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Reference SNP (refSNP) Cluster Report: rs1129038                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.4927/57801 (ExAC)
T=0.1769/886 (1000 Genomes)
C=0.4635/6028 (GO-ESP)
T=0.4526/56833 (TOPMED)
HGVS Names
  • CM000677.2:g.28111713C>T
  • NC_000015.10:g.28111713C>T
  • NC_000015.9:g.28356859C>T
  • NG_016355.1:g.215437G>A
  • NM_004667.5:c.*50G>A
  • NT_187660.1:g.245178T=
  • NT_187660.1:g.245178T>C
  • NW_011332701.1:g.245178T=
  • NW_011332701.1:g.245178T>C
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 ss286924715 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1129038 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
ss1517796LEE|231129fwd/TA/Ggagatgagagcctgagccaggcagcagagcctcgctgctgtgtagactgtaggctgcctg09/13/0010/10/0386cDNAunknown
ss4321391CGAP-GAI|246040fwd/TA/Ggagatgagagcctgagccaggcagcagagcctcgctgctgtgtagactgtaggctgcctg11/28/0110/10/03103cDNAunknown
ss4410160LEE|e231129fwd/TA/Ggagatgagagcctgagccaggcagcagagcctcgctgctgtgtagactgtaggctgcctg04/26/0210/10/03108cDNAunknown
ss16260531CGAP-GAI|1521315fwd/TA/Ggagatgagagcctgagccaggcagcagagcctcgctgctgtgtagactgtaggctgcctg11/18/0311/22/03120cDNAunknown
ss21255932SSAHASNP|WGSA-200403-chr15.chr15.NT_010280.16_722350byFreqrev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc03/19/0405/16/04121Genomicunknown
ss43730882ABI|hCV489033byFreqrev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc07/18/0511/03/06126Genomicunknown
ss74814846AFFY|SNP_M-307548rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc08/09/0708/09/07128Genomicunknown
ss90103929BCMHGSC_JDW|JWB-0834753rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc02/26/0802/29/08129Genomicunknown
ss96746318HUMANGENOME_JCVI|1103645571831rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc03/27/0803/27/08130Genomicunknown
ss1086963511000GENOMES|CEU.trio.12.15.2008_3134738_chr15_26030454rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc12/16/0812/16/08130Genomicunknown
ss134210332ENSEMBL|ENSSNP5792388rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc05/11/0905/15/09131Genomicunknown
ss136931838ENSEMBL|ENSSNP1080517rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc12/08/0810/15/09131Genomicunknown
ss159976973ILLUMINA|HumanOmni1-Quad_v1-0_B_rs1129038-128_B_R_1562629776rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc08/04/0910/01/09131Genomicunknown
ss167716237COMPLETE_GENOMICS|NA07022_36_chr15_26030454rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc09/30/0909/30/09132Genomicunknown
ss168959279ILLUMINA|Human1M-Duov3_B_GA012253-0_B_F_1533435010rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc10/01/0910/01/09132Genomicunknown
ss170884452COMPLETE_GENOMICS|NA20431_36_chr15_26030454rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc10/01/0910/01/09132Genomicunknown
ss207371954BCM-HGSC-SUB|BCM_CMT_1011-2756867rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc03/15/1003/18/10132Genomicunknown
ss2367227241000GENOMES|pilot_1_CEU_6327353_chr15_26030454rev/C/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc05/01/1005/01/10132Genomicunknown
ss244272347ILLUMINA|CVDSNP55v1_A_rs1129038rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc06/10/1006/10/10132Genomicunknown
ss254862162BL|SNP11864_15_26030454rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc08/19/1008/19/10134Genomicunknown
ss286924715GMI|GMI_NA10851_SNP_2937506rev/C/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc12/17/1012/17/10138Genomicunknown
ss291808311PJP|SNP_1314669_chr15_26030454rev/C/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc01/21/1101/21/11134Genomicunknown
ss479517459ILLUMINA|HumanOmni2.5-4v1_B_rs1129038-128_B_R_1616886709rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc01/30/1210/28/16137Genomicunknown
ss479521362ILLUMINA|HumanOmniExpress-12v1_C_rs1129038-131_B_R_1862853210rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc01/30/1210/27/16137Genomicunknown
ss479973661ILLUMINA|HumanOmni1-Quad_v1-0_C_rs1129038-131_B_R_1862853210rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc01/30/1208/28/15146Genomicunknown
ss484557895ILLUMINA|HumanOmni2.5-4v1_D_rs1129038-131_B_R_1862853210rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc01/30/1210/27/16137Genomicunknown
ss4910784061000GENOMES|20110521_exome_586204_chr15_28356859rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc02/10/1202/22/12137Genomicunknown
ss535289487ILLUMINA|HumanOmni5-4v1_B_kgp3060703-0_B_F_1807130359rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc06/22/1208/29/15146Genomicunknown
ss660095885SSMP|15_28356859rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc12/14/1202/13/15138Genomicunknown
ss713214169NHLBI-ESP|ESP6500SI-chr15-28356859rev/BC/Tcaggcagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctcatctc02/20/1302/20/13138Genomicunknown
ss778382864ILLUMINA|HumanOmni25Exome-8v1_A_rs1129038-131_B_R_1862853210rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/30/1307/10/15142Genomicunknown
ss782725609ILLUMINA|HumanOmni2.5-4v1_H_rs1129038-131_B_R_1862853210rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/30/1307/29/15142Genomicunknown
ss783693030ILLUMINA|HumanOmniExpressExome-8v1_A_rs1129038-131_B_R_1908808062rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/31/1306/18/15142Genomicunknown
ss831977271ILLUMINA|HumanOmniExpress-12v1_H_rs1129038-131_B_R_1862853210rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc09/17/1306/18/15144Genomicunknown
ss833837863ILLUMINA|HumanOmni2.5-8v1_A_rs1129038-131_B_R_1862853210rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc09/18/1307/29/15142Genomicunknown
ss991624564EVA-GONL|EVA-GONL_rs1129038rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc04/23/1404/30/14142Genomicunknown
ss1080003544JMKIDD_LAB|HGDP_WGS_chr15_28356859rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc07/10/1407/12/14142Genomicunknown
ss13528224691000GENOMES|PHASE3_V1_66126844rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc08/16/1408/16/14142Genomicunknown
ss1577523061EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1129038rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc02/19/1502/19/15144Genomicunknown
ss1632671702EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_15_28356859_36575857rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc03/04/1503/04/15144Genomicunknown
ss1675665735EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_15_28356859_36575857rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc03/04/1503/04/15144Genomicunknown
ss1691717641EVA_EXAC|EVA_EXAC_7011783rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc03/04/1503/04/15144Genomicunknown
ss1695636210EVA_DECODE|EVA_DECODE_15_26030454_50783_rs1129038rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc03/02/1503/04/15144Genomicunknown
ss1711390109EVA_MGP|EVA_XIMO_505869rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc03/09/1503/09/15144Genomicunknown
ss1752154469ILLUMINA|OmniExpressExome-8v1-1_B_rs1129038-131_B_R_1908808062rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/27/1506/09/15146Genomicunknown
ss1935021729WEILL_CORNELL_DGM|SNV:chr15:28356859rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc10/16/1510/17/15147Genomicunknown
ss1946388509ILLUMINA|HumanCoreExome-12v1-0_C_rs1129038-131_B_R_1919669393rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc10/29/1510/29/15147Genomicunknown
ss1959597524ILLUMINA|rs1129038-131_B_R_1889515898rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc11/13/1511/13/15147Genomicunknown
ss1968070783GENOMED|rs1129038rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc02/16/1602/16/16147Genomicunknown
ss2028291136JJLAB|SNP8793691rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc08/29/1608/31/16149Genomicunknown
ss2095057520ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs1129038-138_B_R_2264353582rev/BC/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc09/27/1609/27/16150Genomicunknown
ss2156688166USC_VALOUEV|NC_000015.9:g.28356859C>Trev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc11/17/1611/17/16150Genomicunknown
ss2205531181HUMAN_LONGEVITY|HLI-15-28111713-C-Trev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc11/18/1611/18/16150Genomicunknown
ss2370066846TOPMED|15_28356859_C/Trev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc11/19/1611/19/16150Genomicunknown
ss2633208751ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_Seq-rs1129038-131_B_R_2130rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc02/02/1702/02/17151Genomicunknown
ss2633208752ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs1129038-131_B_R_19088080rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc02/02/1702/02/17151Genomicunknown
ss2635056530ILLUMINA|Cancer_BeadChip_11459870_A_GA012253-0_B_F_1533435010rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc02/02/1702/02/17151Genomicunknown
ss2701147181GRF|rs1129038rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc02/13/1702/13/17151Genomicunknown
ss2741066596GNOMAD|exomes_rs1129038rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/17/1705/17/17151Genomicunknown
ss2749249785GNOMAD|coding_rs1129038rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/17/1705/17/17151Genomicunknown
ss2932990844GNOMAD|rs1129038rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/23/1705/23/17151Genomicunknown
ss2985667529AFFY|Axiom_Smokesc1_Affx-11382032rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/24/1705/24/17151Genomicunknown
ss3013006529SWEGEN|NC_000015.9:g.28356859C>Trev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc05/30/1705/30/17151Genomicunknown
ss3021616281ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs1129038-138_B_R_2264353582rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc06/28/1706/28/17151Genomicunknown
ss3027969838BIOINF_KMB_FNS_UNIBA|15.28111713C>Trev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc07/05/1707/05/17151Genomicunknown
ss3223242771TOPMED|TOPMed_freeze_5?chr15:28,111,713rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc10/01/1710/01/17151Genomicunknown
ss3351042076CSHL|rs1129038rev/C/Tagcctacagtctacacagcagcgaggctctgctgcctggctcaggctctc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1129038|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CTCCAAGTTC TAGGAATTAA TTGCTCCTCG TTACTCCTAA AGTTGTTTGG ATTATGTTTT
 CTGCTGTTTT GTTCTTAGCA AAAAATATGG TTTTGTGAGC ACGAAGAGTC TAATGAGCAC
 AGTAAAGTAA ACTGCAGCCG TACTCAATTT CTAATCACTT CATGTTTCTG CTCAACAGGT
 GTTGGATAAA TACAACCCTC CAGACCACTT CCTCCCTGAG TCCTACACCT GTTTCTTCTT
 GCTGAAGCTG CCCAGGTATT CCTGCAAGCA GGTGCTGGAG GAGAAGCTCA AGTACGCCAT
 CCACTTCTGC AAGTCCATAG ACACAGATGA CTACGCTCGC ATCGCACTTA CAGGAGAGCC
 AGCCGCCGAC GACAGCAGCG ACGATTCAGA TAACGAGGAT GTCGACTCCT TTGCTTCGGA
 CTCTACACAA GATTATTTAA CAGGACACTA AGATGGGGAA ACGTCCTCGT GAGATGAGAG
 CCTGAGCCAG GCAGCAGAGC
 R
 CTCGCTGCTG TGTAGACTGT AGGCTGCCTG GTGTGTCTGA TGAGAAGCGT CCGTCCTCGA
 GCCAGGCGGG AGGAGGGAGT GGAGAGACTG ACTGGCCGTG ATGGGAATGA CAGTGAGAAG
 GTCCGCCTGT GCGCGTGGAA CACTGTGGAC GCTCGACTTC CAAGGGTCTT CTCACCCGTA
 ATGCTGCATT ACATGTAGGA CTGTGTTTAC TAAAGTGTGT AAATGTTTAT ATAAATACCA
 AATTGCAGCA TCCCCAAAAT GAATAAAGCC TTTTTACTTG TGGGTGCAAT CGATTTTTTT
 TCTTTCTCCT TTCTTTCAAG TGTCGTGAGT CGTCTTGATT GTATATTGGA AATAACTGTG
 TAACAAATCG TATTATAAAT ATTTCAATTA ATTTTACTCT GAATTTGTTT ATTAAAAGAC
 TTTTGAACAT GAAATGATTA GTATTACTTG AATGCATCCA GAGGATATTT AAACCAAAAT
 GAAAAACCAG AAGGCCATTT

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
CGAP-C-24604 NT_010280 ABBA01044293 AW104946 Hs.174087 Hs.266933
dbSNP Blast Analysis
UniGene Cluster ID
434890
OMIM
227220
605837

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1129038 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
HWPA
G
ss134210332ENSEMBL_Watson 2IG1.00000000 1.00000000
ss1352822469EAS 1008AF 0.001000000.99900001
EUR 1006AF 0.635200020.36480001
AFR 1322AF 0.028000000.97200000
AMR 694AF 0.203200000.79679996
SAS 978AF 0.069500000.93049997
ss136931838ENSEMBL_Venter 2IG1.00000000 1.00000000
ss167716237CEUEuropean 2IG1.00000000 1.00000000
ss1691717641ExAc_Aggregated_Populations121394AF 0.497207430.50279254
ss170884452PGP 2IG1.00000000 1.00000000
ss21255932CEPH 184AF 0.759999990.23999999
ss236722724pilot_1_CEU_low_coverage_panel 120AF 0.766666650.23333333
ss43730882AoD_African_American 90AF 0.150000010.85000002
AoD_Caucasian 92AF 0.690000000.31000000
ss96746318J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.500+/-0.0070000ALFRED: 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_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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