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Reference SNP (refSNP) Cluster Report: rs250682                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.4299/2153 (1000 Genomes)
C=0.3288/41284 (TOPMED)
HGVS Names
  • CM000667.2:g.1427688G>C
  • NC_000005.10:g.1427688G>C
  • NC_000005.9:g.1427803G>C
  • NG_015885.1:g.22741C>G
  • NM_001044.4:c.653+4776C>G
  • NT_187547.1:g.82084G=
  • NT_187547.1:g.82084G>C
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 ss1573139 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs250682 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
ss324855KWOK|OVLP-000621-35002fwd/BC/Gatagtaatatggccaccccaactttcgtatattactgtttgtgtggtattatcttttcca06/30/0010/10/0379Genomic99 %
ss616813SC_JCM|AC026748.3_121871fwd/BC/Gatagtaatatggccaccccaactttcgtatattactgtttgtgtggtattatcttttcca07/12/0010/10/0380Genomicunknown
ss1167628KWOK|OVLP-000804-529982fwd/BC/Gatagtaatatggccaccccaactttcgtatattactgtttgtgtggtattatcttttcca09/02/0010/10/0386Genomic99 %
ss1573139KWOK|OVLP-000925-84485byFreqfwd/BC/Gatagtaatatggccaccccaactttcgtatattactgtttgtgtggtattatcttttcca10/04/0008/14/0789Genomic99 %
ss2187814TSC-CSHL|TSC0566281fwd/BC/Gatagtaatatggccaccccaactttcgtatattactgtttgtgtggtattatcttttcca10/19/0010/10/03111Genomic95 %
ss6153531SC_JCM|NT_034766.1_1459356fwd/BC/Gatagtaatatggccaccccaactttcgtatattactgtttgtgtggtattatcttttcca01/10/0310/10/03126Genomicunknown
ss6887153WI_SSAHASNP|NT_037650.1_494717rev/TC/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat02/12/0310/10/03126Genomicunknown
ss19619852CSHL-HAPMAP|CSHL-HuDD-200402.chr5.NT_023089.13_1410541rev/TC/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat02/20/0403/04/04120Genomicunknown
ss20237226CSHL-HAPMAP|CSHL-HuFF-200402.chr5.NT_023089.13_1410541rev/TC/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat02/21/0403/04/04120Genomicunknown
ss22300692SSAHASNP|WGSA-200403-chr5.chr5.NT_023089.13_1410541rev/TC/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat03/21/0403/21/04121Genomicunknown
ss42583252ABI|hCV2960965rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat07/18/0507/18/05126Genomicunknown
ss66445248AFFY|SNP_A-2201773byFreqrev/TC/Gccacacaaacagtaatatacgaaagttggggt10/29/0608/14/07127Genomicunknown
ss76229949AFFY|AFFY_6_1M_SNP_A-2201773byFreqrev/C/Gccacacaaacagtaatatacgaaagttggggt08/28/0703/07/10129Genomicunknown
ss81412404KRIBB_YJKIM|KHS38589fwd/C/Gatagtaatatggccaccccaactttcgtatattactgtttgtgtggtattatcttttcca11/30/0711/30/07130Genomicunknown
ss98689074HUMANGENOME_JCVI|1103654003536rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat04/01/0804/01/08130Genomicunknown
ss105900092BGI|BGI_rs250682rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat09/12/0806/18/09130Genomicunknown
ss1112948601000GENOMES|NA19240_2008_12_16_1065944_chr5_1480803rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat12/17/0812/17/08130Genomicunknown
ss142926445ENSEMBL|ENSSNP8207430rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat12/08/0810/19/09131Genomicunknown
ss154912388GMI|GMI_SNP_94467879rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat06/24/0906/24/09131Genomicunknown
ss161945622COMPLETE_GENOMICS|NA07022_36_chr5_1480803rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat09/28/0909/28/09132Genomicunknown
ss164029977COMPLETE_GENOMICS|NA19240_36_chr5_1480803rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat09/29/0909/29/09132Genomicunknown
ss172896079AFFY|GenomeWideSNP_5_SNP_A-2201773rev/C/Gccacacaaacagtaatatacgaaagttggggt10/01/0910/02/09132Genomicunknown
ss206951159BCM-HGSC-SUB|BCM_CMT_1011-1116471rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat03/15/1003/18/10132Genomicunknown
ss2214673891000GENOMES|pilot_1_YRI_3277072_chr5_1480803rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat04/22/1004/22/10132Genomicunknown
ss2327926861000GENOMES|pilot_1_CEU_2397315_chr5_1480803rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat05/01/1005/01/10132Genomicunknown
ss2399973321000GENOMES|pilot_1_CHB+JPT_1882409_chr5_1480803rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat05/01/1005/01/10132Genomicunknown
ss278133770GMI|GMI_AK_SNP_2454003rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat12/16/1012/16/10137Genomicunknown
ss285103014GMI|GMI_NA10851_SNP_1115787rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat12/17/1012/17/10138Genomicunknown
ss293340779PJP|SNP_2847137_chr5_1480803rev/C/Gtggaaaagataataccacacaaacagtaatatacgaaagttggggtggccatattactat01/21/1101/21/11134Genomicunknown
ss558147187TISHKOFF|snp_chr5_1427803rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt11/22/1211/23/12138Genomicunknown
ss651991197SSMP|5_1427803rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt12/14/1202/10/15138Genomicunknown
ss981165229EVA-GONL|EVA-GONL_rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt04/23/1404/24/14142Genomicunknown
ss1072326014JMKIDD_LAB|HGDP_WGS_chr5_1427803rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt07/10/1407/11/14142Genomicunknown
ss13136051061000GENOMES|PHASE3_V1_25280300rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt08/16/1408/16/14142Genomicunknown
ss1430216849DDI|DDI_rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt11/04/1411/05/14144Genomicunknown
ss1580976354EVA_GENOME_DK|EVA_GENOME_DK_snv_rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt02/19/1502/20/15144Genomicunknown
ss1590681143EVA_DECODE|EVA_DECODE_5_1480803_11822_rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt03/02/1503/03/15144Genomicunknown
ss1612111344EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_1427803_13987046rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt03/04/1503/04/15144Genomicunknown
ss1612111345EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_1427803_13987047rev/A/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt03/04/1503/04/15144Genomicunknown
ss1655105377EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_1427803_13987046rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt03/04/1503/04/15144Genomicunknown
ss1655105378EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_1427803_13987047rev/A/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt03/04/1503/04/15144Genomicunknown
ss1712736961EVA_SVP|EVA_SVP_431328rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt03/12/1503/12/15144Genomicunknown
ss1802923475HAMMER_LAB|Hsieh_2691916rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt07/15/1507/15/15146Genomicunknown
ss1924421537WEILL_CORNELL_DGM|SNV:chr5:1427803rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt10/16/1510/17/15147Genomicunknown
ss1969991255GENOMED|rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt02/16/1602/16/16147Genomicunknown
ss2022803988JJLAB|SNP3306543rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt08/29/1608/30/16149Genomicunknown
ss2150954100USC_VALOUEV|NC_000005.9:g.1427803G>Crev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt11/17/1611/17/16150Genomicunknown
ss2270768818HUMAN_LONGEVITY|HLI-5-1427688-G-A,Crev/A/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt11/18/1611/18/16150Genomicunknown
ss2438756671TOPMED|5_1427803_G/Crev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt11/20/1611/20/16150Genomicunknown
ss2625900426SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV2116744rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt01/06/1701/06/17151Genomicunknown
ss2706475486GRF|rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt02/13/1702/13/17151Genomicunknown
ss2820334119GNOMAD|rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt05/18/1705/18/17151Genomicunknown
ss2996316011SWEGEN|NC_000005.9:g.1427803G>Crev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt05/30/1705/30/17151Genomicunknown
ss3025184772BIOINF_KMB_FNS_UNIBA|5.1427688G>Crev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt07/05/1707/05/17151Genomicunknown
ss3346200809CSHL|rs250682rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt10/02/1710/02/17151Genomicunknown
ss3454365870TOPMED|TOPMed_freeze_5?chr5:1,427,688rev/C/Gaagataataccacacaaacagtaatatacgaaagttggggtggccatatt10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs250682|allelePos=929|totalLen=3481|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=151
 CTTCTTGGGC AGCAGCCCAC CCACCAGAGG GAGGTGGCAG AAATGGTTCC TGGAGAGAAA
 TAAAAGGAAC CCTTCCTTGT AGGAACCTGG AGATTATTGA ttggctgcat cccacacatt
 tgatatgctg tgttttcatt TCAAAACCCC AACACAGGAC CACATAACTG TGACCAGTTT
 ACAGTTTCCC CACTTCCATA AATACTTATC GACACTGACT AATATAAATT ATAAAGTTAT
 AAAttaaagc tattaatttg cctcaaatgg actgcattag ctgcatccca caaagtttga
 tatgctgtgt tttcatttca ttcagttcaa agtattccct aatctttctt ttgatttcta
 tttgactaac agggcatttt tagaagtttg ttgtttaatt tgaaatattt ggaagtttgc
 taggtatttt tgttattgat ttctaattta attctgtttt ggcaagatga tatgcttata
 catctttaat attttaaaat atattgagac ttgtttatga cctactagat ggtttacact
 ggtgaatgtt ccacatgcac ctagaaagaa tatgtattct gctgtctttg gttggaaagt
 tgcataaatg tcagagaggt tatgttaggt cactgtgttt ttcaggtttt ctacatcctt
 actggttttc tgtccacttg ctctatcagt tactgagaaa ggggtactga aatctcaact
 ataactgtag atttgtctat ttcttttcac ttctatcagt atttgcttca ttcacatatt
 ttgaaactct gctatgaagt gcatacatgt ttattattat tagtctttga attgaccgct
 ttaccatttg aactatcctt ctgggttaga tttctcattc tgaagtctac tttgtctgat
 agtaatatgg ccaccccaac tttcgtat
 S
 attactgttt gtgtggtatt atcttttcca gccttttatt tttaaactat atgtgtcatt
 atatataaaa tggatttatt gtagacacca tcgagttggt tgtgcttttt atccaatatg
 gcaatctctg ttttttaatt agagtttcca ttcaataatt gtcagcatgg ctggctttaa
 gtctttcatt gtgctaattt tttgccccct ctcttctttg tttcttgttt cctctattta
 ttccctgttt tgaattaatt ttttaggctt tcattttatc aacactatta gctaataaac
 tatagctttc tgttttcatt tcttcgtgga ttttataggg tttacaacac tgaccttcaa
 GTGACATGAT ACCGTTTCAC AGAGCAGAAG GGCCTACAAC AGTAGACTTC TGTtttcctc
 acatcctttg tgcaattgtt gtcatagatt ttttctacaa tatgtatcaa ctccatgata
 ccttgctgtt atttctgctt taagcattta cattttaaat aaatctaaca aagaaatgtt
 ttatatttac ctgcataggc accatctcta gtgctgtccg gtcctgtatg tagattgggg
 tttccattta agaccatctt ccttccatct aaagaatttc ctttaacatt tctcatagcg
 tagacttgct ggcagtgatt cagcttGGGC TTTACACAAA AGTATTTTGC CTTCTTGGGG
 GGCTattgtg gtaagctata catagcattg cttttaccac cttagccatt tttcagtgca
 cagttcagtg gcattaggta caatcacatg ttgtgcaacc atcaccatca tccattggaa
 ctttctcctc ctccaaagct gaaattttgt ccccattaaa tactaagtcc ccatcctccc
 tcactgcagc ccctggcagc taccattcta ctttctgtct ctgtgaattt gtctactcta
 ggtccctcct ctgagtagaa tcacttattt ttttgtgact gccttatttt ccttagcata
 tgtcttcaag gtttattgaa gaatttcaga accagaattt cattcctttt taaggccaaa
 taatatttca attccattgt atggatatat catgttttgt ttatccattt atctttttcc
 tttttagaga caggatctca ctctgttgtc caggctggag tgtgcagtgg tatgatcacg
 gctcactgca ggcttgacct tctgggctca agcaatcctc ctgcctcaga ctcccaagta
 gctgggacta caggtatgtg acaccacatc cagctaattt tttaaaattt tttgtaaagt
 ggggtcttgc catgttgccc aggcctgtct taaactcctg ggctcaagta atcctcccgc
 ctcagcctcc cagagcactg caattacaaa tgtaagccac cacacctggc cagatctatt
 tatcttttga tggacatttg ggttgcttcc acattttggc tactgtaaaa acatgctgct
 atgaacctca atattgagta cctacttttg agtagatacc cagaagttga attgctggag
 ctatgtgata attctgtgtt taattttttg aggaaccacc acactgtttc ccacagtgga
 tgcaaatcgg aacaagggtt ctgatttccc cgcatccttg acaacactta ctttctgctt
 gtttgttttg atcatagcca tcctaatggg tgtgaagtgg tctatcattg tatttttgat
 ttgtatttcc ttaatgatta gtgactgttg ggcatctctt catgtgttta ttggccattt
 gtataccatc tttggagcaa tgtctattca agtcctttgc ccatttttga attgggctgt
 cagttttttt gttgttgagt tttaggagtt ctttacatat tttagatatt attctctttt
 cagattaata ggtgatttgc gaatattttc tctcattctg tagttttcct ttttactctg
 ttgatagcat ccttcagtgc acaaaagttt taaattttga tgaagtctaa ttcatctttt
 gtgtcatatc taagaaaaca ttgccaagtc caagattgtg aaaatttacc ctatgttctc
 ttccaagagt tttatggttt tagcccttat atttggctct tttatccatt ttgggttaat
 ttttctatat catgtgaagt agCTGTTCAC TGATTTTCCT CTGGTTGTAG ATCACATTTC
 TTGCTTCTTG TCATGTCTAG TAATTTTTTA TTAGATGCTA GACTTGGTGA GTTTTATACT
 AATGGGTATT TAGCTCTTGT CGTCTTTGTT TAGAGAGTGT TAGATTTGTT CTAATAGGAA
 GTTAACGTGC TTTGGCACAA TTTTATCCTT TGGAAGCTTG TTTCACCACC TCACTGCCTT
 GGCTCCCTCT TGGTAAAACG GGGTGAGAGG GCTGCTGTGA GGTCATCACA ATGATGCATG
 GGAGGCCTGA GCATGCCTGG ATCACCACCA GTGGCTCCAC TGTCACCCAA TTGAATCATG
 GCCAGGAATT CACCAGGAAA AAGAGCCCAG TA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_034766.1 ABBA01034203 AC009170 AC022130 AC022130.3
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs250682 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/G
G/G
HWPC
G
ss1313605106EAS 1008AF 0.489099980.51089996
EUR 1006AF 0.751499950.24850000
AFR 1322AF 0.459899990.54009998
AMR 694AF 0.691600020.30840001
SAS 978AF 0.529699980.47029999
ss142926445ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss1573139HapMap-CEUEuropean 226IG0.557522120.389380540.053097340.654721000.752212410.24778761
HapMap-HCBAsian 86IG0.186046510.604651150.209302320.200325000.488372090.51162791
HapMap-JPTAsian 172IG0.151162790.534883740.313953490.371093000.418604640.58139533
HapMap-YRISub-Saharan African 226IG0.185840710.495575220.318584081.000000000.433628320.56637168
HAPMAP-ASW 98IG0.163265300.551020380.285714300.438578000.438775510.56122446
HAPMAP-CHBAsian 82IG0.243902440.439024390.317073170.479500000.463414640.53658539
HAPMAP-CHD 170IG0.223529410.517647090.258823540.751830000.482352940.51764709
HAPMAP-GIH 176IG0.306818190.454545470.238636360.438578000.534090940.46590909
HAPMAP-LWK 180IG0.111111110.566666660.322222230.099721000.394444440.60555553
HAPMAP-MEX 100IG0.400000010.460000010.140000001.000000000.630000000.37000000
HAPMAP-MKK 286IG0.363636370.489510480.146853150.751830000.608391580.39160839
HAPMAP-TSI 176IG0.590909060.352272720.056818181.000000000.767045440.23295455
ENSEMBL_Watson 2IG1.00000000 1.00000000
ss161945622CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss164029977YRISub-Saharan African 2IG 1.00000000 1.00000000
ss221467389pilot_1_YRI_low_coverage_panel 118AF 0.423728820.57627118
ss232792686pilot_1_CEU_low_coverage_panel 120AF 0.708333310.29166666
ss239997332pilot_1_CHB+JPT_low_coverage_panel 120AF 0.483333320.51666665
ss66445248HapMap-CEUEuropean 118IG0.474576260.440677970.084745761.000000000.694915240.30508474
HapMap-HCBAsian 90IG0.177777780.600000020.222222220.200325000.477777780.52222222
HapMap-JPTAsian 90IG0.222222220.577777800.200000000.317310000.511111140.48888889
HapMap-YRISub-Saharan African 120IG0.200000000.466666670.333333340.751830000.433333340.56666666
ss76229949ICMHP 10IG0.200000000.600000020.20000000 0.500000000.50000000
ss98689074J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.490+/-0.0690000

  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, NCBI
UNKNOWNUNKNOWNUNKNOWN

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