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Reference SNP (refSNP) Cluster Report: rs6856902                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.3510/1758 (1000 Genomes)
A=0.3201/40197 (TOPMED)
HGVS Names
  • CM000666.2:g.162594146A>G
  • NC_000004.11:g.163515298A>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 ss278024444 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6856902 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
ss10185578BCM_SSAHASNP|chr4.NT_016606.15_25034963byFreqfwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca06/27/0310/25/06116Genomicunknown
ss17778469CSHL-HAPMAP|CSHL-HuCC-200402.chr4.NT_016606.16_25063354fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca02/19/0403/04/04120Genomicunknown
ss22073557SSAHASNP|WGSA-200403-chr4.chr4.NT_016606.16_25063354fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca03/20/0403/20/04121Genomicunknown
ss44562433ABI|hCV30731891fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca07/19/0507/19/05126Genomicunknown
ss66848126ILLUMINA|HumanHap300v1.1_rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca11/09/0611/09/06127Genomicunknown
ss67508670ILLUMINA|HumanHap550v1.1_rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca11/14/0611/14/06127Genomicunknown
ss67871917ILLUMINA|HumanHap650Yv1.0_rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca11/14/0611/14/06127Genomicunknown
ss70891704ILLUMINA|HumanHap550v3.0__rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca04/20/0703/31/08130Genomicunknown
ss71484795ILLUMINA|HumanHap650Yv3.0_rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca04/23/0704/23/07127Genomicunknown
ss75919388ILLUMINA|ILMN_Human_1M_rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca08/28/0708/29/07129Genomicunknown
ss79236641ILLUMINA|HumanHap300v2.0_rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca04/18/0711/18/07130Genomicunknown
ss81018999HGSV|Cor18507_SNV_20070510.chr4_163872903byFreqfwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca11/26/0709/05/14130Genomicunknown
ss84378951HGSV|Cor18555_SNV_20070510.chr4_163872903fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca11/27/0712/07/07130Genomicunknown
ss84562865KRIBB_YJKIM|KHS744558fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca12/04/0712/07/07130Genomicunknown
ss1085284741000GENOMES|CEU.trio.12.15.2008_1134143_chr4_163734748fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca12/16/0812/16/08130Genomicunknown
ss1109231691000GENOMES|NA19240_2008_12_16_1020524_chr4_163734748fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca12/17/0812/17/08130Genomicunknown
ss117270612ILLUMINA-UK|NA18507_000217191_NCBI36.1_chr4_163734748fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca01/18/0901/19/09130Genomic99 %
ss122635077ILLUMINA|HumanCNV370v1_C_rs6856902fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca04/14/0904/15/09131Genomicunknown
ss135063511ENSEMBL|ENSSNP2324601fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca12/08/0810/15/09131Genomicunknown
ss154387862ILLUMINA|Human610_Quadv1_B_rs6856902-127_T_F_1501827783fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca06/18/0906/20/09131Genomicunknown
ss159563562ILLUMINA|Human660W-Quad_v1_A_rs6856902-128_T_F_1501827783fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca07/06/0907/07/09131Genomicunknown
ss160818100ILLUMINA|HumanOmni1-Quad_v1-0_B_rs6856902-128_T_F_1512201119fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca08/04/0910/04/09131Genomicunknown
ss162735985COMPLETE_GENOMICS|NA07022_36_chr4_163734748fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca09/28/0909/29/09132Genomicunknown
ss167375040COMPLETE_GENOMICS|NA20431_36_chr4_163734748fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca09/30/0909/30/09132Genomicunknown
ss172208103ILLUMINA|HumanCNV370-Quadv3_C_rs6856902-127_T_F_1501827783fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca10/01/0910/04/09132Genomicunknown
ss174142743ILLUMINA|Human1M-Duov3_B_rs6856902-127_T_F_1501827783fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca10/01/0910/04/09132Genomicunknown
ss199454887BUSHMAN|BUSHMAN-chr4-163734747byFreqfwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca02/16/1009/05/14132Genomicunknown
ss206297208BCM-HGSC-SUB|BCM_CMT_1011-817804fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca03/15/1003/17/10132Genomicunknown
ss2213365331000GENOMES|pilot_1_YRI_3146216_chr4_163734748fwd/A/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca04/22/1004/22/10132Genomicunknown
ss2326910941000GENOMES|pilot_1_CEU_2295723_chr4_163734748fwd/A/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca05/01/1005/01/10132Genomicunknown
ss2399186281000GENOMES|pilot_1_CHB+JPT_1803705_chr4_163734748fwd/A/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca05/01/1005/01/10132Genomicunknown
ss253692076BL|SNP178232_4_163734748fwd/TA/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca08/18/1008/18/10134Genomicunknown
ss278024444GMI|GMI_AK_SNP_2344677fwd/A/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca12/16/1012/16/10137Genomicunknown
ss293242284PJP|SNP_2748642_chr4_163734748fwd/A/Gtgattaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaagaaaca01/21/1101/21/11134Genomicunknown
ss482384127ILLUMINA|HumanOmni1-Quad_v1-0_C_rs6856902-131_T_F_1863193735fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag01/30/1208/28/15146Genomicunknown
ss537402364ILLUMINA|HumanOmni5-4v1_B_rs6856902-131_T_F_1908502410fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag06/22/1208/28/15146Genomicunknown
ss557998575TISHKOFF|snp_chr4_163515298fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag11/22/1211/23/12138Genomicunknown
ss651822371SSMP|4_163515298fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag12/14/1202/10/15138Genomicunknown
ss825567159ILLUMINA|HumanCNV370v1_C_rs6856902-126_T_F_IFB1137693046:0fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag06/24/1311/21/14147Genomicunknown
ss833074703ILLUMINA|Human660W-Quad_v1_C_rs6856902-131_T_F_1863193735fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag09/18/1307/02/15142Genomicunknown
ss833665531ILLUMINA|Human660W-Quad_v1_H_rs6856902-131_T_F_1863193735fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag09/18/1307/02/15142Genomicunknown
ss980922311EVA-GONL|EVA-GONL_rs6856902fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag04/23/1404/24/14142Genomicunknown
ss1072141583JMKIDD_LAB|HGDP_WGS_chr4_163515298fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag07/10/1407/11/14142Genomicunknown
ss13127333111000GENOMES|PHASE3_V1_24368703fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag08/16/1408/16/14142Genomicunknown
ss1430127820DDI|DDI_rs6856902fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag11/04/1411/05/14144Genomicunknown
ss1580873282EVA_GENOME_DK|EVA_GENOME_DK_snv_rs6856902fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag02/19/1502/20/15144Genomicunknown
ss1590438717EVA_DECODE|EVA_DECODE_4_163734748_1282957_rs6856902fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag03/02/1503/03/15144Genomicunknown
ss1611657506EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_4_163515298_13485364fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag03/04/1503/04/15144Genomicunknown
ss1654651539EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_4_163515298_13485364fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag03/04/1503/04/15144Genomicunknown
ss1712721481EVA_SVP|EVA_SVP_415848fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag03/12/1503/12/15144Genomicunknown
ss1802513331HAMMER_LAB|Hsieh_2578063fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag07/15/1507/15/15146Genomicunknown
ss1924162993WEILL_CORNELL_DGM|SNV:chr4:163515298fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag10/16/1510/17/15147Genomicunknown
ss1969928799GENOMED|rs6856902fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag02/16/1602/16/16147Genomicunknown
ss2022670294JJLAB|SNP3172849fwd/TA/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag08/29/1608/30/16149Genomicunknown
ss2150802225USC_VALOUEV|NC_000004.11:g.163515298A>Gfwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag11/17/1611/17/16150Genomicunknown
ss2269037575HUMAN_LONGEVITY|HLI-4-162594146-A-Gfwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag11/18/1611/18/16150Genomicunknown
ss2436980221TOPMED|4_163515298_A/Gfwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag11/20/1611/20/16150Genomicunknown
ss2625829773SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV2025023fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag01/06/1701/06/17151Genomicunknown
ss2706304011GRF|rs6856902fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag02/13/1702/13/17151Genomicunknown
ss2817888599GNOMAD|rs6856902fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag05/18/1705/18/17151Genomicunknown
ss2995926482SWEGEN|NC_000004.11:g.163515298A>Gfwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag05/30/1705/30/17151Genomicunknown
ss3025113860BIOINF_KMB_FNS_UNIBA|4.162594146A>Gfwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag07/05/1707/05/17151Genomicunknown
ss3346070340CSHL|rs6856902fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag10/02/1710/02/17151Genomicunknown
ss3448803239TOPMED|TOPMed_freeze_5?chr4:162,594,146fwd/A/Gaggtagagtaactcttccagttgttggaagagaaaaagaaattttaaaag10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6856902|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 GATTATAGTG CTGTCGCATT TGCTGCCTCC GAGAGCTAGG TGATTTTAAG TAAGGATAAT
 AGCAGAGGTA CGCACTATCA TGCTCTCTTC TAGGATACTG TTAATCTGTA CTTCAAACTC
 ATCAAGCAAG GCTCAAGCTA GCAACTGGCT TTAGCTATTC CACCATGGTA CACATCATGA
 ATATAGCTCC AAAGCATAAG AACTCACAGA AAAATAAAAA TTTAATATAC TACAATTAAA
 AGGAAAAGAA TCTAGAGTAG ATTAAGCAGA ATTTACATTT TCAATAAGCA ATCATTTAAA
 ACAAGCATAT TTAATATCTG CAAAAATATA AGGGAAGATG AAGAAAGCAC AAGAAGTCAT
 AAAATATAAA TGAGGTATAA TTTATGGAAA GAACTAATTG AGATAAAGGA CTTAACAGAT
 GGAATGAGTT CTAGAACGAA AATGAGAGAG GGATGAATTA TTGACCTGCA TGATTAGGTA
 GAGTAACTCT TCCAGTTGTT
 R
 GGAAGAGAAA AAGAAATTTT AAAAGAAACA TGAAAGGGAT ATGGATGTTA GAAATATAAT
 TTCCAATGTA AAACATTACA GATTTACTAG AAATAAAGAG TAATGAGGCA ATATTTTTTA
 AAAAATTATG GAGAAGGCCA GGTGTGATGG CTCACGCCTG TAATCCCAGA ACTTTGGGAG
 GCCAAGATGG GCGGATCACA AGGTCAGGAG ATCGAGACGA TCCTGGCTAA CATGGCGAAA
 CCCCGTCTCT ACTAAAAATA CAAAAAATTA GCCATGCGTG GTGTCGGGCG CCTGTAGTCC
 CAGCTACTCT GGAGGCTGAG GCAGGAGAAT GGCGTGAACC CGGGAGGTGG AGCTTGCAGA
 GAGCCAAGAT TGTGCCACTG CACTCCAGCC TGGGCGACAG AGGGAGACTC CGTCTCAAAA
 ATAAATAAAT AAATATAAAT AAATAAATAA ATAAATAAAT AAATAAATAA ATAAATAAAT
 AAAATAAATT ATGGAGAAAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_016606
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.
SourceA/A
A/G
G/G
HWPA
G
ss117270612YRI 2IG 1.00000000 1.00000000
ss1312733311EAS 1008AF 0.487100010.51289999
EUR 1006AF 0.276299980.72369999
AFR 1322AF 0.396399970.60360003
AMR 694AF 0.239200010.76079994
SAS 978AF 0.305700000.69430000
ss135063511ENSEMBL_Venter 2IG 1.00000000 1.00000000
ENSEMBL_celera 2IG 1.00000000 1.00000000
ss162735985CEUEuropean 2IG 1.00000000 1.00000000
ss167375040PGP 2IG 1.00000000 0.500000000.50000000
ss199454887BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss221336533pilot_1_YRI_low_coverage_panel 118AF 0.389830500.61016947
ss232691094pilot_1_CEU_low_coverage_panel 120AF 0.266666680.73333335
ss239918628pilot_1_CHB+JPT_low_coverage_panel 120AF 0.500000000.50000000
ss81018999HapMap-CEUEuropean 120IG0.033333340.449999990.516666650.200325000.258333330.74166667
HapMap-HCBAsian 90IG0.222222220.533333360.244444440.654721000.488888890.51111114
HapMap-JPTAsian 88IG0.295454530.454545470.250000000.583882000.522727250.47727272
HapMap-YRISub-Saharan African 216IG0.138888900.509259280.351851850.527089000.393518510.60648149
HAPMAP-CHD 162IG0.345679010.481481490.172839511.000000000.586419760.41358024
ENSEMBL_Watson 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.456+/-0.1420000

  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
UNKNOWNUNKNOWNUNKNOWN

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