dbSNP Short Genetic Variations
Welcome to the Reference SNP (rs) Report
All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.
Reference SNP (rs) Report
This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.
rs2542151
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr18:12779948 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
- Alleles
- G>T
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
G=0.169209 (44788/264690, TOPMED)G=0.157499 (29628/188116, ALFA)G=0.169073 (23699/140170, GnomAD) (+ 21 more)
- Clinical Significance
- Not Reported in ClinVar
- Gene : Consequence
-
None
- Publications
- 71 citations
- Genomic View
- See rs on genome
ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.
Release Version: 20230706150541
| Population | Group | Sample Size | Ref Allele | Alt Allele |
|---|---|---|---|---|
| Total | Global | 188332 | G=0.157514 | T=0.842486 |
| European | Sub | 158152 | G=0.156122 | T=0.843878 |
| African | Sub | 8408 | G=0.2006 | T=0.7994 |
| African Others | Sub | 298 | G=0.272 | T=0.728 |
| African American | Sub | 8110 | G=0.1980 | T=0.8020 |
| Asian | Sub | 6348 | G=0.1563 | T=0.8437 |
| East Asian | Sub | 4498 | G=0.1490 | T=0.8510 |
| Other Asian | Sub | 1850 | G=0.1741 | T=0.8259 |
| Latin American 1 | Sub | 610 | G=0.162 | T=0.838 |
| Latin American 2 | Sub | 3160 | G=0.1085 | T=0.8915 |
| South Asian | Sub | 294 | G=0.187 | T=0.813 |
| Other | Sub | 11360 | G=0.15827 | T=0.84173 |
Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").
Download| Study | Population | Group | Sample Size | Ref Allele | Alt Allele |
|---|---|---|---|---|---|
| TopMed | Global | Study-wide | 264690 | G=0.169209 | T=0.830791 |
| Allele Frequency Aggregator | Total | Global | 188116 | G=0.157499 | T=0.842501 |
| Allele Frequency Aggregator | European | Sub | 157972 | G=0.156097 | T=0.843903 |
| Allele Frequency Aggregator | Other | Sub | 11338 | G=0.15823 | T=0.84177 |
| Allele Frequency Aggregator | African | Sub | 8394 | G=0.2009 | T=0.7991 |
| Allele Frequency Aggregator | Asian | Sub | 6348 | G=0.1563 | T=0.8437 |
| Allele Frequency Aggregator | Latin American 2 | Sub | 3160 | G=0.1085 | T=0.8915 |
| Allele Frequency Aggregator | Latin American 1 | Sub | 610 | G=0.162 | T=0.838 |
| Allele Frequency Aggregator | South Asian | Sub | 294 | G=0.187 | T=0.813 |
| gnomAD - Genomes | Global | Study-wide | 140170 | G=0.169073 | T=0.830927 |
| gnomAD - Genomes | European | Sub | 75916 | G=0.15604 | T=0.84396 |
| gnomAD - Genomes | African | Sub | 41996 | G=0.20788 | T=0.79212 |
| gnomAD - Genomes | American | Sub | 13656 | G=0.14118 | T=0.85882 |
| gnomAD - Genomes | Ashkenazi Jewish | Sub | 3322 | G=0.0939 | T=0.9061 |
| gnomAD - Genomes | East Asian | Sub | 3128 | G=0.1685 | T=0.8315 |
| gnomAD - Genomes | Other | Sub | 2152 | G=0.1654 | T=0.8346 |
| The PAGE Study | Global | Study-wide | 78700 | G=0.17104 | T=0.82896 |
| The PAGE Study | AfricanAmerican | Sub | 32514 | G=0.19739 | T=0.80261 |
| The PAGE Study | Mexican | Sub | 10810 | G=0.11341 | T=0.88659 |
| The PAGE Study | Asian | Sub | 8318 | G=0.1312 | T=0.8688 |
| The PAGE Study | PuertoRican | Sub | 7918 | G=0.1604 | T=0.8396 |
| The PAGE Study | NativeHawaiian | Sub | 4534 | G=0.2431 | T=0.7569 |
| The PAGE Study | Cuban | Sub | 4230 | G=0.1598 | T=0.8402 |
| The PAGE Study | Dominican | Sub | 3828 | G=0.1735 | T=0.8265 |
| The PAGE Study | CentralAmerican | Sub | 2450 | G=0.1588 | T=0.8412 |
| The PAGE Study | SouthAmerican | Sub | 1982 | G=0.1398 | T=0.8602 |
| The PAGE Study | NativeAmerican | Sub | 1260 | G=0.1476 | T=0.8524 |
| The PAGE Study | SouthAsian | Sub | 856 | G=0.189 | T=0.811 |
| 14KJPN | JAPANESE | Study-wide | 28258 | G=0.10493 | T=0.89507 |
| 8.3KJPN | JAPANESE | Study-wide | 16760 | G=0.10626 | T=0.89374 |
| 1000Genomes_30x | Global | Study-wide | 6404 | G=0.1747 | T=0.8253 |
| 1000Genomes_30x | African | Sub | 1786 | G=0.2055 | T=0.7945 |
| 1000Genomes_30x | Europe | Sub | 1266 | G=0.1343 | T=0.8657 |
| 1000Genomes_30x | South Asian | Sub | 1202 | G=0.1747 | T=0.8253 |
| 1000Genomes_30x | East Asian | Sub | 1170 | G=0.1932 | T=0.8068 |
| 1000Genomes_30x | American | Sub | 980 | G=0.149 | T=0.851 |
| 1000Genomes | Global | Study-wide | 5008 | G=0.1741 | T=0.8259 |
| 1000Genomes | African | Sub | 1322 | G=0.1997 | T=0.8003 |
| 1000Genomes | East Asian | Sub | 1008 | G=0.1925 | T=0.8075 |
| 1000Genomes | Europe | Sub | 1006 | G=0.1392 | T=0.8608 |
| 1000Genomes | South Asian | Sub | 978 | G=0.175 | T=0.825 |
| 1000Genomes | American | Sub | 694 | G=0.148 | T=0.852 |
| Genetic variation in the Estonian population | Estonian | Study-wide | 4480 | G=0.1379 | T=0.8621 |
| The Avon Longitudinal Study of Parents and Children | PARENT AND CHILD COHORT | Study-wide | 3854 | G=0.1661 | T=0.8339 |
| UK 10K study - Twins | TWIN COHORT | Study-wide | 3708 | G=0.1739 | T=0.8261 |
| KOREAN population from KRGDB | KOREAN | Study-wide | 2930 | G=0.1294 | T=0.8706 |
| HapMap | Global | Study-wide | 1882 | G=0.1339 | T=0.8661 |
| HapMap | American | Sub | 766 | G=0.136 | T=0.864 |
| HapMap | African | Sub | 688 | G=0.145 | T=0.855 |
| HapMap | Asian | Sub | 252 | G=0.103 | T=0.897 |
| HapMap | Europe | Sub | 176 | G=0.125 | T=0.875 |
| Korean Genome Project | KOREAN | Study-wide | 1832 | G=0.1326 | T=0.8674 |
| Genome-wide autozygosity in Daghestan | Global | Study-wide | 1128 | G=0.1578 | T=0.8422 |
| Genome-wide autozygosity in Daghestan | Daghestan | Sub | 626 | G=0.157 | T=0.843 |
| Genome-wide autozygosity in Daghestan | Near_East | Sub | 140 | G=0.129 | T=0.871 |
| Genome-wide autozygosity in Daghestan | Central Asia | Sub | 122 | G=0.164 | T=0.836 |
| Genome-wide autozygosity in Daghestan | Europe | Sub | 108 | G=0.222 | T=0.778 |
| Genome-wide autozygosity in Daghestan | South Asian | Sub | 96 | G=0.15 | T=0.85 |
| Genome-wide autozygosity in Daghestan | Caucasus | Sub | 36 | G=0.11 | T=0.89 |
| Genome of the Netherlands Release 5 | Genome of the Netherlands | Study-wide | 998 | G=0.164 | T=0.836 |
| CNV burdens in cranial meningiomas | Global | Study-wide | 786 | G=0.142 | T=0.858 |
| CNV burdens in cranial meningiomas | CRM | Sub | 786 | G=0.142 | T=0.858 |
| Northern Sweden | ACPOP | Study-wide | 600 | G=0.188 | T=0.812 |
| SGDP_PRJ | Global | Study-wide | 542 | G=0.135 | T=0.865 |
| Qatari | Global | Study-wide | 216 | G=0.171 | T=0.829 |
| A Vietnamese Genetic Variation Database | Global | Study-wide | 214 | G=0.201 | T=0.799 |
| Ancient Sardinia genome-wide 1240k capture data generation and analysis | Global | Study-wide | 80 | G=0.07 | T=0.93 |
| Siberian | Global | Study-wide | 56 | G=0.07 | T=0.93 |
| The Danish reference pan genome | Danish | Study-wide | 40 | G=0.17 | T=0.82 |
Help
Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.
Genomic Placements
| Sequence name | Change |
|---|---|
| GRCh38.p14 chr 18 | NC_000018.10:g.12779948G>T |
| GRCh37.p13 chr 18 | NC_000018.9:g.12779947G>T |
Help
Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.
Not Reported in ClinVar
Help
Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".
| Placement | G= | T |
|---|---|---|
| GRCh38.p14 chr 18 | NC_000018.10:g.12779948= | NC_000018.10:g.12779948G>T |
| GRCh37.p13 chr 18 | NC_000018.9:g.12779947= | NC_000018.9:g.12779947G>T |
Help
Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.
126 SubSNP,
24 Frequency
submissions
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | SC_JCM | ss3564000 | Sep 28, 2001 (100) |
| 2 | WI_SSAHASNP | ss14418689 | Dec 05, 2003 (119) |
| 3 | CSHL-HAPMAP | ss16785766 | Feb 27, 2004 (120) |
| 4 | SSAHASNP | ss21505482 | Apr 05, 2004 (121) |
| 5 | ABI | ss44111455 | Mar 14, 2006 (126) |
| 6 | AFFY | ss66422898 | Nov 30, 2006 (127) |
| 7 | ILLUMINA | ss75169352 | Dec 07, 2007 (129) |
| 8 | AFFY | ss76189761 | Dec 08, 2007 (130) |
| 9 | HGSV | ss78243689 | Dec 07, 2007 (129) |
| 10 | KRIBB_YJKIM | ss81815231 | Dec 15, 2007 (130) |
| 11 | HGSV | ss82412408 | Dec 15, 2007 (130) |
| 12 | HGSV | ss84979315 | Dec 15, 2007 (130) |
| 13 | BCMHGSC_JDW | ss90719956 | Mar 24, 2008 (129) |
| 14 | HUMANGENOME_JCVI | ss96493667 | Feb 05, 2009 (130) |
| 15 | BGI | ss106531457 | Feb 05, 2009 (130) |
| 16 | 1000GENOMES | ss110184269 | Jan 24, 2009 (130) |
| 17 | 1000GENOMES | ss114096096 | Jan 25, 2009 (130) |
| 18 | ILLUMINA-UK | ss117795211 | Feb 14, 2009 (130) |
| 19 | WTCCC | ss120252804 | Dec 01, 2009 (131) |
| 20 | ENSEMBL | ss132656180 | Dec 01, 2009 (131) |
| 21 | ENSEMBL | ss137273409 | Dec 01, 2009 (131) |
| 22 | GMI | ss154874408 | Dec 01, 2009 (131) |
| 23 | COMPLETE_GENOMICS | ss167839169 | Jul 04, 2010 (132) |
| 24 | AFFY | ss172754290 | Jul 04, 2010 (132) |
| 25 | ILLUMINA | ss173385727 | Jul 04, 2010 (132) |
| 26 | BUSHMAN | ss203008631 | Jul 04, 2010 (132) |
| 27 | BCM-HGSC-SUB | ss208086905 | Jul 04, 2010 (132) |
| 28 | 1000GENOMES | ss227751858 | Jul 14, 2010 (132) |
| 29 | WTCCC | ss230385061 | Jul 04, 2010 (132) |
| 30 | 1000GENOMES | ss237389679 | Jul 15, 2010 (132) |
| 31 | 1000GENOMES | ss243656001 | Jul 15, 2010 (132) |
| 32 | ILLUMINA | ss244291019 | Jul 04, 2010 (132) |
| 33 | BL | ss255504933 | May 09, 2011 (134) |
| 34 | GMI | ss282910541 | May 04, 2012 (137) |
| 35 | GMI | ss287247276 | Apr 25, 2013 (138) |
| 36 | PJP | ss292133061 | May 09, 2011 (134) |
| 37 | EXOME_CHIP | ss491531488 | May 04, 2012 (137) |
| 38 | ILLUMINA | ss537102229 | Sep 08, 2015 (146) |
| 39 | TISHKOFF | ss565520209 | Apr 25, 2013 (138) |
| 40 | SSMP | ss661339281 | Apr 25, 2013 (138) |
| 41 | ILLUMINA | ss780683658 | Sep 08, 2015 (146) |
| 42 | ILLUMINA | ss783357069 | Sep 08, 2015 (146) |
| 43 | EVA-GONL | ss993512193 | Aug 21, 2014 (142) |
| 44 | JMKIDD_LAB | ss1081345268 | Aug 21, 2014 (142) |
| 45 | 1000GENOMES | ss1360199095 | Aug 21, 2014 (142) |
| 46 | HAMMER_LAB | ss1397740183 | Sep 08, 2015 (146) |
| 47 | DDI | ss1428153405 | Apr 01, 2015 (144) |
| 48 | EVA_GENOME_DK | ss1578319769 | Apr 01, 2015 (144) |
| 49 | EVA_UK10K_ALSPAC | ss1636445716 | Apr 01, 2015 (144) |
| 50 | EVA_UK10K_TWINSUK | ss1679439749 | Apr 01, 2015 (144) |
| 51 | EVA_DECODE | ss1697565172 | Apr 01, 2015 (144) |
| 52 | EVA_SVP | ss1713611081 | Apr 01, 2015 (144) |
| 53 | ILLUMINA | ss1752247447 | Sep 08, 2015 (146) |
| 54 | HAMMER_LAB | ss1808966124 | Sep 08, 2015 (146) |
| 55 | ILLUMINA | ss1917925766 | Feb 12, 2016 (147) |
| 56 | WEILL_CORNELL_DGM | ss1936984207 | Feb 12, 2016 (147) |
| 57 | ILLUMINA | ss1946489076 | Feb 12, 2016 (147) |
| 58 | ILLUMINA | ss1959789641 | Feb 12, 2016 (147) |
| 59 | GENOMED | ss1968475726 | Jul 19, 2016 (147) |
| 60 | JJLAB | ss2029265082 | Sep 14, 2016 (149) |
| 61 | ILLUMINA | ss2094896539 | Dec 20, 2016 (150) |
| 62 | ILLUMINA | ss2095077941 | Dec 20, 2016 (150) |
| 63 | ILLUMINA | ss2095077942 | Dec 20, 2016 (150) |
| 64 | USC_VALOUEV | ss2157761069 | Dec 20, 2016 (150) |
| 65 | HUMAN_LONGEVITY | ss2219948919 | Dec 20, 2016 (150) |
| 66 | SYSTEMSBIOZJU | ss2629130317 | Nov 08, 2017 (151) |
| 67 | ILLUMINA | ss2633449946 | Nov 08, 2017 (151) |
| 68 | ILLUMINA | ss2633449947 | Nov 08, 2017 (151) |
| 69 | GRF | ss2702334157 | Nov 08, 2017 (151) |
| 70 | GNOMAD | ss2954295745 | Nov 08, 2017 (151) |
| 71 | AFFY | ss2985113203 | Nov 08, 2017 (151) |
| 72 | AFFY | ss2985749918 | Nov 08, 2017 (151) |
| 73 | SWEGEN | ss3016185749 | Nov 08, 2017 (151) |
| 74 | ILLUMINA | ss3021826071 | Nov 08, 2017 (151) |
| 75 | BIOINF_KMB_FNS_UNIBA | ss3028459909 | Nov 08, 2017 (151) |
| 76 | CSHL | ss3351927910 | Nov 08, 2017 (151) |
| 77 | ILLUMINA | ss3627765501 | Oct 12, 2018 (152) |
| 78 | ILLUMINA | ss3627765502 | Oct 12, 2018 (152) |
| 79 | ILLUMINA | ss3634697267 | Oct 12, 2018 (152) |
| 80 | ILLUMINA | ss3638184893 | Oct 12, 2018 (152) |
| 81 | ILLUMINA | ss3640404576 | Oct 12, 2018 (152) |
| 82 | ILLUMINA | ss3643161380 | Oct 12, 2018 (152) |
| 83 | ILLUMINA | ss3644701482 | Oct 12, 2018 (152) |
| 84 | URBANLAB | ss3650745216 | Oct 12, 2018 (152) |
| 85 | ILLUMINA | ss3652245540 | Oct 12, 2018 (152) |
| 86 | ILLUMINA | ss3652245541 | Oct 12, 2018 (152) |
| 87 | ILLUMINA | ss3652245542 | Oct 12, 2018 (152) |
| 88 | ILLUMINA | ss3653885053 | Oct 12, 2018 (152) |
| 89 | EGCUT_WGS | ss3683041167 | Jul 13, 2019 (153) |
| 90 | EVA_DECODE | ss3701254401 | Jul 13, 2019 (153) |
| 91 | ILLUMINA | ss3725661217 | Jul 13, 2019 (153) |
| 92 | ACPOP | ss3742369565 | Jul 13, 2019 (153) |
| 93 | ILLUMINA | ss3744452384 | Jul 13, 2019 (153) |
| 94 | ILLUMINA | ss3744997434 | Jul 13, 2019 (153) |
| 95 | EVA | ss3755141524 | Jul 13, 2019 (153) |
| 96 | PAGE_CC | ss3771960411 | Jul 13, 2019 (153) |
| 97 | ILLUMINA | ss3772495002 | Jul 13, 2019 (153) |
| 98 | KHV_HUMAN_GENOMES | ss3820407491 | Jul 13, 2019 (153) |
| 99 | EVA | ss3835070391 | Apr 27, 2020 (154) |
| 100 | EVA | ss3841149792 | Apr 27, 2020 (154) |
| 101 | EVA | ss3846649702 | Apr 27, 2020 (154) |
| 102 | SGDP_PRJ | ss3886587837 | Apr 27, 2020 (154) |
| 103 | KRGDB | ss3936398056 | Apr 27, 2020 (154) |
| 104 | KOGIC | ss3979641319 | Apr 27, 2020 (154) |
| 105 | EVA | ss3984729921 | Apr 26, 2021 (155) |
| 106 | EVA | ss3985814005 | Apr 26, 2021 (155) |
| 107 | EVA | ss4017787616 | Apr 26, 2021 (155) |
| 108 | TOPMED | ss5049271593 | Apr 26, 2021 (155) |
| 109 | TOMMO_GENOMICS | ss5224241028 | Apr 26, 2021 (155) |
| 110 | 1000G_HIGH_COVERAGE | ss5304533728 | Oct 16, 2022 (156) |
| 111 | EVA | ss5315919252 | Oct 16, 2022 (156) |
| 112 | EVA | ss5430091629 | Oct 16, 2022 (156) |
| 113 | HUGCELL_USP | ss5497428684 | Oct 16, 2022 (156) |
| 114 | EVA | ss5511867126 | Oct 16, 2022 (156) |
| 115 | 1000G_HIGH_COVERAGE | ss5608895964 | Oct 16, 2022 (156) |
| 116 | SANFORD_IMAGENETICS | ss5624408885 | Oct 16, 2022 (156) |
| 117 | SANFORD_IMAGENETICS | ss5660885036 | Oct 16, 2022 (156) |
| 118 | TOMMO_GENOMICS | ss5781032396 | Oct 16, 2022 (156) |
| 119 | YY_MCH | ss5816883355 | Oct 16, 2022 (156) |
| 120 | EVA | ss5827264804 | Oct 16, 2022 (156) |
| 121 | EVA | ss5847483129 | Oct 16, 2022 (156) |
| 122 | EVA | ss5847815349 | Oct 16, 2022 (156) |
| 123 | EVA | ss5851972867 | Oct 16, 2022 (156) |
| 124 | EVA | ss5873265895 | Oct 16, 2022 (156) |
| 125 | EVA | ss5952286424 | Oct 16, 2022 (156) |
| 126 | EVA | ss5979521611 | Oct 16, 2022 (156) |
| 127 | 1000Genomes | NC_000018.9 - 12779947 | Oct 12, 2018 (152) |
| 128 | 1000Genomes_30x | NC_000018.10 - 12779948 | Oct 16, 2022 (156) |
| 129 | The Avon Longitudinal Study of Parents and Children | NC_000018.9 - 12779947 | Oct 12, 2018 (152) |
| 130 | Genome-wide autozygosity in Daghestan | NC_000018.8 - 12769947 | Apr 27, 2020 (154) |
| 131 | Genetic variation in the Estonian population | NC_000018.9 - 12779947 | Oct 12, 2018 (152) |
| 132 | The Danish reference pan genome | NC_000018.9 - 12779947 | Apr 27, 2020 (154) |
| 133 | gnomAD - Genomes | NC_000018.10 - 12779948 | Apr 26, 2021 (155) |
| 134 | Genome of the Netherlands Release 5 | NC_000018.9 - 12779947 | Apr 27, 2020 (154) |
| 135 | HapMap | NC_000018.10 - 12779948 | Apr 27, 2020 (154) |
| 136 | KOREAN population from KRGDB | NC_000018.9 - 12779947 | Apr 27, 2020 (154) |
| 137 | Korean Genome Project | NC_000018.10 - 12779948 | Apr 27, 2020 (154) |
| 138 | Northern Sweden | NC_000018.9 - 12779947 | Jul 13, 2019 (153) |
| 139 | The PAGE Study | NC_000018.10 - 12779948 | Jul 13, 2019 (153) |
| 140 | Ancient Sardinia genome-wide 1240k capture data generation and analysis | NC_000018.9 - 12779947 | Apr 26, 2021 (155) |
| 141 | CNV burdens in cranial meningiomas | NC_000018.9 - 12779947 | Apr 26, 2021 (155) |
| 142 | Qatari | NC_000018.9 - 12779947 | Apr 27, 2020 (154) |
| 143 | SGDP_PRJ | NC_000018.9 - 12779947 | Apr 27, 2020 (154) |
| 144 | Siberian | NC_000018.9 - 12779947 | Apr 27, 2020 (154) |
| 145 | 8.3KJPN | NC_000018.9 - 12779947 | Apr 26, 2021 (155) |
| 146 | 14KJPN | NC_000018.10 - 12779948 | Oct 16, 2022 (156) |
| 147 | TopMed | NC_000018.10 - 12779948 | Apr 26, 2021 (155) |
| 148 | UK 10K study - Twins | NC_000018.9 - 12779947 | Oct 12, 2018 (152) |
| 149 | A Vietnamese Genetic Variation Database | NC_000018.9 - 12779947 | Jul 13, 2019 (153) |
| 150 | ALFA | NC_000018.10 - 12779948 | Apr 26, 2021 (155) |
Help
History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).
| Associated ID | History Updated (Build) |
|---|---|
| rs56547811 | May 25, 2008 (130) |
| rs59359578 | May 25, 2008 (130) |
| rs59874292 | Feb 27, 2009 (130) |
Added to this RefSNP Cluster:
| Submission IDs | Observation SPDI | Canonical SPDI | Source RSIDs |
|---|---|---|---|
| 209950, ss66422898, ss76189761, ss78243689, ss82412408, ss84979315, ss90719956, ss110184269, ss114096096, ss117795211, ss167839169, ss172754290, ss203008631, ss208086905, ss255504933, ss282910541, ss287247276, ss292133061, ss1397740183, ss1697565172, ss1713611081, ss2094896539, ss3643161380 | NC_000018.8:12769946:G:T | NC_000018.10:12779947:G:T | (self) |
| 73499462, 40726678, 28779415, 4515351, 18145412, 43575450, 15654430, 1039932, 279473, 19026129, 38604817, 10277423, 82210335, 40726678, 9002810, ss227751858, ss237389679, ss243656001, ss491531488, ss537102229, ss565520209, ss661339281, ss780683658, ss783357069, ss993512193, ss1081345268, ss1360199095, ss1428153405, ss1578319769, ss1636445716, ss1679439749, ss1752247447, ss1808966124, ss1917925766, ss1936984207, ss1946489076, ss1959789641, ss1968475726, ss2029265082, ss2095077941, ss2095077942, ss2157761069, ss2629130317, ss2633449946, ss2633449947, ss2702334157, ss2954295745, ss2985113203, ss2985749918, ss3016185749, ss3021826071, ss3351927910, ss3627765501, ss3627765502, ss3634697267, ss3638184893, ss3640404576, ss3644701482, ss3652245540, ss3652245541, ss3652245542, ss3653885053, ss3683041167, ss3742369565, ss3744452384, ss3744997434, ss3755141524, ss3772495002, ss3835070391, ss3841149792, ss3886587837, ss3936398056, ss3984729921, ss3985814005, ss4017787616, ss5224241028, ss5315919252, ss5430091629, ss5511867126, ss5624408885, ss5660885036, ss5827264804, ss5847483129, ss5847815349, ss5952286424, ss5979521611 | NC_000018.9:12779946:G:T | NC_000018.10:12779947:G:T | (self) |
| 96421899, 518472862, 1557927, 36019320, 1181880, 114869500, 264817256, 6251098514, ss2219948919, ss3028459909, ss3650745216, ss3701254401, ss3725661217, ss3771960411, ss3820407491, ss3846649702, ss3979641319, ss5049271593, ss5304533728, ss5497428684, ss5608895964, ss5781032396, ss5816883355, ss5851972867, ss5873265895 | NC_000018.10:12779947:G:T | NC_000018.10:12779947:G:T | (self) |
| ss14418689, ss16785766, ss21505482 | NT_010859.13:12769946:G:T | NC_000018.10:12779947:G:T | (self) |
| ss3564000, ss44111455, ss75169352, ss81815231, ss96493667, ss106531457, ss120252804, ss132656180, ss137273409, ss154874408, ss173385727, ss230385061, ss244291019 | NT_010859.14:12769946:G:T | NC_000018.10:12779947:G:T | (self) |
Help
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
71
citations for rs2542151
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 17554260 | Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. | Todd JA et al. | 2007 | Nature genetics |
| 18224312 | Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. | Brockmöller J et al. | 2008 | European journal of clinical pharmacology |
| 18252225 | On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. | Luca D et al. | 2008 | American journal of human genetics |
| 18423522 | Estimating odds ratios in genome scans: an approximate conditional likelihood approach. | Ghosh A et al. | 2008 | American journal of human genetics |
| 18438406 | Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. | Fisher SA et al. | 2008 | Nature genetics |
| 18533027 | Worldwide population differentiation at disease-associated SNPs. | Myles S et al. | 2008 | BMC medical genomics |
| 18587394 | Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. | Barrett JC et al. | 2008 | Nature genetics |
| 18853133 | Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. | Rafiq S et al. | 2008 | Diabetologia |
| 19140132 | Unbiased estimation of odds ratios: combining genomewide association scans with replication studies. | Bowden J et al. | 2009 | Genetic epidemiology |
| 19359276 | Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes. | Barton A et al. | 2009 | Human molecular genetics |
| 19474294 | Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. | Hindorff LA et al. | 2009 | Proceedings of the National Academy of Sciences of the United States of America |
| 19565500 | Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis. | Prahalad S et al. | 2009 | Arthritis and rheumatism |
| 19639606 | Correcting "winner's curse" in odds ratios from genomewide association findings for major complex human diseases. | Zhong H et al. | 2010 | Genetic epidemiology |
| 19776214 | SimCT: a generic tool to visualize ontology-based relationships for biological objects. | Herrmann C et al. | 2009 | Bioinformatics (Oxford, England) |
| 19915572 | Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. | Barrett JC et al. | 2009 | Nature genetics |
| 19953089 | Differences in genetic background between active smokers, passive smokers, and non-smokers with Crohn's disease. | van der Heide F et al. | 2010 | The American journal of gastroenterology |
| 20228799 | Genome-wide association identifies multiple ulcerative colitis susceptibility loci. | McGovern DP et al. | 2010 | Nature genetics |
| 20362271 | Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. | Ritchie MD et al. | 2010 | American journal of human genetics |
| 20369022 | Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. | Nica AC et al. | 2010 | PLoS genetics |
| 20403149 | PTPN2 but not PTPN22 is associated with Crohn's disease in a New Zealand population. | Morgan AR et al. | 2010 | Tissue antigens |
| 20570966 | Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. | McGovern DP et al. | 2010 | Human molecular genetics |
| 20722033 | The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. | Thompson SD et al. | 2010 | Arthritis and rheumatism |
| 20805105 | Synthetic associations in the context of genome-wide association scan signals. | Orozco G et al. | 2010 | Human molecular genetics |
| 20885991 | Advances and challenges in biomarker development for type 1 diabetes prediction and prevention using omic technologies. | Carey C et al. | 2010 | Expert opinion on medical diagnostics |
| 20923970 | Bayesian epistasis association mapping via SNP imputation. | Zhang Y et al. | 2011 | Biostatistics (Oxford, England) |
| 20976797 | P-value based analysis for shared controls design in genome-wide association studies. | Zaykin DV et al. | 2010 | Genetic epidemiology |
| 21217814 | Presymptomatic risk assessment for chronic non-communicable diseases. | Padhukasahasram B et al. | 2010 | PloS one |
| 21246196 | A polymorphism in PTPN2 gene is associated with an earlier onset of type 1 diabetes. | Espino-Paisan L et al. | 2011 | Immunogenetics |
| 21304977 | An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. | Juyal G et al. | 2011 | PloS one |
| 21333900 | The role of genetics in IBS. | Saito YA et al. | 2011 | Gastroenterology clinics of North America |
| 21487504 | Immunopathogenesis of inflammatory bowel disease. | Matricon J et al. | 2010 | Self/nonself |
| 21548950 | Evaluation of 22 genetic variants with Crohn's disease risk in the Ashkenazi Jewish population: a case-control study. | Peter I et al. | 2011 | BMC medical genetics |
| 21730793 | Influence of Crohn's disease risk alleles and smoking on disease location. | Chen H et al. | 2011 | Diseases of the colon and rectum |
| 21752155 | Genetic susceptibility to inflammation and colonic transit in lower functional gastrointestinal disorders: preliminary analysis. | Camilleri M et al. | 2011 | Neurogastroenterology and motility |
| 21818367 | Investigation of multiple susceptibility loci for inflammatory bowel disease in an Italian cohort of patients. | Latiano A et al. | 2011 | PloS one |
| 21830272 | Distinct and overlapping genetic loci in Crohn's disease and ulcerative colitis: correlations with pathogenesis. | Waterman M et al. | 2011 | Inflammatory bowel diseases |
| 21852963 | Pervasive sharing of genetic effects in autoimmune disease. | Cotsapas C et al. | 2011 | PLoS genetics |
| 22021207 | Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy. | Scharl M et al. | 2012 | Inflammatory bowel diseases |
| 22426692 | Confirmation of three inflammatory bowel disease susceptibility loci in a Chinese cohort. | Lv C et al. | 2012 | International journal of colorectal disease |
| 22457781 | PTPN2 gene variants are associated with susceptibility to both Crohn's disease and ulcerative colitis supporting a common genetic disease background. | Glas J et al. | 2012 | PloS one |
| 22654555 | The genetic basis of graves' disease. | Płoski R et al. | 2011 | Current genomics |
| 22984424 | Both baseline clinical factors and genetic polymorphisms influence the development of severe functional status in ankylosing spondylitis. | Schiotis R et al. | 2012 | PloS one |
| 23000205 | Gene network analysis of small molecules with autoimmune disease associated genes predicts a novel strategy for drug efficacy. | Maiti AK et al. | 2013 | Autoimmunity reviews |
| 23300620 | Genotype/phenotype analyses for 53 Crohn's disease associated genetic polymorphisms. | Jung C et al. | 2012 | PloS one |
| 23518806 | Association between the PTPN2 gene and Crohn's disease: dissection of potential causal variants. | Marcil V et al. | 2013 | Inflammatory bowel diseases |
| 23804260 | Protein tyrosine phosphatases and type 1 diabetes: genetic and functional implications of PTPN2 and PTPN22. | Cerosaletti K et al. | 2012 | The review of diabetic studies |
| 24127071 | Associations between PTPN2 polymorphisms and susceptibility to ulcerative colitis and Crohn's disease: a meta-analysis. | Zhang JX et al. | 2014 | Inflammation research |
| 24274136 | Biobanking across the phenome - at the center of chronic disease research. | Imboden M et al. | 2013 | BMC public health |
| 25061809 | Analyzing genome-wide association studies with an FDR controlling modification of the Bayesian Information Criterion. | Dolejsi E et al. | 2014 | PloS one |
| 25369137 | A multilocus genetic study in a cohort of Italian SLE patients confirms the association with STAT4 gene and describes a new association with HCP5 gene. | Ciccacci C et al. | 2014 | PloS one |
| 25460303 | Epistasis amongst PTPN2 and genes of the vitamin D pathway contributes to risk of juvenile idiopathic arthritis. | Ellis JA et al. | 2015 | The Journal of steroid biochemistry and molecular biology |
| 25652333 | Genetics of serum concentration of IL-6 and TNFα in systemic lupus erythematosus and rheumatoid arthritis: a candidate gene analysis. | Solus JF et al. | 2015 | Clinical rheumatology |
| 26344020 | Genetic Variants of PTPN2 Gene in Chinese Children with Type 1 Diabetes Mellitus. | Peng H et al. | 2015 | Medical science monitor |
| 26734582 | Genetic Variations of PTPN2 and PTPN22: Role in the Pathogenesis of Type 1 Diabetes and Crohn's Disease. | Sharp RC et al. | 2015 | Frontiers in cellular and infection microbiology |
| 26798662 | Genetic Factors in Systemic Lupus Erythematosus: Contribution to Disease Phenotype. | Ceccarelli F et al. | 2015 | Journal of immunology research |
| 26811645 | Protein tyrosine phosphatase non-receptor type 2 and inflammatory bowel disease. | Spalinger MR et al. | 2016 | World journal of gastroenterology |
| 26833331 | Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn Disease. | Jiang D et al. | 2016 | American journal of human genetics |
| 26865700 | Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data. | Sanjak JS et al. | 2016 | G3 (Bethesda, Md.) |
| 26928573 | The Clinical Relevance of the IBD-Associated Variation within the Risk Gene Locus Encoding Protein Tyrosine Phosphatase Non-Receptor Type 2 in Patients of the Swiss IBD Cohort. | Spalinger MR et al. | 2016 | Digestion |
| 26993061 | Accounting for selection and correlation in the analysis of two-stage genome-wide association studies. | Robertson DS et al. | 2016 | Biostatistics (Oxford, England) |
| 27153677 | Assessing statistical significance in multivariable genome wide association analysis. | Buzdugan L et al. | 2016 | Bioinformatics (Oxford, England) |
| 27331016 | ERBB3-rs2292239 as primary type 1 diabetes association locus among non-HLA genes in Chinese. | Sun C et al. | 2016 | Meta gene |
| 27336838 | Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci. | Di Narzo AF et al. | 2016 | Clinical and translational gastroenterology |
| 27342690 | Polymorphisms in STAT-4, IL-10, PSORS1C1, PTPN2 and MIR146A genes are associated differently with prognostic factors in Italian patients affected by rheumatoid arthritis. | Ciccacci C et al. | 2016 | Clinical and experimental immunology |
| 27670835 | Systematic meta-analyses and field synopsis of genetic and epigenetic studies in paediatric inflammatory bowel disease. | Li X et al. | 2016 | Scientific reports |
| 27812365 | Shared Genetic Etiology of Autoimmune Diseases in Patients from a Biorepository Linked to De-identified Electronic Health Records. | Restrepo NA et al. | 2016 | Frontiers in genetics |
| 27892471 | Combining Multiple Hypothesis Testing with Machine Learning Increases the Statistical Power of Genome-wide Association Studies. | Mieth B et al. | 2016 | Scientific reports |
| 29954342 | LPG: A four-group probabilistic approach to leveraging pleiotropy in genome-wide association studies. | Yang Y et al. | 2018 | BMC genomics |
| 30888520 | Genetic Mechanisms Highlight Shared Pathways for the Pathogenesis of Polygenic Type 1 Diabetes and Monogenic Autoimmune Diabetes. | Johnson MB et al. | 2019 | Current diabetes reports |
| 32807638 | Genetic susceptibility of increased intestinal permeability is associated with progressive liver disease and diabetes in patients with non-alcoholic fatty liver disease. | Miele L et al. | 2020 | Nutrition, metabolism, and cardiovascular diseases |
| 34198814 | Gene Polymorphisms of NOD2, IL23R, PTPN2 and ATG16L1 in Patients with Crohn's Disease: On the Way to Personalized Medicine? | Hoffmann P et al. | 2021 | Genes |
Help
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genome context:
Select flank length:
Genomic regions, transcripts, and products
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NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.