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dbSNP Short Genetic Variations

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.

rs4582

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr2:27381412 (GRCh38.p12) 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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.46665 (58596/125568, TOPMED)
G=0.4746 (14875/31344, GnomAD)
G=0.462 (2313/5008, 1000G) (+ 5 more)
G=0.398 (1785/4480, Estonian)
G=0.377 (1454/3854, ALSPAC)
G=0.405 (1502/3708, TWINSUK)
G=0.45 (269/600, NorthernSweden)
G=0.17 (36/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PPM1G : 3 Prime UTR Variant
ZNF513 : 2KB Upstream Variant
Publications
0 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.p12 chr 2 NC_000002.12:g.27381412A>G
GRCh37.p13 chr 2 NC_000002.11:g.27604279A>G
ZNF513 RefSeqGene NG_028219.1:g.4333T>C
Gene: PPM1G, protein phosphatase, Mg2+/Mn2+ dependent 1G (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PPM1G transcript NM_177983.3:c. N/A 3 Prime UTR Variant
Gene: ZNF513, zinc finger protein 513 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
ZNF513 transcript variant 2 NM_001201459.1:c. N/A Upstream Transcript Variant
ZNF513 transcript variant 1 NM_144631.6:c. N/A Upstream Transcript Variant
ZNF513 transcript variant X1 XM_005264142.2:c. N/A Upstream Transcript Variant
ZNF513 transcript variant X2 XM_005264143.3:c. N/A N/A
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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
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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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.53335 G=0.46665
gnomAD - Genomes Global Study-wide 31344 A=0.5254 G=0.4746
gnomAD - Genomes European Sub 18860 A=0.6035 G=0.3965
gnomAD - Genomes African Sub 8708 A=0.294 G=0.706
gnomAD - Genomes East Asian Sub 1556 A=0.844 G=0.156
gnomAD - Genomes Other Sub 1082 A=0.591 G=0.409
gnomAD - Genomes American Sub 848 A=0.44 G=0.56
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.68 G=0.32
1000Genomes Global Study-wide 5008 A=0.538 G=0.462
1000Genomes African Sub 1322 A=0.238 G=0.762
1000Genomes East Asian Sub 1008 A=0.834 G=0.166
1000Genomes Europe Sub 1006 A=0.626 G=0.374
1000Genomes South Asian Sub 978 A=0.56 G=0.44
1000Genomes American Sub 694 A=0.52 G=0.48
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.602 G=0.398
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.623 G=0.377
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.595 G=0.405
Northern Sweden ACPOP Study-wide 600 A=0.55 G=0.45
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.83 G=0.17
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 A= G Note
GRCh38.p12 chr 2 NC_000002.12:g.27381412= NC_000002.12:g.27381412A>G
GRCh37.p13 chr 2 NC_000002.11:g.27604279= NC_000002.11:g.27604279A>G
ZNF513 RefSeqGene NG_028219.1:g.4333= NG_028219.1:g.4333T>C
PPM1G transcript NM_177983.3:c.*187= NM_177983.3:c.*187T>C
PPM1G transcript NM_177983.2:c.*187= NM_177983.2:c.*187T>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#.

89 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 UWGC ss7381 Sep 19, 2000 (52)
2 UWGC ss7416 Sep 19, 2000 (52)
3 CGAP-GAI ss8717 Sep 19, 2000 (52)
4 LEE ss1515700 Oct 04, 2000 (86)
5 LEE ss4408479 May 29, 2002 (106)
6 WI_SSAHASNP ss11453775 Jul 11, 2003 (116)
7 WUGSC_SSAHASNP ss14492242 Dec 05, 2003 (119)
8 CGAP-GAI ss16252149 Feb 27, 2004 (120)
9 CSHL-HAPMAP ss19439179 Feb 27, 2004 (120)
10 ABI ss44143635 Mar 15, 2006 (126)
11 ILLUMINA ss65728317 Oct 16, 2006 (127)
12 ILLUMINA ss74855839 Dec 07, 2007 (129)
13 BGI ss103467570 Dec 01, 2009 (131)
14 1000GENOMES ss109344033 Jan 24, 2009 (130)
15 1000GENOMES ss109988020 Jan 24, 2009 (130)
16 ILLUMINA-UK ss117633015 Feb 14, 2009 (130)
17 KRIBB_YJKIM ss119337420 Dec 01, 2009 (131)
18 ILLUMINA ss160689167 Dec 01, 2009 (131)
19 ENSEMBL ss161254789 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss163221106 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss164048601 Jul 04, 2010 (132)
22 ILLUMINA ss173756502 Jul 04, 2010 (132)
23 BUSHMAN ss200191806 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss205969521 Jul 04, 2010 (132)
25 1000GENOMES ss219133789 Jul 14, 2010 (132)
26 1000GENOMES ss231086141 Jul 14, 2010 (132)
27 1000GENOMES ss238659984 Jul 15, 2010 (132)
28 BL ss252989202 May 09, 2011 (134)
29 GMI ss276394814 May 04, 2012 (137)
30 PJP ss292532047 May 09, 2011 (134)
31 ILLUMINA ss410833484 Sep 17, 2011 (135)
32 ILLUMINA ss480974296 May 04, 2012 (137)
33 ILLUMINA ss480994617 May 04, 2012 (137)
34 ILLUMINA ss481970713 Sep 08, 2015 (146)
35 ILLUMINA ss485282039 May 04, 2012 (137)
36 ILLUMINA ss537247404 Sep 08, 2015 (146)
37 TISHKOFF ss555432765 Apr 25, 2013 (138)
38 SSMP ss649013056 Apr 25, 2013 (138)
39 ILLUMINA ss778539284 Sep 08, 2015 (146)
40 ILLUMINA ss783086942 Sep 08, 2015 (146)
41 ILLUMINA ss784044445 Sep 08, 2015 (146)
42 ILLUMINA ss832345365 Sep 08, 2015 (146)
43 ILLUMINA ss833995893 Sep 08, 2015 (146)
44 EVA-GONL ss976614518 Aug 21, 2014 (142)
45 JMKIDD_LAB ss1068952544 Aug 21, 2014 (142)
46 1000GENOMES ss1296395368 Aug 21, 2014 (142)
47 DDI ss1428514475 Apr 01, 2015 (144)
48 EVA_GENOME_DK ss1578790534 Apr 01, 2015 (144)
49 EVA_DECODE ss1586019056 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1603067900 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1646061933 Apr 01, 2015 (144)
52 EVA_MGP ss1710957540 Apr 01, 2015 (144)
53 EVA_SVP ss1712440157 Apr 01, 2015 (144)
54 ILLUMINA ss1752350509 Sep 08, 2015 (146)
55 HAMMER_LAB ss1796454455 Sep 08, 2015 (146)
56 WEILL_CORNELL_DGM ss1919846708 Feb 12, 2016 (147)
57 GENOMED ss1968721895 Jul 19, 2016 (147)
58 JJLAB ss2020451898 Sep 14, 2016 (149)
59 USC_VALOUEV ss2148496333 Dec 20, 2016 (150)
60 HUMAN_LONGEVITY ss2228525752 Dec 20, 2016 (150)
61 TOPMED ss2394441326 Dec 20, 2016 (150)
62 SYSTEMSBIOZJU ss2624741393 Nov 08, 2017 (151)
63 ILLUMINA ss2633587514 Nov 08, 2017 (151)
64 ILLUMINA ss2635087321 Nov 08, 2017 (151)
65 GRF ss2703057393 Nov 08, 2017 (151)
66 GNOMAD ss2771097024 Nov 08, 2017 (151)
67 SWEGEN ss2989172369 Nov 08, 2017 (151)
68 BIOINF_KMB_FNS_UNIBA ss3023992277 Nov 08, 2017 (151)
69 TOPMED ss3302442639 Nov 08, 2017 (151)
70 CSHL ss3344130223 Nov 08, 2017 (151)
71 ILLUMINA ss3628018674 Oct 11, 2018 (152)
72 ILLUMINA ss3631556022 Oct 11, 2018 (152)
73 ILLUMINA ss3633192916 Oct 11, 2018 (152)
74 ILLUMINA ss3633904251 Oct 11, 2018 (152)
75 ILLUMINA ss3634756789 Oct 11, 2018 (152)
76 ILLUMINA ss3635590695 Oct 11, 2018 (152)
77 ILLUMINA ss3636442693 Oct 11, 2018 (152)
78 ILLUMINA ss3637342525 Oct 11, 2018 (152)
79 ILLUMINA ss3638248847 Oct 11, 2018 (152)
80 ILLUMINA ss3640464093 Oct 11, 2018 (152)
81 ILLUMINA ss3643219832 Oct 11, 2018 (152)
82 OMUKHERJEE_ADBS ss3646259325 Oct 11, 2018 (152)
83 EGCUT_WGS ss3657127011 Jul 13, 2019 (153)
84 EVA_DECODE ss3703489062 Jul 13, 2019 (153)
85 ACPOP ss3728256806 Jul 13, 2019 (153)
86 ILLUMINA ss3745056740 Jul 13, 2019 (153)
87 EVA ss3756503677 Jul 13, 2019 (153)
88 ILLUMINA ss3772553623 Jul 13, 2019 (153)
89 KHV_HUMAN_GENOMES ss3800884335 Jul 13, 2019 (153)
90 1000Genomes NC_000002.11 - 27604279 Oct 11, 2018 (152)
91 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 27604279 Oct 11, 2018 (152)
92 Genetic variation in the Estonian population NC_000002.11 - 27604279 Oct 11, 2018 (152)
93 gnomAD - Genomes NC_000002.11 - 27604279 Jul 13, 2019 (153)
94 Northern Sweden NC_000002.11 - 27604279 Jul 13, 2019 (153)
95 TopMed NC_000002.12 - 27381412 Oct 11, 2018 (152)
96 UK 10K study - Twins NC_000002.11 - 27604279 Oct 11, 2018 (152)
97 A Vietnamese Genetic Variation Database NC_000002.11 - 27604279 Jul 13, 2019 (153)
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)
rs3185357 Jul 03, 2002 (106)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss109344033, ss109988020, ss117633015, ss163221106, ss164048601, ss200191806, ss205969521, ss252989202, ss276394814, ss292532047, ss480974296, ss1586019056, ss1712440157, ss2635087321, ss3643219832 NC_000002.10:27457782:A:G NC_000002.12:27381411:A:G (self)
7313696, 4059822, 2865259, 19914258, 1541671, 4059822, 884870, ss219133789, ss231086141, ss238659984, ss480994617, ss481970713, ss485282039, ss537247404, ss555432765, ss649013056, ss778539284, ss783086942, ss784044445, ss832345365, ss833995893, ss976614518, ss1068952544, ss1296395368, ss1428514475, ss1578790534, ss1603067900, ss1646061933, ss1710957540, ss1752350509, ss1796454455, ss1919846708, ss1968721895, ss2020451898, ss2148496333, ss2394441326, ss2624741393, ss2633587514, ss2703057393, ss2771097024, ss2989172369, ss3344130223, ss3628018674, ss3631556022, ss3633192916, ss3633904251, ss3634756789, ss3635590695, ss3636442693, ss3637342525, ss3638248847, ss3640464093, ss3646259325, ss3657127011, ss3728256806, ss3745056740, ss3756503677, ss3772553623 NC_000002.11:27604278:A:G NC_000002.12:27381411:A:G (self)
188529422, ss2228525752, ss3023992277, ss3302442639, ss3703489062, ss3800884335 NC_000002.12:27381411:A:G NC_000002.12:27381411:A:G (self)
ss11453775 NT_022184.12:6420211:A:G NC_000002.12:27381411:A:G (self)
ss14492242, ss19439179 NT_022184.13:6420211:A:G NC_000002.12:27381411:A:G (self)
ss7381, ss7416, ss8717, ss1515700, ss4408479, ss16252149, ss44143635, ss65728317, ss74855839, ss103467570, ss119337420, ss160689167, ss161254789, ss173756502, ss410833484 NT_022184.15:6426165:A:G NC_000002.12:27381411:A:G (self)
Help

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

No publications for rs4582

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.

Software version is: 2.0.1.post270+ab078da