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Reference SNP (refSNP) Cluster Report: rs5029939                 **Clinical Channel**
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 PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.1396/699 (1000 Genomes)
G=0.1341/16834 (TOPMED)
HGVS Names
  • CM000668.2:g.137874586C>G
  • NC_000006.11:g.138195723C>G
  • NC_000006.12:g.137874586C>G
  • NG_032761.1:g.12143C>G
  • NM_001270507.1:c.296-259C>G
  • NM_001270508.1:c.296-259C>G
  • NM_006290.3:c.296-259C>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 ss279042550 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5029939 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
ss7984946PGA-UW-FHCRC|TNFAIP3-009094byFreqfwd/BC/Gcccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct03/19/0304/07/04113Genomicunknown
ss10324843BCM_SSAHASNP|chr6.NT_025741.12_42300152byFreqfwd/BC/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct06/29/0310/25/06116Genomicunknown
ss14536261WUGSC_SSAHASNP|chr6.NT_025741.13_42300152fwd/BC/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct11/05/0311/22/03119Genomicunknown
ss66465675AFFY|SNP_A-2255250byFreqrev/TC/Gcttggttctagcttaatctgctcctaactagt10/29/0603/31/08127Genomicunknown
ss76268581AFFY|AFFY_6_1M_SNP_A-2255250rev/C/Gcttggttctagcttaatctgctcctaactagt08/28/0708/30/07130Genomicunknown
ss79053529HGSV|Cor18507_SNV_20070510.chr6_138237416fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct10/19/0710/22/07129Genomicunknown
ss82182604KRIBB_YJKIM|KHS202308fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct11/30/0712/02/07130Genomicunknown
ss85707648HGSV|Cor18517_SNV_20070510.chr6_138237416fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct12/06/0712/10/07130Genomicunknown
ss116735767ILLUMINA-UK|NA18507_000184519_NCBI36.1_chr6_138237416fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct01/17/0901/18/09130Genomic99 %
ss160737352ILLUMINA|HumanOmni1-Quad_v1-0_B_rs5029939-128_B_F_1518202867fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct08/04/0910/04/09131Genomicunknown
ss173046223AFFY|GenomeWideSNP_5_SNP_A-2255250rev/C/Gcttggttctagcttaatctgctcctaactagt10/01/0910/02/09132Genomicunknown
ss173907368ILLUMINA|Human1M-Duov3_B_rs5029939-128_B_F_1518202867fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct10/01/0910/04/09132Genomicunknown
ss202474156BUSHMAN|BUSHMAN-chr6-138237415byFreqfwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct02/16/1009/05/14132Genomicunknown
ss2227068241000GENOMES|pilot_1_YRI_4516507_chr6_138237416fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct04/22/1004/22/10132Genomicunknown
ss2337055531000GENOMES|pilot_1_CEU_3310182_chr6_138237416fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct05/01/1005/01/10132Genomicunknown
ss2407151191000GENOMES|pilot_1_CHB+JPT_2600196_chr6_138237416fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct05/01/1005/01/10132Genomicunknown
ss279042550GMI|GMI_AK_SNP_3362792fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct12/16/1012/16/10137Genomicunknown
ss293735015PJP|SNP_3241373_chr6_138237416fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct01/21/1101/21/11134Genomicunknown
ss481130187ILLUMINA|HumanOmni2.5-4v1_B_rs5029939-128_B_F_1617299147fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg01/30/1210/28/16137Genomicunknown
ss481152226ILLUMINA|HumanOmniExpress-12v1_C_rs5029939-131_B_F_1857741275fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg01/30/1210/27/16137Genomicunknown
ss482141721ILLUMINA|HumanOmni1-Quad_v1-0_C_rs5029939-131_B_F_1865215866fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg01/30/1208/28/15146Genomicunknown
ss485360123ILLUMINA|HumanOmni2.5-4v1_D_rs5029939-131_B_F_1857741275fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg01/30/1210/28/16137Genomicunknown
ss491392262EXOME_CHIP|.GWAS._108488_chr_6_138195723fwd/C/Gtccaggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctggctcct03/05/1203/05/12137Genomicunknown
ss537304611ILLUMINA|HumanOmni5-4v1_B_rs5029939-131_B_F_1885472587fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg06/22/1208/29/15146Genomicunknown
ss559561877TISHKOFF|snp_chr6_138195723fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg11/22/1211/23/12138Genomicunknown
ss653855365SSMP|6_138195723fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg12/14/1202/11/15138Genomicunknown
ss778718043ILLUMINA|HumanOmni25Exome-8v1_A_rs5029939-131_B_F_1865215866fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/30/1307/09/15142Genomicunknown
ss783125751ILLUMINA|HumanOmni2.5-4v1_H_rs5029939-131_B_F_1857741275fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/30/1307/28/15142Genomicunknown
ss784082375ILLUMINA|HumanOmniExpressExome-8v1_A_rs5029939-131_B_F_1885472587fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/31/1306/19/15142Genomicunknown
ss832384588ILLUMINA|HumanOmniExpress-12v1_H_rs5029939-131_B_F_1857741275fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg09/17/1306/18/15144Genomicunknown
ss834177388ILLUMINA|HumanOmni2.5-8v1_A_rs5029939-131_B_F_1865215866fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg09/18/1307/28/15142Genomicunknown
ss983561240EVA-GONL|EVA-GONL_rs5029939fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg04/23/1404/24/14142Genomicunknown
ss1074079918JMKIDD_LAB|HGDP_WGS_chr6_138195723fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg07/10/1407/11/14142Genomicunknown
ss13225087861000GENOMES|PHASE3_V1_34567562fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg08/16/1408/16/14142Genomicunknown
ss1397472808HAMMER_LAB|HAMMER_LAB_rs5029939fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg09/30/1409/30/14146Genomicunknown
ss1581919406EVA_GENOME_DK|EVA_GENOME_DK_snv_rs5029939fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg02/19/1502/20/15144Genomicunknown
ss1593133165EVA_DECODE|EVA_DECODE_6_138237416_1097213_rs5029939fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg03/02/1503/03/15144Genomicunknown
ss1616824890EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_138195723_19168847fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg03/04/1503/04/15144Genomicunknown
ss1659818923EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_138195723_19168847fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg03/04/1503/04/15144Genomicunknown
ss1712904353EVA_SVP|EVA_SVP_598720fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg03/12/1503/12/15144Genomicunknown
ss1752604167ILLUMINA|OmniExpressExome-8v1-1_B_rs5029939-131_B_F_2087479502fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/27/1506/09/15146Genomicunknown
ss1804697837HAMMER_LAB|Hsieh_3709060fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg07/15/1507/16/15146Genomicunknown
ss1926807223WEILL_CORNELL_DGM|SNV:chr6:138195723fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg10/16/1510/17/15147Genomicunknown
ss1958954796ILLUMINA|rs5029939-138_B_F_2264361976fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg11/13/1511/13/15147Genomicunknown
ss2024061070JJLAB|SNP4563625fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg08/29/1608/30/16149Genomicunknown
ss2094967079ILLUMINA|Immuno_BeadChip_11419691_B_imm_6_138237416-1_T_R_1670197154fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg09/27/1609/27/16150Genomicunknown
ss2095191160ILLUMINA|InfiniumImmunoArray-24v2-0_A_imm_6_138237416-1_T_R_2310716526fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg09/27/1609/27/16150Genomicunknown
ss2095191161ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs5029939-138_B_F_2264361976fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg09/27/1609/27/16150Genomicunknown
ss2288888540HUMAN_LONGEVITY|HLI-6-137874586-C-Gfwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg11/18/1611/18/16150Genomicunknown
ss2457563258TOPMED|6_138195723_C/Gfwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg11/20/1611/20/16150Genomicunknown
ss2634518302ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-rs5029939-131_B_F_2131fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg02/02/1702/02/17151Genomicunknown
ss2634518303ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs5029939-131_B_F_20874795fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg02/02/1702/02/17151Genomicunknown
ss2634518304ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs5029939-131_B_F_2130fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg02/02/1702/02/17151Genomicunknown
ss2707886775GRF|rs5029939fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg02/13/1702/13/17151Genomicunknown
ss2845796232GNOMAD|rs5029939fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/18/1705/18/17151Genomicunknown
ss2985388211AFFY|Axiom_PsorMich_Affx-27789018fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/24/1705/24/17151Genomicunknown
ss2986014584AFFY|Axiom_Smokesc1_Affx-27789018fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/24/1705/24/17151Genomicunknown
ss3000043253SWEGEN|NC_000006.11:g.138195723C>Gfwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg05/30/1705/30/17151Genomicunknown
ss3022671706ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs5029939-138_B_F_2264361976fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg06/28/1706/28/17151Genomicunknown
ss3513436243TOPMED|TOPMed_freeze_5?chr6:137,874,586fwd/C/Ggtcacctaaactagttaggagcagattaagctagaaccaaggtcccctgg10/05/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5029939|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=151
 AACCTGTTTT TTTGTTTGTT TTTCTTCTCA AAATGTTAGC CCTAAACACT GAATTATTTT
 CAAATTTAGA CACCCAGGTG CTTTTTAACT TTTGTACTTT ACAGTTACTA ACAAGCAGGT
 TTGCATAAGG CATTTTTGAG AGCCGGACTA GCAGGCCATA GGTAATTCCG TGTTGTCAAT
 ACGACTTTCC ACACCAGGAG AGGAAACTCC CAGGGCCCAA AGGCTAAAGT GGAATGGTCA
 AGTCATTTGC CATTGAGTCA TAGCCAGACC ATCCCTATCT AGCAAGCCAT GCCTGCTTCC
 TGGTTTGTGC ATGTTGCCCT GTGTGCTCCT CCTTAGAACT AGAGAGCAGC AATGCCAGTG
 CCTTCACCAG CAAATCAAGG GATGGTAGGA AGGGATAGGG CTTTAGAGAT CATCACTTAC
 TGCCCTCATT TCACAAGAGG AAAAATGCCC AGTGAACTTA AGGAATTTCC TCCAGGTCAC
 CTAAACTAGT TAGGAGCAGA
 S
 TTAAGCTAGA ACCAAGGTCC CCTGGCTCCT TTGCAGTTGG TGTCATTCAT TAAAAAGAAG
 AATAAAAAGA ACTCTTTTTT TCTTAAAGCT GTCATCATCT TGTGAAATAT CAGTTTGCCC
 TTGACTAGGA AATTACATCA AATTAAACCA TTCAGTCCCC TAGAATAGCA GTAGGGCTGG
 TTTATTCTGA AAACCTTTGC TGGGTCTTAC ATGCAGATAA CTTGACTTTC CTTCTCTTCT
 CCTCCTTTCT GTCCTCAGGT GACGGCAATT GCCTCATGCA TGCCACTTCT CAGTACATGT
 GGGGCGTTCA GGACACAGAC TTGGTACTGA GGAAGGCGCT GTTCAGCACG CTCAAGGAAA
 CAGACACACG CAACTTTAAA TTCCGCTGGC AACTGGAGTC TCTCAAATCT CAGGAATTTG
 TTGAAACGGG GCTTTGCTAT GATACTCGGG TAGGTTTTTC CCCCTAATTA TCTACTAACA
 GAGCTCCATG GTGGGCATAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_025741
dbSNP Blast Analysis
OMIM
612378

  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
ss10324843HapMap-CEUEuropean 224IG0.946428600.05357143 1.000000000.973214270.02678571
HapMap-HCBAsian 86IG0.837209280.16279070 1.000000000.918604670.08139535
HapMap-JPTAsian 170IG0.788235310.188235300.023529410.402784000.882352950.11764706
HapMap-YRISub-Saharan African 226IG0.309734520.486725660.203539821.000000000.553097370.44690266
HAPMAP-ASW 98IG0.551020380.306122450.142857150.099721000.704081650.29591838
HAPMAP-CHBAsian 82IG0.853658560.14634146 1.000000000.926829280.07317073
HAPMAP-CHD 170IG0.870588240.12941177 1.000000000.935294090.06470589
HAPMAP-GIH 176IG0.943181810.05681818 1.000000000.971590940.02840909
HAPMAP-LWK 180IG0.366666670.577777800.055555560.010028000.655555550.34444445
HAPMAP-MEX 100IG0.959999980.04000000 1.000000000.980000020.02000000
HAPMAP-MKK 284IG0.408450690.464788730.126760561.000000000.640845060.35915494
HAPMAP-TSI 176IG0.920454560.07954545 1.000000000.960227250.03977273
ENSEMBL_Watson 2IG1.00000000 1.00000000
ss116735767YRI 2IG 1.00000000 0.500000000.50000000
ss1322508786EAS 1008AF 0.949400010.05060000
EUR 1006AF 0.976100030.02390000
AFR 1322AF 0.591499980.40849999
AMR 694AF 0.922199960.07780000
SAS 978AF 0.969300030.03070000
ss202474156BUSHMAN_POP 2IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss222706824pilot_1_YRI_low_coverage_panel 118AF 0.500000000.50000000
ss233705553pilot_1_CEU_low_coverage_panel 120AF 0.958333310.04166667
ss240715119pilot_1_CHB+JPT_low_coverage_panel 120AF 0.850000020.15000001
ss66465675HapMap-CEUEuropean 118IG0.915254240.08474576 1.000000000.957627120.04237288
HapMap-HCBAsian 90IG0.822222230.17777778 1.000000000.911111120.08888889
HapMap-JPTAsian 90IG0.644444470.311111120.044444451.000000000.800000010.20000000
HapMap-YRISub-Saharan African 120IG0.216666670.566666660.216666670.317310000.500000000.50000000
ss76268581ICMHP 10IG1.00000000 1.00000000
ss7984946PGA-AFRICAN-PANELAfrican American 40IG0.449999990.400000010.150000010.654721000.649999980.34999999
PGA-EUROPEAN-PANELEuropean 44IG0.954545440.04545455 1.000000000.977272750.02272727

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.240+/-0.2500000

  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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