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Reference SNP (refSNP) Cluster Report: rs4988235                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:113/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G/T (REV)
Allele Origin:C:germline
T:germline
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:A=0.1613/808 (1000 Genomes)
A=0.3877/48678 (TOPMED)
HGVS Names
  • CM000664.2:g.135851076G>A
  • NC_000002.11:g.136608646G>A
  • NC_000002.12:g.135851076G>A
  • NG_008104.2:g.9094C>T
  • NG_008958.1:g.30366C>T
  • NM_005915.5:c.1917+326C>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 ss284442913 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4988235 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
ss6905277EGP_SNPS|MCM6-026638byFreqfwd/BC/Ttgcgctggcaatacagataagataatgtagccctggcctcaaaggaactctcctccttag02/21/0304/07/04113Genomicunknown
ss21718943SSAHASNP|WGSA-200403-chr2.chr2.NT_005058.14_5217655rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca03/20/0403/20/04121Genomicunknown
ss41791584ABI|hCV2104745byFreqrev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca07/17/0511/03/06126Genomicunknown
ss66536930DSWALLOW|13910*Tfwd/BC/Ttgcgctggcaatacagataagataatgtagccctggcctcaaaggaactctcctccttag10/30/0610/30/06127Genomicunknown
ss75046935ILLUMINA|ILMN_Human_1M_rs4988235fwd/BC/Ttgcgctggcaatacagataagataatgtagccctggcctcaaaggaactctcctccttag08/28/0708/29/07129Genomicunknown
ss77533811HGSV|Cor12156_SNV_20070510.chr2_136442378rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca10/09/0710/13/07129Genomicunknown
ss78390960HGSV|Cor12878_SNV_20070510.chr2_136442378rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca10/17/0710/19/07129Genomicunknown
ss91358492BCMHGSC_JDW|JWB-1311115rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca02/26/0803/01/08129Genomicunknown
ss96429678HUMANGENOME_JCVI|1103658227841rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca03/26/0803/26/08130Genomicunknown
ss105437324SNP500CANCER|MCM6-04byFreqfwd/BC/Ttgcrctggcaatacagataagataakgyagcystggcctcaaaggaactctcctccttag09/05/0809/05/14130Genomicunknown
ss1099115581000GENOMES|CEU.trio.12.15.2008_475889_chr2_136325116rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca12/16/0812/16/08130Genomicunknown
ss119497200KRIBB_YJKIM|KHS1659447fwd/BC/Ttgcgctggcaatacagataagataatgtagccctggcctcaaaggaactctcctccttag02/04/0902/04/09131Genomicunknown
ss136140189ENSEMBL|ENSSNP1615512rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca12/08/0810/15/09131Genomicunknown
ss160735894ILLUMINA|HumanOmni1-Quad_v1-0_B_rs4988235-128_T_R_1514008997rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca08/04/0910/04/09131Genomicunknown
ss165275741COMPLETE_GENOMICS|NA07022_36_chr2_136325116rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca09/29/0909/30/09132Genomicunknown
ss167206869COMPLETE_GENOMICS|NA20431_36_chr2_136325116rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca09/30/0909/30/09132Genomicunknown
ss173903967ILLUMINA|Human1M-Duov3_B_rs4988235-128_T_R_1514008997rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca10/01/0910/04/09132Genomicunknown
ss205615294BCM-HGSC-SUB|BCM_CMT_1011-286678rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca03/15/1003/16/10132Genomicunknown
ss2313738881000GENOMES|pilot_1_CEU_978517_chr2_136325116rev/A/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca05/01/1005/01/10132Genomicunknown
ss253507113BL|SNP144002_2_136325116rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca08/18/1008/18/10134Genomicunknown
ss284442913GMI|GMI_NA10851_SNP_455684rev/A/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca12/17/1012/17/10138Genomicunknown
ss292373850PJP|SNP_1880208_chr2_136325116rev/A/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca01/21/1101/21/11134Genomicunknown
ss410938247ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs4988235rev/TA/Gctaaggaggagagttcctttgaggccagggctacattatcttatctgtattgccagcgca06/07/1106/07/11135Genomicunknown
ss481126268ILLUMINA|HumanOmni2.5-4v1_B_rs4988235-128_T_R_1615265951rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca01/30/1210/28/16137Genomicunknown
ss481148421ILLUMINA|HumanOmniExpress-12v1_C_rs4988235-131_T_R_1863803852rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca01/30/1210/27/16137Genomicunknown
ss482137356ILLUMINA|HumanOmni1-Quad_v1-0_C_rs4988235-131_T_R_1863803852rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca01/30/1208/28/15146Genomicunknown
ss485358206ILLUMINA|HumanOmni2.5-4v1_D_rs4988235-131_T_R_1863803852rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca01/30/1210/28/16137Genomicunknown
ss537302999ILLUMINA|HumanOmni5-4v1_B_rs4988235-131_T_R_1911620025rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca06/22/1208/28/15146Genomicunknown
ss778555721ILLUMINA|HumanOmni25Exome-8v1_A_rs4988235-131_T_R_1866552214rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca05/30/1307/09/15146Genomicunknown
ss783124812ILLUMINA|HumanOmni2.5-4v1_H_rs4988235-131_T_R_1863803852rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca05/30/1307/28/15142Genomicunknown
ss784081462ILLUMINA|HumanOmniExpressExome-8v1_A_rs4988235-131_T_R_1911620025rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca05/31/1306/19/15146Genomicunknown
ss832383636ILLUMINA|HumanOmniExpress-12v1_H_rs4988235-131_T_R_1863803852rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca09/17/1306/18/15144Genomicunknown
ss834012514ILLUMINA|HumanOmni2.5-8v1_A_rs4988235-131_T_R_1866552214rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca09/18/1307/28/15146Genomicunknown
ss977391047EVA-GONL|EVA-GONL_rs4988235rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca04/23/1404/23/14142Genomicunknown
ss1069520152JMKIDD_LAB|HGDP_WGS_chr2_136608646rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca07/10/1407/10/14142Genomicunknown
ss12994608621000GENOMES|PHASE3_V1_10535148rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca08/16/1408/16/14142Genomicunknown
ss1397305328HAMMER_LAB|HAMMER_LAB_rs4988235rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca09/30/1409/30/14146Genomicunknown
ss1428750137DDI|DDI_rs4988235rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca11/04/1411/04/14144Genomicunknown
ss1505810855OMIM-CURATED-RECORDS|SCV000028329fwd/BC/Ttgcgctggcaatacagataagataatgtagccctggcctcaaaggaactctcctccttag12/08/1412/08/14142Genomicunknown
ss1579099368EVA_GENOME_DK|EVA_GENOME_DK_snv_rs4988235rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca02/19/1502/20/15144Genomicunknown
ss1586819657EVA_DECODE|EVA_DECODE_2_136325116_1021568_rs4988235rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca03/02/1503/02/15144Genomicunknown
ss1604632304EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_136608646_5771110rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca03/04/1503/04/15144Genomicunknown
ss1604632305EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_136608646_5771111rev/C/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca03/04/1503/04/15144Genomicunknown
ss1647626337EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_136608646_5771110rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca03/04/1503/04/15144Genomicunknown
ss1647626338EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_136608646_5771111rev/C/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca03/04/1503/04/15144Genomicunknown
ss1712492313EVA_SVP|EVA_SVP_186865rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca03/12/1503/12/15144Genomicunknown
ss1752312553ILLUMINA|OmniExpressExome-8v1-1_B_rs4988235-131_T_R_1911620025rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca05/27/1506/09/15146Genomicunknown
ss1920650265WEILL_CORNELL_DGM|SNV:chr2:136608646rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca10/16/1510/16/15147Genomicunknown
ss1958461414ILLUMINA|2:136608646-G-A-0_T_F_2304233041rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca11/13/1511/13/15147Genomicunknown
ss1968896143GENOMED|rs4988235rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca02/16/1602/16/16147Genomicunknown
ss2020848212JJLAB|SNP1350767rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca08/29/1608/30/16149Genomicunknown
ss2094807482ILLUMINA|Immuno_BeadChip_11419691_B_rs4988235-131_T_R_1866552214rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca09/27/1609/27/16150Genomicunknown
ss2095101017ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs4988235-131_T_R_1866552214rev/TA/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca09/27/1609/27/16150Genomicunknown
ss2148915016USC_VALOUEV|NC_000002.11:g.136608646G>Arev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca11/17/1611/17/16150Genomicunknown
ss2234547850HUMAN_LONGEVITY|HLI-2-135851076-G-Arev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca11/18/1611/18/16150Genomicunknown
ss2400908848TOPMED|2_136608646_G/Arev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca11/19/1611/19/16150Genomicunknown
ss2633676742ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs4988235-131_T_R_19116200rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca02/02/1702/02/17151Genomicunknown
ss2710912514ILLUMINA|Consortium-OncoArray_15047405_A_rs4988235-131_T_R_1911620025rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca03/22/1703/22/17151Genomicunknown
ss2780042566GNOMAD|rs4988235rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca05/17/1705/17/17151Genomicunknown
ss2990481553SWEGEN|NC_000002.11:g.136608646G>Arev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca05/30/1705/30/17151Genomicunknown
ss3022020033ILLUMINA|MEGA_Consortium_v2_15070954_A2_2:136608646-G-A-0_T_F_2304233041rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca06/28/1706/28/17151Genomicunknown
ss3024187558BIOINF_KMB_FNS_UNIBA|2.135851076G>Arev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca07/05/1707/05/17151Genomicunknown
ss3323859101TOPMED|TOPMed_freeze_5?chr2:135,851,076rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca10/02/1710/02/17151Genomicunknown
ss3344495711CSHL|rs4988235rev/A/Ggaggagagttcctttgaggccagggctacattatcttatctgtattgcca10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4988235|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/G/T'|mol=Genomic|build=151
 TGATCTGAAA CAGATTTCCA AAGAGTCAGA GGACTTCATT GTGGAGCAAT ATAAACATCT
 CCGCCAGAGA GATGGTTCTG GAGTGACCAA GTCTTCATGG AGGATTACAG TGCGACAGCT
 TGAGAGCATG ATTCGTCTCT CTGAAGCTAT GGCTCGGATG CACTGCTGTG ATGAGGTATC
 AGAGTCACTT TGATATGATG AGAGCAGAGA TAAACAGATT TGTTGCATGT TTTTAATCTT
 TGGTATGGGA CATACTAGAA TTCACTGCAA ATACATTTTT ATGTAACTGT TGAATGCTCA
 TACGACCATG GAATTCTTCC CTTTAAAGAG CTTGGTAAGC ATTTGAGTGT AGTTGTTAGA
 CGGAGACGAT CACGTCATAG TTTATAGAGT GCATAAAGAC GTAAGTTACC ATTTAATACC
 TTTCATTCAG GAAAAATGTA CTTAGACCCT ACAATGTACT AGTAGGCCTC TGCGCTGGCA
 ATACAGATAA GATAATGTAG
 B
 CCCTGGCCTC AAAGGAACTC TCCTCCTTAG GTTGCATTTG TATAATGTTT GATTTTTAGA
 TTGTTCTTTG AGCCCTGCAT TCCACGAGGA TAGGTCAGTG GGTATTAACG AGGTAAAAGG
 GGAGTAGTAC GAAAGGGCAT TCAAGCGTCC CATCTTCGCT TCAACCAAAG CAGCCCTGCG
 TTTTCCTAGT TTTATTAATA GGTTTGATGT AAGGTCGTCT TTGAAAAGGG GGTTTGGCTT
 TTTTTTACAG TGTGACTGAG GTATAATTTA TAAAAAGGGA AATGTATGGC ATGGTGAGTT
 TTTTCACATA CATCCTTGTG AATACCCAGC TCAAGATCCA AAACATTTCC ATAATTTCAG
 AAAGTTCCAA ACCCCTGCCT CTTTTCAGTC TTAGCCCTCT TCCCCTGAAG TAACCACTGT
 TCCGACTTCA ATCACTACTT TTATCCCACA GGTTAATTTT TTGGCTTTTT TCCACTAAAT
 TTTCAAATTC TTTGATATGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005058 ABBA01028160
dbSNP Blast Analysis
OMIM
223100

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs4988235 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss105437324P1 200GF0.610000010.190000000.200000000.001000000.704999980.29499999
CAUC1 60GF0.266666680.133333340.600000020.001000000.333333340.66666669
AFR1 48GF0.791666690.20833333 1.000000000.895833310.10416666
HISP1 46GF0.521739130.391304340.086956521.000000000.717391310.28260869
PAC1 46GF0.956521750.04347826 1.000000000.978260870.02173913
ss1299460862EAS 1008AF 1.00000000
EUR 1006AF 0.491999980.50800002
AFR 1322AF 0.972800020.02720000
AMR 694AF 0.783900020.21610001
SAS 978AF 0.886500000.11350000
ss136140189ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss165275741CEUEuropean 2IG 1.00000000 1.00000000
ss167206869PGP 2IG 1.00000000 1.00000000
ss231373888pilot_1_CEU_low_coverage_panel 120AF 0.224999990.77499998
ss41791584HapMap-CEUEuropean 226IG0.088495570.362831860.548672560.402784000.269911500.73008847
HapMap-HCBAsian 90IG1.00000000 1.00000000
HapMap-JPTAsian 90IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 116IG1.00000000 1.00000000
Africa/MiddleEast 1044AF 0.940000000.06000000
HAPMAP-ASW 98IG0.775510190.163265300.061224490.020022000.857142870.14285715
HAPMAP-GIH 176IG0.715909060.261363630.022727271.000000000.846590940.15340909
HAPMAP-MEX 100IG0.500000000.400000010.100000000.751830000.699999990.30000001
HAPMAP-TSI 176IG0.818181810.159090910.022727270.250592000.897727250.10227273
ss6905277PDR90Global 170IG0.552941200.341176480.105882350.200325000.723529400.27647060
ss96429678J. Craig Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.271+/-0.2490000ALFRED: 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
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNYES

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