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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs7154773

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr14:60282400 (GRCh38.p7) 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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.45359 (56957/125568, TOPMED)
C=0.4273 (13214/30924, GnomAD)
C=0.448 (2244/5008, 1000G) (+ 2 more)
C=0.348 (1341/3854, ALSPAC)
C=0.357 (1324/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PPM1A : Intron Variant
Publications
3 citations
Genomic View
See rs on genome
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.p7 chr 14 NC_000014.9:g.60282400G>C
GRCh37.p13 chr 14 NC_000014.8:g.60749118G>C
PPM1A RefSeqGene NG_029698.1:g.41649G>C
Gene: PPM1A, protein phosphatase, Mg2+/Mn2+ dependent 1A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PPM1A transcript variant 1 NM_021003.4:c. N/A Intron Variant
PPM1A transcript variant 2 NM_177951.2:c. N/A Intron Variant
PPM1A transcript variant 3 NM_177952.2:c. N/A Intron Variant
PPM1A transcript variant X13 XM_005267779.1:c. N/A Intron Variant
PPM1A transcript variant X14 XM_005267781.1:c. N/A Intron Variant
PPM1A transcript variant X3 XM_011536872.1:c. N/A Intron Variant
PPM1A transcript variant X4 XM_011536876.1:c. N/A Intron Variant
PPM1A transcript variant X5 XM_011536877.1:c. N/A Intron Variant
PPM1A transcript variant X7 XM_011536878.1:c. N/A Intron Variant
PPM1A transcript variant X8 XM_011536879.2:c. N/A Intron Variant
PPM1A transcript variant X9 XM_011536880.2:c. N/A Intron Variant
PPM1A transcript variant X10 XM_011536881.2:c. N/A Intron Variant
PPM1A transcript variant X16 XM_011536882.2:c. N/A Intron Variant
PPM1A transcript variant X17 XM_011536883.1:c. N/A Intron Variant
PPM1A transcript variant X14 XM_011536884.1:c. N/A Intron Variant
PPM1A transcript variant X1 XM_017021381.1:c. N/A Intron Variant
PPM1A transcript variant X2 XM_017021382.1:c. N/A Intron Variant
PPM1A transcript variant X6 XM_017021383.1:c. N/A Intron Variant
PPM1A transcript variant X11 XM_017021384.1:c. N/A Intron Variant
PPM1A transcript variant X12 XM_017021385.1:c. N/A Intron Variant
PPM1A transcript variant X15 XM_017021386.1:c. N/A Intron Variant
PPM1A transcript variant X18 XM_017021387.1:c. N/A Intron Variant
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

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
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.54641 C=0.45359
The Genome Aggregation Database Global Study-wide 30924 G=0.5727 C=0.4273
The Genome Aggregation Database European Sub 18488 G=0.6867 C=0.3133
The Genome Aggregation Database African Sub 8710 G=0.255 C=0.745
The Genome Aggregation Database East Asian Sub 1612 G=0.852 C=0.148
The Genome Aggregation Database Other Sub 976 G=0.67 C=0.33
The Genome Aggregation Database American Sub 836 G=0.73 C=0.27
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=0.53 C=0.47
1000Genomes Global Study-wide 5008 G=0.552 C=0.448
1000Genomes African Sub 1322 G=0.188 C=0.812
1000Genomes East Asian Sub 1008 G=0.850 C=0.150
1000Genomes Europe Sub 1006 G=0.669 C=0.331
1000Genomes South Asian Sub 978 G=0.52 C=0.48
1000Genomes American Sub 694 G=0.68 C=0.32
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.652 C=0.348
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.643 C=0.357
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= C Note
GRCh38.p7 chr 14 NC_000014.9:g.60282400G= NC_000014.9:g.60282400G>C
GRCh37.p13 chr 14 NC_000014.8:g.60749118G= NC_000014.8:g.60749118G>C
PPM1A RefSeqGene NG_029698.1:g.41649G= NG_029698.1:g.41649G>C
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#.

5 Frequency, 47 SubSNP submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10749010 Jul 11, 2003 (116)
2 PERLEGEN ss24616665 Sep 20, 2004 (123)
3 ABI ss43627282 Mar 14, 2006 (126)
4 AFFY ss66275951 Jul 04, 2010 (132)
5 AFFY ss75927741 Dec 07, 2007 (129)
6 HGSV ss79014003 Dec 07, 2007 (129)
7 KRIBB_YJKIM ss82394873 Dec 15, 2007 (130)
8 HGSV ss83944871 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss89967462 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss96922591 Feb 06, 2009 (130)
11 1000GENOMES ss113399721 Jan 25, 2009 (130)
12 ILLUMINA-UK ss118514946 Feb 14, 2009 (130)
13 ENSEMBL ss134004970 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss168162568 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss169685426 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss171206935 Jul 04, 2010 (132)
17 BUSHMAN ss200147552 Jul 04, 2010 (132)
18 1000GENOMES ss226600926 Jul 14, 2010 (132)
19 1000GENOMES ss236565329 Jul 15, 2010 (132)
20 1000GENOMES ss242994501 Jul 15, 2010 (132)
21 BL ss255031833 May 09, 2011 (134)
22 GMI ss286852506 Apr 25, 2013 (138)
23 PJP ss291612828 May 09, 2011 (134)
24 TISHKOFF ss564128783 Apr 25, 2013 (138)
25 SSMP ss659811517 Apr 25, 2013 (138)
26 EVA-GONL ss991209106 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1079703087 Aug 21, 2014 (142)
28 1000GENOMES ss1351243845 Aug 21, 2014 (142)
29 DDI ss1427443635 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1577293330 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1631861081 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1674855114 Apr 01, 2015 (144)
33 EVA_DECODE ss1695210686 Apr 01, 2015 (144)
34 EVA_SVP ss1713449096 Apr 01, 2015 (144)
35 HAMMER_LAB ss1807950065 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1934583741 Feb 12, 2016 (147)
37 JJLAB ss2028070606 Sep 14, 2016 (149)
38 USC_VALOUEV ss2156446530 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2202476166 Dec 20, 2016 (150)
40 TOPMED ss2366838386 Dec 20, 2016 (150)
41 SYSTEMSBIOZJU ss2628525525 Nov 08, 2017 (151)
42 GRF ss2700872496 Nov 08, 2017 (151)
43 GNOMAD ss2928377111 Nov 08, 2017 (151)
44 SWEGEN ss3012298130 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3027861475 Nov 08, 2017 (151)
46 TOPMED ss3212756493 Nov 08, 2017 (151)
47 CSHL ss3350835094 Nov 08, 2017 (151)
48 1000Genomes NC_000014.8 - 60749118 Jul 20, 2018 (151)
49 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 60749118 Jul 20, 2018 (151)
50 The Genome Aggregation Database NC_000014.8 - 60749118 Jul 20, 2018 (151)
51 Trans-Omics for Precision Medicine NC_000014.9 - 60282400 Jul 20, 2018 (151)
52 UK 10K study - Twins NC_000014.8 - 60749118 Jul 20, 2018 (151)
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)
rs17834382 Oct 08, 2004 (123)
rs59776898 Feb 27, 2009 (130)
rs60623923 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss75927741, ss79014003, ss83944871, ss89967462, ss113399721, ss118514946, ss168162568, ss169685426, ss171206935, ss200147552, ss255031833, ss286852506, ss291612828, ss1695210686, ss1713449096 NC_000014.7:59818870:G= NC_000014.9:60282399:G= (self)
64233538, 35682443, 62078636, 35682443, ss226600926, ss236565329, ss242994501, ss564128783, ss659811517, ss991209106, ss1079703087, ss1351243845, ss1427443635, ss1577293330, ss1631861081, ss1674855114, ss1807950065, ss1934583741, ss2028070606, ss2156446530, ss2366838386, ss2628525525, ss2700872496, ss2928377111, ss3012298130, ss3350835094 NC_000014.8:60749117:G= NC_000014.9:60282399:G= (self)
117810724, ss2202476166, ss3027861475, ss3212756493 NC_000014.9:60282399:G= NC_000014.9:60282399:G= (self)
ss10749010 NT_026437.10:40669158:G= NC_000014.9:60282399:G= (self)
ss24616665, ss43627282, ss82394873, ss96922591, ss134004970 NT_026437.12:41749117:G= NC_000014.9:60282399:G= (self)
ss66275951 NT_026437.13:42058876:G= NC_000014.9:60282399:G= (self)
ss75927741, ss79014003, ss83944871, ss89967462, ss113399721, ss118514946, ss168162568, ss169685426, ss171206935, ss200147552, ss255031833, ss286852506, ss291612828, ss1695210686, ss1713449096 NC_000014.7:59818870:G>C NC_000014.9:60282399:G>C (self)
64233538, 35682443, 62078636, 35682443, ss226600926, ss236565329, ss242994501, ss564128783, ss659811517, ss991209106, ss1079703087, ss1351243845, ss1427443635, ss1577293330, ss1631861081, ss1674855114, ss1807950065, ss1934583741, ss2028070606, ss2156446530, ss2366838386, ss2628525525, ss2700872496, ss2928377111, ss3012298130, ss3350835094 NC_000014.8:60749117:G>C NC_000014.9:60282399:G>C (self)
117810724, ss2202476166, ss3027861475, ss3212756493 NC_000014.9:60282399:G>C NC_000014.9:60282399:G>C (self)
ss10749010 NT_026437.10:40669158:G>C NC_000014.9:60282399:G>C (self)
ss24616665, ss43627282, ss82394873, ss96922591, ss134004970 NT_026437.12:41749117:G>C NC_000014.9:60282399:G>C (self)
ss66275951 NT_026437.13:42058876:G>C NC_000014.9:60282399:G>C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

3 citations for rs7154773
PMID Title Author Year Journal
22554139 Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis. Ueki M et al. 2012 BMC bioinformatics
23281810 Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data. Liu Y et al. 2012 BMC systems biology
24812308 Detecting local haplotype sharing and haplotype association. Xu H et al. 2014 Genetics

Genomic regions, transcripts, and products
Top Help

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.

Software version is: 0.1.4.post833+d3ba21e