr2-47496961byFreqfwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/06/1209/05/14137Genomicunknown
ss537302816ILLUMINA|HumanOmni5-4v1_B_rs4987188-131_B_R_1908454223fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg06/22/1208/28/15146Genomicunknown
ss538293146MMR_WOODS|MSH2_c.965G>Afwd/TA/Gtttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa07/31/1210/24/12137Genomicunknown
ss778927518ILLUMINA|HumanOmni25Exome-8v1_A_rs4987188-131_B_R_1865486741fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/30/1307/09/15146Genomicunknown
ss780777447ILLUMINA|HumanOmni25Exome-8v1_A_exm192212-0_B_R_1918977250fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/30/1307/09/15146Genomicunknown
ss783124750ILLUMINA|HumanOmni2.5-4v1_H_rs4987188-131_B_R_1853527113fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/30/1307/28/15146Genomicunknown
ss783457487ILLUMINA|HumanOmniExpressExome-8v1_A_exm192212-0_B_R_1918977250fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/31/1306/19/15146Genomicunknown
ss784081402ILLUMINA|HumanOmniExpressExome-8v1_A_rs4987188-131_B_R_1908454223fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/31/1306/19/15146Genomicunknown
ss832383573ILLUMINA|HumanOmniExpress-12v1_H_rs4987188-131_B_R_1853527113fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg09/17/1306/18/15146Genomicunknown
ss834389019ILLUMINA|HumanOmni2.5-8v1_A_rs4987188-131_B_R_1865486741fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg09/18/1307/28/15146Genomicunknown
ss974442141JMKIDD_LAB|KhoeSan_Exomes_chr2_47643457fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/06/1403/06/14142Genomicunknown
ss976785727EVA-GONL|EVA-GONL_rs4987188fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg04/23/1404/23/14142Genomicunknown
ss12970516281000GENOMES|PHASE3_V1_8031226fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg08/16/1408/16/14142Genomicunknown
ss1457621369CLINVAR|SCV000186696fwd/BG/Ttttactagggttctgttgaagataccactgctctcagtctctggctgccttgctgaataa11/23/1411/23/14142Genomicunknown
ss1578861446EVA_GENOME_DK|EVA_GENOME_DK_snv_rs4987188fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg02/19/1502/20/15144Genomicunknown
ss1584018420EVA_FINRISK|EVA_FINRISK_rs4987188fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg02/27/1502/27/15144Genomicunknown
ss1586195899EVA_DECODE|EVA_DECODE_2_47496961_397790_rs4987188fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/02/1503/02/15144Genomicunknown
ss1603417862EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_47643457_4440457fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/04/1503/04/15144Genomicunknown
ss1646411895EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_47643457_4440457fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/04/1503/04/15144Genomicunknown
ss1686299686EVA_EXAC|EVA_EXAC_1165341fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/04/1503/04/15144Genomicunknown
ss1686299687EVA_EXAC|EVA_EXAC_1165342fwd/G/Ttagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/04/1503/04/15144Genomicunknown
ss1710962407EVA_MGP|EVA_XIMO_79159fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/09/1503/09/15144Genomicunknown
ss1752359254ILLUMINA|OmniExpressExome-8v1-1_B_exm192212-0_B_R_1918977250fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/27/1506/09/15146Genomicunknown
ss1752359255ILLUMINA|OmniExpressExome-8v1-1_B_rs4987188-131_B_R_1908454223fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/27/1506/09/15146Genomicunknown
ss1917749006ILLUMINA|HumanExome-12v1-1_B_exm192212-0_B_R_1918977250fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg10/16/1510/16/15147Genomicunknown
ss1920020951WEILL_CORNELL_DGM|SNV:chr2:47643457fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg10/16/1510/16/15147Genomicunknown
ss1946039713ILLUMINA|HumanCoreExome-12v1-0_C_exm192212-0_B_R_1918977250fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg10/29/1510/29/15147Genomicunknown
ss1958415020ILLUMINA|exm192212-0_B_R_1918977250fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg11/13/1511/13/15147Genomicunknown
ss2020543965JJLAB|SNP1046520fwd/TA/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg08/29/1608/30/16149Genomicunknown
ss2148588127USC_VALOUEV|NC_000002.11:g.47643457G>Afwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg11/17/1611/17/16150Genomicunknown
ss2229892862HUMAN_LONGEVITY|HLI-2-47416318-G-A,Tfwd/A/G/Ttagggttctgttgaagataccactgctctcagtctctggctgccttgctg11/18/1611/18/16150Genomicunknown
ss2395823059TOPMED|2_47643457_G/Afwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg11/19/1611/19/16150Genomicunknown
ss2395823060TOPMED|2_47643457_G/Tfwd/G/Ttagggttctgttgaagataccactgctctcagtctctggctgccttgctg11/19/1611/19/16150Genomicunknown
ss2633609385ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs4987188-131_B_R_19084542fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg02/02/1702/02/17151Genomicunknown
ss2710899731ILLUMINA|Consortium-OncoArray_15047405_A_rs4987188-131_B_R_1908454223fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg03/22/1703/22/17151Genomicunknown
ss2732652183GNOMAD|exomes_rs4987188fwd/A/G/Ttagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/17/1705/17/17151Genomicunknown
ss2746676372GNOMAD|coding_rs4987188fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/17/1705/17/17151Genomicunknown
ss2772940433GNOMAD|rs4987188fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/17/1705/17/17151Genomicunknown
ss2985167591AFFY|Axiom_PsorMich_Affx-20140583fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/24/1705/24/17151Genomicunknown
ss2989432999SWEGEN|NC_000002.11:g.47643457G>Afwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg05/30/1705/30/17151Genomicunknown
ss3021968022ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm192212-0_B_R_1918977250fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg06/28/1706/28/17151Genomicunknown
ss3306700722TOPMED|TOPMed_freeze_5?chr2:47,416,318-01fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg10/02/1710/02/17151Genomicunknown
ss3306700723TOPMED|TOPMed_freeze_5?chr2:47,416,318-02fwd/G/Ttagggttctgttgaagataccactgctctcagtctctggctgccttgctg10/02/1710/02/17151Genomicunknown
ss3344209329CSHL|rs4987188fwd/A/Gtagggttctgttgaagataccactgctctcagtctctggctgccttgctg10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4987188|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=151
 TCAACAAATA AAATAAAACT GTAGTAATTA TAAAGTGGTT TTGGCTGGGG GAGAAATGTA
 CAGTTGAACA TACGGATTAA GAGGTTGAAA GTTGGTCTTA GGAAGAGGAA CTTTTTGTGG
 AAATTTCTTA ATATTTGAAG AATATTATGT TATTGTTCCT CTGTTTTTCA TGGCGTAGTA
 AGGTTTTCAC TAATGAGCTT GCCATTCTTT CTATTTTATT TTTTGTTTAC TAGGGTTCTG
 TTGAAGATAC CACTG
 D
 CTCTCAGTCT CTGGCTGCCT TGCTGAATAA GTGTAAAACC CCTCAAGGAC AAAGACTTGT
 TAACCAGTGG ATTAAGCAGC CTCTCATGGA TAAGAACAGA ATAGAGGAGA GGTATGTTAT
 TAGTTTATAC TTTCGTTAGT TTTATGTAAC CTGCAGTTAC CCACATGATT ATACCACTTA
 TTGTAATATG CAGTTTTGGA AGTATATGTT ACCATTTAAC TGTACAGAGT ACATAGTAAT
 AGAGTGGTAA TTATT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_034483.2
dbSNP Blast Analysis
UniGene Cluster ID
156519
3D structure mapping
NP_000242  NP_001245210  
OMIM
609309.0010

  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.
SourceA/A
A/G
G/G
HWPA
G
T
ss1297051628EAS 1008AF 1.00000000
EUR 1006AF 0.016900000.98310000
AFR 1322AF 0.001500000.99849999
AMR 694AF 0.005800000.99419999
SAS 978AF 0.008200000.99180001
ss166553971PGP 2IG 1.00000000 0.500000000.50000000
ss1686299686ExAc_Aggregated_Populations121407AF 0.014076620.98592341
ss1686299687ExAc_Aggregated_Populations119703AF 0.999958220.00004177
ss231153107pilot_1_CEU_low_coverage_panel 120AF 0.025000000.97500002
ss23140883PDR90Global 166IG 0.012048190.987951821.000000000.006024100.99397588
HapMap-CEUEuropean 226IG 0.061946900.938053071.000000000.030973450.96902657
HapMap-HCBAsian 86IG 0.023255810.976744171.000000000.011627910.98837209
HapMap-JPTAsian 168IG 0.023809520.976190451.000000000.011904760.98809522
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.040816330.959183691.000000000.020408160.97959185
HAPMAP-CHBAsian 82IG 1.00000000 1.00000000
HAPMAP-CHD 170IG 0.011764710.988235291.000000000.005882350.99411762
HAPMAP-GIH 174IG 0.034482760.965517221.000000000.017241380.98275864
HAPMAP-MEX 100IG 0.080000000.920000021.000000000.040000000.95999998
HAPMAP-TSI 176IG 0.034090910.965909061.000000000.017045460.98295456
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss342059036ESP_Cohort_Populations 4552GF0.000439370.014059750.985500870.020022000.007469240.99253076
ss491782996CSAgilent 1323GF 0.023000000.977000001.000000000.011500000.98850000
ss6903873P1 204AF 0.020000000.980000021.000000000.010000000.99000001
CAUC1 62AF 0.065000010.935000001.000000000.032000000.96799999
AFR1 48AF 1.00000000 1.00000000
HISP1 46AF 1.00000000 1.00000000
PAC1 48AF 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.028+/-0.1150000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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