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Reference SNP (refSNP) Cluster Report: rs1040288                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.4928/2468 (1000 Genomes)
C=0.4999/62773 (TOPMED)
HGVS Names
  • CM000666.2:g.148126966G>C
  • NC_000004.11:g.149048117G>C
  • NC_000004.12:g.148126966G>C
  • NG_013350.1:g.320556C>G
  • NM_000901.4:c.2511-6678C>G
  • NM_001166104.1:c.2160-6678C>G
  • NM_001354819.1:c.2160-6678C>G
  • NR_148974.1:n.2378-6678C>G
  • XR_244631.1:n.2378-6678C>G
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 ss1506766 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1040288 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
ss1506766TSC-CSHL|TSC0346655byFreqfwd/BC/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca09/07/0004/07/0486Genomic95 %
ss6304648SC_JCM|NT_006258.11_1066012fwd/BC/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca01/10/0310/10/03111Genomicunknown
ss19604209CSHL-HAPMAP|CSHL-HuDD-200402.chr4.NT_016606.16_10596173fwd/BC/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca02/20/0403/04/04120Genomicunknown
ss22192016SSAHASNP|WGSA-200403-chr4.chr4.NT_016606.16_10596173fwd/BC/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca03/20/0403/21/04121Genomicunknown
ss44509226ABI|hCV1796069byFreqfwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca07/19/0511/03/06126Genomicunknown
ss66372793AFFY|SNP_A-2022214byFreqrev/TC/Gaaaaagggccaaaaatattactcagcttggca10/29/0608/14/07127Genomicunknown
ss76100594AFFY|AFFY_6_1M_SNP_A-2022214byFreqrev/C/Gaaaaagggccaaaaatattactcagcttggca08/28/0703/07/10130Genomicunknown
ss78771073HGSV|Cor12878_SNV_20070510.chr4_149405722fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca10/17/0710/20/07129Genomicunknown
ss81452581KRIBB_YJKIM|KHS78766fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca11/30/0711/30/07130Genomicunknown
ss86217048RSG_JCVI|NR3C2-051197_051198-C_GbyFreqfwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca12/12/0709/05/14129Genomicunknown
ss92823226BCMHGSC_JDW|JWB-1870370fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca02/26/0803/03/08129Genomicunknown
ss99019952HUMANGENOME_JCVI|1103654581392fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca04/02/0804/02/08130Genomicunknown
ss105873436BGI|BGI_rs1040288fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca09/12/0806/18/09130Genomicunknown
ss1084397671000GENOMES|CEU.trio.12.15.2008_1111513_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca12/15/0812/15/08130Genomicunknown
ss1107747311000GENOMES|NA19240_2008_12_16_1002394_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca12/17/0812/17/08130Genomicunknown
ss117232496ILLUMINA-UK|NA18507_000198093_NCBI36.1_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca01/18/0901/19/09130Genomic99 %
ss120241544ILLUMINA|GS0006564-OPA_rs1040288-111.3_T_R_59936rev/C/Gtgtatgactctggaaaaaagggccaaaaatattactcagcttggcacacagagaaaggag03/17/0903/17/09131Genomicunknown
ss133298216ENSEMBL|ENSSNP2304309byFreqfwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca12/08/0803/07/10131Genomicunknown
ss139950834ENSEMBL|ENSSNP12693258fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca05/18/0905/19/09131Genomicunknown
ss158043615GMI|GMI_SNP_135644855fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca06/24/0906/25/09131Genomicunknown
ss164663880COMPLETE_GENOMICS|NA19240_36_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca09/29/0909/30/09132Genomicunknown
ss167280816COMPLETE_GENOMICS|NA20431_36_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca09/30/0909/30/09132Genomicunknown
ss172506241AFFY|GenomeWideSNP_5_SNP_A-2022214rev/C/Gaaaaagggccaaaaatattactcagcttggca10/01/0910/02/09132Genomicunknown
ss199327566BUSHMAN|BUSHMAN-chr4-149267566fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca02/16/1003/06/10132Genomicunknown
ss206454169BCM-HGSC-SUB|BCM_CMT_1011-897432fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca03/15/1003/17/10132Genomicunknown
ss2212806011000GENOMES|pilot_1_YRI_3090284_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca04/22/1004/22/10132Genomicunknown
ss2326481821000GENOMES|pilot_1_CEU_2252811_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca05/01/1005/01/10132Genomicunknown
ss2398851781000GENOMES|pilot_1_CHB+JPT_1770255_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca05/01/1005/01/10132Genomicunknown
ss277983591GMI|GMI_AK_SNP_2303824fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca12/16/1012/16/10137Genomicunknown
ss285028963GMI|GMI_NA10851_SNP_1041736fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca12/17/1012/17/10138Genomicunknown
ss293222114PJP|SNP_2728472_chr4_149267567fwd/C/Gctcctttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtcataca01/21/1101/21/11134Genomicunknown
ss557934745TISHKOFF|snp_chr4_149048117fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc11/22/1211/23/12138Genomicunknown
ss651754809SSMP|4_149048117fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc12/14/1202/10/15138Genomicunknown
ss980813465EVA-GONL|EVA-GONL_rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc04/23/1404/24/14142Genomicunknown
ss1072058451JMKIDD_LAB|HGDP_WGS_chr4_149048117fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc07/10/1407/11/14142Genomicunknown
ss13123280481000GENOMES|PHASE3_V1_23945626fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc08/16/1408/16/14142Genomicunknown
ss1430092918DDI|DDI_rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc11/04/1411/05/14144Genomicunknown
ss1580829503EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc02/19/1502/20/15144Genomicunknown
ss1590326114EVA_DECODE|EVA_DECODE_4_149267567_1170354_rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc03/02/1503/03/15144Genomicunknown
ss1611439570EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_4_149048117_13245546fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc03/04/1503/04/15144Genomicunknown
ss1654433603EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_4_149048117_13245546fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc03/04/1503/04/15144Genomicunknown
ss1712714663EVA_SVP|EVA_SVP_409030fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc03/12/1503/12/15144Genomicunknown
ss1802374019HAMMER_LAB|Hsieh_2534678fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc07/15/1507/15/15146Genomicunknown
ss1924055146WEILL_CORNELL_DGM|SNV:chr4:149048117fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc10/16/1510/17/15147Genomicunknown
ss1969902402GENOMED|rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc02/16/1602/16/16147Genomicunknown
ss2022613253JJLAB|SNP3115808fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc08/29/1608/30/16149Genomicunknown
ss2150745396USC_VALOUEV|NC_000004.11:g.149048117G>Cfwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc11/17/1611/17/16150Genomicunknown
ss2268185900HUMAN_LONGEVITY|HLI-4-148126966-G-Cfwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc11/18/1611/18/16150Genomicunknown
ss2436121203TOPMED|4_149048117_G/Cfwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc11/20/1611/20/16150Genomicunknown
ss2625803108SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV1988003fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc01/06/1701/06/17151Genomicunknown
ss2706241299GRF|rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc02/13/1702/13/17151Genomicunknown
ss2816735647GNOMAD|rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc05/18/1705/18/17151Genomicunknown
ss2995763386SWEGEN|NC_000004.11:g.149048117G>Cfwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc05/30/1705/30/17151Genomicunknown
ss3025083591BIOINF_KMB_FNS_UNIBA|4.148126966G>Cfwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc07/05/1707/05/17151Genomicunknown
ss3346020703CSHL|rs1040288fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc10/02/1710/02/17151Genomicunknown
ss3446151512TOPMED|TOPMed_freeze_5?chr4:148,126,966fwd/C/Gttctctgtgtgccaagctgagtaatatttttggcccttttttccagagtc10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1040288|allelePos=435|totalLen=1381|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=151
 TAGAACATGA GAACGGAACA CCTCCATGTC AGAGTGTTTC TGTTATCAGA TGTGTTAACA
 AAACATCCAC ACACAGATTA AAGATTAAAG AGAGACCTCA GATTCCACTT GAAAACAGAT
 TAGAACGTTA ATGTGTGACA ACACACCTAA AGAAAGCATT TTTTTTGCCA CTGCAGTATG
 AACAGCATCT CTTTTTAACT CTTTGTGAGG TATTAACTAA ATAACCTCTA CAGTCTCCAT
 AGCTATCATT TATGGATTAC CCGCCACCCA CCAGAGCTAA ATTTCTTCTT GCTAAATCTC
 AAAATGCCCT GTGAGGAATT ATTCTCATAT TCATGATAAG GAATTTTAGG TACATGTGAA
 GCCAGGATCC AAACCCAGGT TTTTTACTTC AAAACTCAGG CCTTCTCCTT TCTCTGTGTG
 CCAAGCTGAG TAAT
 S
 ATTTTTGGCC CTTTTTTCCA GAGTCATACA ACTCTATTCA GTACCTCCAG TGTTTTGTTA
 TTACAGTCAC TCATTTGTTT ATTCTTTGCT CCCCATTATG TGGTAACATT TTGTGTTTTC
 AAATTCCATT GCTGTTTCCA TTGCATGAAA TCGAATTCTC TAAATGAAGA GTACTGAGCA
 CTCAATATAG CTTGAAATTT CAAGAAAATA GGTCATCTTG AAAATGCATT TTATATCACA
 TCATTTTTGC ACAATTTTTT GTGCAATTGT GCATTTTTTT GCACAATTAA ATTAAATGTA
 TAGAAATGTA CATGCAAGGA AGTTGAAATA AGGACAATCT TTTGGCATAA TATTGGTATT
 AATTTTGCAA TATCGCTTTA CAGAATATAC TCTTTGCTAC GTGCTTTTAT TCATGTTATA
 ATTTTACCTC ATTTTGAATA GAATAATGTA AAAATATACT GACTACTTTG GGAAAGAGAA
 GCAAGCTCAT ATAATGCTTC TGTAAAACAA AAGTAAATCC ATGACCAAAA GTCACCCTTG
 AACAGTGGAC TAATACAAAT GTGGTAATAG ATTACTGATG TAGAAAACAG CCATATAGTG
 AACATCAGAC CTGAGTAACT AACAGCTGCT AGTCTCTACT TAAGAACCGT GAGTACTAAT
 ATACTTGCAC ATGTCAGCCA TTTCTAAATA TCTTCTTATT TGCAGGAACA GAATAAAAAC
 TTTACTTTTG GATAAATAAA CACAGCAGCC AAAGTGGGTC TAGAGACCCA TTCCAGAGGT
 TGGGTTAAAA TGAATAATAG TTCTAAAATA TTTTTTAAAA AACACTTCAA TAGTTTTGTA
 AACTTGAAAT TTTCTCAAAT GAGGAAGCCA ATTTTATTTG TAGCTATAAC TTCATCTGGT
 CTTCTCTTAG AACATCCATT GTACTAAACT AAAATCATAT GATCAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_016606 ABBA01070063
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/G
G/G
HWPC
G
ss117232496YRI 2IG 1.00000000 0.500000000.50000000
ss1312328048EAS 1008AF 0.719200020.28079998
EUR 1006AF 0.544700030.45530000
AFR 1322AF 0.343400000.65660000
AMR 694AF 0.510100010.48989999
SAS 978AF 0.469300000.53069997
ss133298216ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ENSEMBL_celera 4IG0.50000000 0.50000000 0.500000000.50000000
ss139950834ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss1506766HapMap-CEUEuropean 226IG0.283185840.566371680.150442480.150222000.566371680.43362832
HapMap-HCBAsian 86IG0.581395330.348837200.069767450.751830000.755813960.24418604
HapMap-JPTAsian 172IG0.534883740.441860470.023255810.099721000.755813960.24418604
HapMap-YRISub-Saharan African 226IG0.123893800.539823000.336283180.200325000.393805300.60619467
HAPMAP-ASW 98IG0.102040820.510204080.387755100.438578000.357142870.64285713
HAPMAP-CHBAsian 82IG0.560975610.341463420.097560970.438578000.731707330.26829270
HAPMAP-CHD 168IG0.488095220.380952390.130952390.250592000.678571400.32142857
HAPMAP-GIH 176IG0.238636360.522727250.238636360.751830000.500000000.50000000
HAPMAP-LWK 180IG0.222222220.511111140.266666681.000000000.477777780.52222222
HAPMAP-MEX 100IG0.360000010.419999990.220000000.317310000.569999990.43000001
HAPMAP-MKK 286IG0.195804190.454545470.349650350.438578000.423076930.57692307
HAPMAP-TSI 176IG0.352272720.431818190.215909090.273322000.568181810.43181819
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss164663880YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss167280816PGP 2IG1.00000000 1.00000000
ss221280601pilot_1_YRI_low_coverage_panel 118AF 0.364406790.63559324
ss232648182pilot_1_CEU_low_coverage_panel 120AF 0.558333340.44166666
ss239885178pilot_1_CHB+JPT_low_coverage_panel 120AF 0.725000020.27500001
ss44509226AoD_African_American 90AF 0.400000010.60000002
AoD_Caucasian 92AF 0.589999970.41000003
ss66372793HapMap-CEUEuropean 118IG0.220338990.661016940.118644070.010028000.550847470.44915253
HapMap-HCBAsian 90IG0.555555580.355555560.088888890.583882000.733333350.26666668
HapMap-JPTAsian 90IG0.577777800.400000010.022222220.294266000.777777790.22222222
HapMap-YRISub-Saharan African 120IG0.133333340.533333360.333333340.402784000.400000010.60000002
ss76100594ICMHP 6IG0.333333340.333333340.33333334 0.500000000.50000000
ss86217048R44_ISDP1 522AF 0.478927200.52107280
ss99019952J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.500+/-0.0070000

  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: ILLUMINAPERLEGEN
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNYES

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