NCBI
dbSNP
dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
Re-designed RefSNP Report page!
Clean, modern design that makes it easy to find the information that you are looking for. Report any problems by sending us an email.
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP (refSNP) Cluster Report: rs2599404                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.4391/53073 (ExAC)
C=0.3512/1759 (1000 Genomes)
C=0.4610/5994 (GO-ESP)
C=0.4397/55209 (TOPMED)
HGVS Names
  • CM000674.2:g.11133489A>C
  • NC_000012.11:g.11286088A>C
  • NC_000012.12:g.11133489A>C
  • NM_001097643.1:c.756T>G
  • NM_001291314.1:c.-295+37933T>G
  • NM_001291315.1:c.-134+37933T>G
  • NM_001316893.1:c.-134+37933T>G
  • NP_001091112.1:p.Phe252Leu
  • NR_037918.2:n.204+37933T>G
  • NR_133575.1:n.202+37933T>G
  • NT_187658.1:g.328523C=
  • NT_187658.1:g.328523C>A
  • NW_003571047.1:g.328535C=
  • NW_003571047.1:g.328535C>A
  • NW_003571050.1:g.364143A>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 ss281275550 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2599404 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
ss3655842SC_JCM|AC018743.13_173464fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga09/24/0110/10/03100Genomicunknown
ss40117836ABI|hCV1317468fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga07/16/0507/16/05126Genomicunknown
ss88968546BCMHGSC_JDW|JWB-0519236fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga02/26/0802/28/08129Genomicunknown
ss97286625HUMANGENOME_JCVI|1103649367787fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga03/28/0803/28/08130Genomicunknown
ss1114885681000GENOMES|CEU.trio.12.15.2008_2677771_chr12_11177355fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga12/17/0812/17/08130Genomicunknown
ss1131699911000GENOMES|NA19240_2008_12_16_2412530_chr12_11177355fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga12/18/0812/18/08130Genomicunknown
ss132064167ENSEMBL|ENSSNP668211fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga12/08/0810/14/09131Genomicunknown
ss133003307ENSEMBL|ENSSNP10553711fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga05/11/0905/14/09131Genomicunknown
ss167792824COMPLETE_GENOMICS|NA07022_36_chr12_11177355fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga09/30/0909/30/09132Genomicunknown
ss169070757COMPLETE_GENOMICS|NA19240_36_chr12_11177355fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga10/01/0910/01/09132Genomicunknown
ss170407295COMPLETE_GENOMICS|NA20431_36_chr12_11177355fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga10/01/0910/05/09132Genomicunknown
ss203549002BUSHMAN|BUSHMAN-chr12-11177354fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga02/16/1003/09/10132Genomicunknown
ss2256069221000GENOMES|pilot_1_YRI_7416605_chr12_11177355fwd/A/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga04/22/1004/22/10132Genomicunknown
ss2358247321000GENOMES|pilot_1_CEU_5429361_chr12_11177355fwd/A/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga05/01/1005/01/10132Genomicunknown
ss2424035611000GENOMES|pilot_1_CHB+JPT_4288638_chr12_11177355fwd/A/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga05/01/1005/01/10132Genomicunknown
ss254881917BL|SNP15702_12_11177355fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga08/19/1008/19/10134Genomicunknown
ss281275550GMI|GMI_AK_SNP_5595939fwd/A/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga12/16/1012/16/10137Genomicunknown
ss291380382PJP|SNP_886740_chr12_11177355fwd/A/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga01/21/1101/21/11134Genomicunknown
ss482019532ILLUMINA|HumanOmni2.5-4v1_D_kgp1988536-0_T_F_1803102487fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg01/30/1210/27/16137Genomicunknown
ss482976180ILLUMINA|HumanOmni2.5-4v1_B_SNP12-11177355-0_T_F_1619936085fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg01/30/1210/28/16137Genomicunknown
ss491464514EXOME_CHIP|nonsyn_180740_chr_12_11286088fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga03/05/1203/05/12137Genomicunknown
ss491660739CLINSEQ_SNP|SNV-chr12-11177355byFreqfwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg03/06/1209/05/14137Genomicunknown
ss534471039ILLUMINA|HumanOmni5-4v1_B_kgp1988536-0_T_F_1803102487fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg06/22/1208/29/15146Genomicunknown
ss562992951TISHKOFF|snp_chr12_11286088fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg11/22/1211/23/12138Genomicunknown
ss658525097SSMP|12_11286088fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg12/14/1202/13/15138Genomicunknown
ss713077367NHLBI-ESP|ESP6500SI-chr12-11286088fwd/TA/Ccatgaagacaggttgcttttccagcctcccaaattacaaactgatatgatcatggacaga02/20/1302/20/13138Genomicunknown
ss779490516ILLUMINA|HumanOmni25Exome-8v1_A_kgp1988536-0_T_F_1803102487fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg05/30/1307/10/15142Genomicunknown
ss781627237ILLUMINA|HumanOmni2.5-4v1_H_kgp1988536-0_T_F_1803102487fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg05/30/1307/29/15142Genomicunknown
ss834960635ILLUMINA|HumanOmni2.5-8v1_A_kgp1988536-0_T_F_1803102487fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg09/18/1307/29/15142Genomicunknown
ss989238677EVA-GONL|EVA-GONL_rs2599404fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg04/23/1404/25/14142Genomicunknown
ss1078246914JMKIDD_LAB|HGDP_WGS_chr12_11286088fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg07/10/1407/12/14142Genomicunknown
ss13439137731000GENOMES|PHASE3_V1_56829602fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg08/16/1408/16/14142Genomicunknown
ss1397625654HAMMER_LAB|HAMMER_LAB_rs2599404fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg09/30/1409/30/14146Genomicunknown
ss1426844737DDI|DDI_rs2599404fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg11/04/1411/04/14144Genomicunknown
ss1576113604EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2599404fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg02/19/1502/19/15144Genomicunknown
ss1598907691EVA_DECODE|EVA_DECODE_12_11177355_87112_rs2599404fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg03/02/1503/04/15144Genomicunknown
ss1628013014EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_12_11286088_31437761fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg03/04/1503/04/15144Genomicunknown
ss1671007047EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_12_11286088_31437761fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg03/04/1503/04/15144Genomicunknown
ss1690796578EVA_EXAC|EVA_EXAC_6013901fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg03/04/1503/04/15144Genomicunknown
ss1711321407EVA_MGP|EVA_XIMO_437167fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg03/09/1503/09/15144Genomicunknown
ss1807120562HAMMER_LAB|Hsieh_6141420fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg07/15/1507/16/15146Genomicunknown
ss1932604374WEILL_CORNELL_DGM|SNV:chr12:11286088fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg10/16/1510/17/15147Genomicunknown
ss1967523288GENOMED|rs2599404fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg02/16/1602/16/16147Genomicunknown
ss2027046915JJLAB|SNP7549470fwd/TA/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg08/29/1608/30/16149Genomicunknown
ss2155371213USC_VALOUEV|NC_000012.11:g.11286088A>Cfwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg11/17/1611/17/16150Genomicunknown
ss2351414561TOPMED|12_11286088_A/Cfwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg11/19/1611/19/16150Genomicunknown
ss2628002524SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV4796983fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg01/06/1701/06/17151Genomicunknown
ss2632925017ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp1988536-0_T_F_180310248fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg02/02/1702/02/17151Genomicunknown
ss2699696018GRF|rs2599404fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg02/13/1702/13/17151Genomicunknown
ss2739640969GNOMAD|exomes_rs2599404fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg05/17/1705/17/17151Genomicunknown
ss2748816020GNOMAD|coding_rs2599404fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg05/17/1705/17/17151Genomicunknown
ss2907347871GNOMAD|rs2599404fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg05/22/1705/22/17151Genomicunknown
ss2984968073AFFY|Axiom_PsorMich_Affx-6896667fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg05/24/1705/24/17151Genomicunknown
ss3009210016SWEGEN|NC_000012.11:g.11286088A>Cfwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg05/30/1705/30/17151Genomicunknown
ss3023067495EVA_SAMSUNG_MC|EXOMES.12:g11286088a>cfwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg07/03/1707/03/17151Genomicunknown
ss3027328751BIOINF_KMB_FNS_UNIBA|12.11133489A>Cfwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg07/05/1707/05/17151Genomicunknown
ss3162962310TOPMED|TOPMed_freeze_5?chr12:11,133,489fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg09/30/1709/30/17151Genomicunknown
ss3349924652CSHL|rs2599404fwd/A/Cagacaggttgcttttccagcctcccaaattacaaactgatatgatcatgg10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2599404|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 AATATAAAAT ACATGTATGA AATAAACATG GCTTCATAAT TGAGGAATTT TTGTCATATT
 TTCTATAATT TGGCAGTTTT TGTGAAAAAA CAATAAAAAG CATGTTATTG TCAATGTTCT
 TCAGTTTTTC ATACACACAC ACACACACAC ACACATCTAT ATATATGTAC TTTTCTAGAC
 TAACTTTAGG TAAAAGACTT TTCTAGGTAT ACATGTGGAA ATTATTCATA TACATATATT
 ACAGAAAACC CAGTAAGAAA TATAAAATGT TTCATACACC ACCAGTTTGT TTTCTGCTAG
 AAGACACACA ATGCCCCTCT TGTGAATCTA TGGAGACGAA GGCTTCTGTC TTTCACCCAG
 TACCTCACAT GCCGCAAAAC TGAAAGAAAA ATCTGCTTTA GCTTCTTGTT TCCCAAAATC
 AGGATGAATG GGTGGGTTGA AGGATAGCTG AATATAATAG CTTGGCAGAA CATGAAGACA
 GGTTGCTTTT CCAGCCTCCC
 M
 AAATTACAAA CTGATATGAT CATGGACAGA AAGTAAATGG CACATAACAG AAGAAAGGAG
 GTCACAGTTT GCAAAGCTTT TATGTGGACC TTGGTGCTGG GATCTTGAGA TCCTTTGCCA
 TGGAGCTGCA TCTTCTTGAG ATGTTTACAC AGAGAACAGA TTAACAGCAG AAAAGATATC
 AGGGTCAGAG TGAGGGGTAC AAAGTTTGCT AGCATGGTTA GAGTCATATT TGAATGGTAC
 ATTGCACTCC TCAATTTGAT CTTCCAAGTC ACGTTTCCTT CATATTCTTT TGTCCATACA
 GTCTCATCCA TGTTTATCAC AAAAAGATGA CAAACCAAAA ATAGCAAAGG CCCCAACAGT
 ATCACCAGAA CAACACTCTT AACTCTCCTC TTTATGCGAA GAAAAATAAG GTTGGAGAAA
 TTGGCAATCC TGAGCAAATA AAACATGCTG AGGCTAGTAG CAAGCCAGCT GCTGAAATGG
 TTGGTTACTG CCCAGACATT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000012 ABBA01067813 AC018630 AC018851 AC079625
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/C
C/C
HWPA
C
ss132064167ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss133003307ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss1343913773EAS 1008AF 0.805599990.19440000
EUR 1006AF 0.489100010.51090002
AFR 1322AF 0.643000010.35699999
AMR 694AF 0.530300020.46970001
SAS 978AF 0.743400040.25659999
ss167792824CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss169070757YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss1690796578ExAc_Aggregated_Populations121390AF 0.561388910.43861109
ss170407295PGP 2IG 1.00000000 0.500000000.50000000
ss203549002BANTU 2IG 1.00000000 0.500000000.50000000
ss225606922pilot_1_YRI_low_coverage_panel 118AF 0.610169470.38983050
ss235824732pilot_1_CEU_low_coverage_panel 120AF 0.458333340.54166669
ss242403561pilot_1_CHB+JPT_low_coverage_panel 120AF 0.808333340.19166666
ss491660739CSAgilent 594GF0.262737270.464535440.272727280.250592000.495004980.50499499
ss97286625J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.493+/-0.0600000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement