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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.

rs2375005

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:95407564 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.464574 (122968/264690, TOPMED)
T=0.474515 (66414/139962, GnomAD)
T=0.09049 (2557/28258, 14KJPN) (+ 16 more)
A=0.48117 (10144/21082, ALFA)
T=0.08945 (1499/16758, 8.3KJPN)
T=0.3413 (2186/6404, 1000G_30x)
T=0.3373 (1689/5008, 1000G)
A=0.4667 (2091/4480, Estonian)
A=0.4582 (1766/3854, ALSPAC)
A=0.4504 (1670/3708, TWINSUK)
T=0.0973 (285/2930, KOREAN)
A=0.466 (465/998, GoNL)
T=0.485 (291/600, NorthernSweden)
T=0.201 (100/498, SGDP_PRJ)
T=0.348 (115/330, HapMap)
A=0.394 (85/216, Qatari)
T=0.196 (42/214, Vietnamese)
T=0.28 (14/50, Siberian)
A=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PON2 : Intron Variant
LOC107986822 : Intron Variant
Publications
2 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 21082 T=0.51883 A=0.48117
European Sub 16440 T=0.54951 A=0.45049
African Sub 2946 T=0.4328 A=0.5672
African Others Sub 114 T=0.368 A=0.632
African American Sub 2832 T=0.4354 A=0.5646
Asian Sub 112 T=0.170 A=0.830
East Asian Sub 86 T=0.19 A=0.81
Other Asian Sub 26 T=0.12 A=0.88
Latin American 1 Sub 146 T=0.459 A=0.541
Latin American 2 Sub 610 T=0.308 A=0.692
South Asian Sub 98 T=0.32 A=0.68
Other Sub 730 T=0.444 A=0.556


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
TopMed Global Study-wide 264690 T=0.464574 A=0.535426
gnomAD - Genomes Global Study-wide 139962 T=0.474515 A=0.525485
gnomAD - Genomes European Sub 75816 T=0.52416 A=0.47584
gnomAD - Genomes African Sub 41912 T=0.42432 A=0.57568
gnomAD - Genomes American Sub 13628 T=0.38648 A=0.61352
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.6157 A=0.3843
gnomAD - Genomes East Asian Sub 3132 T=0.1833 A=0.8167
gnomAD - Genomes Other Sub 2154 T=0.4666 A=0.5334
14KJPN JAPANESE Study-wide 28258 T=0.09049 A=0.90951
Allele Frequency Aggregator Total Global 21082 T=0.51883 A=0.48117
Allele Frequency Aggregator European Sub 16440 T=0.54951 A=0.45049
Allele Frequency Aggregator African Sub 2946 T=0.4328 A=0.5672
Allele Frequency Aggregator Other Sub 730 T=0.444 A=0.556
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.308 A=0.692
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.459 A=0.541
Allele Frequency Aggregator Asian Sub 112 T=0.170 A=0.830
Allele Frequency Aggregator South Asian Sub 98 T=0.32 A=0.68
8.3KJPN JAPANESE Study-wide 16758 T=0.08945 A=0.91055
1000Genomes_30x Global Study-wide 6404 T=0.3413 A=0.6587
1000Genomes_30x African Sub 1786 T=0.3835 A=0.6165
1000Genomes_30x Europe Sub 1266 T=0.5032 A=0.4968
1000Genomes_30x South Asian Sub 1202 T=0.2895 A=0.7105
1000Genomes_30x East Asian Sub 1170 T=0.1821 A=0.8179
1000Genomes_30x American Sub 980 T=0.309 A=0.691
1000Genomes Global Study-wide 5008 T=0.3373 A=0.6627
1000Genomes African Sub 1322 T=0.3812 A=0.6188
1000Genomes East Asian Sub 1008 T=0.1746 A=0.8254
1000Genomes Europe Sub 1006 T=0.5000 A=0.5000
1000Genomes South Asian Sub 978 T=0.291 A=0.709
1000Genomes American Sub 694 T=0.318 A=0.682
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5333 A=0.4667
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.5418 A=0.4582
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.5496 A=0.4504
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0973 A=0.9027, C=0.0000, G=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.534 A=0.466
Northern Sweden ACPOP Study-wide 600 T=0.485 A=0.515
SGDP_PRJ Global Study-wide 498 T=0.201 A=0.799
HapMap Global Study-wide 330 T=0.348 A=0.652
HapMap African Sub 120 T=0.400 A=0.600
HapMap American Sub 120 T=0.492 A=0.508
HapMap Asian Sub 90 T=0.09 A=0.91
Qatari Global Study-wide 216 T=0.606 A=0.394
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.196 A=0.804
Siberian Global Study-wide 50 T=0.28 A=0.72
The Danish reference pan genome Danish Study-wide 40 T=0.62 A=0.38
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 7 NC_000007.14:g.95407564T>A
GRCh38.p14 chr 7 NC_000007.14:g.95407564T>C
GRCh38.p14 chr 7 NC_000007.14:g.95407564T>G
GRCh37.p13 chr 7 NC_000007.13:g.95036876T>A
GRCh37.p13 chr 7 NC_000007.13:g.95036876T>C
GRCh37.p13 chr 7 NC_000007.13:g.95036876T>G
PON2 RefSeqGene NG_008725.1:g.32509A>T
PON2 RefSeqGene NG_008725.1:g.32509A>G
PON2 RefSeqGene NG_008725.1:g.32509A>C
Gene: PON2, paraoxonase 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PON2 transcript variant 1 NM_000305.3:c.696-496A>T N/A Intron Variant
PON2 transcript variant 2 NM_001018161.2:c.660-496A…

NM_001018161.2:c.660-496A>T

N/A Intron Variant
PON2 transcript variant X1 XM_005250453.2:c.492-496A…

XM_005250453.2:c.492-496A>T

N/A Intron Variant
PON2 transcript variant X2 XM_017012357.3:c.486-496A…

XM_017012357.3:c.486-496A>T

N/A Intron Variant
Gene: LOC107986822, uncharacterized LOC107986822 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107986822 transcript variant X2 XR_007060439.1:n. N/A Intron Variant
LOC107986822 transcript variant X1 XR_001745283.2:n. N/A Genic Downstream Transcript 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

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 T= A C G
GRCh38.p14 chr 7 NC_000007.14:g.95407564= NC_000007.14:g.95407564T>A NC_000007.14:g.95407564T>C NC_000007.14:g.95407564T>G
GRCh37.p13 chr 7 NC_000007.13:g.95036876= NC_000007.13:g.95036876T>A NC_000007.13:g.95036876T>C NC_000007.13:g.95036876T>G
PON2 RefSeqGene NG_008725.1:g.32509= NG_008725.1:g.32509A>T NG_008725.1:g.32509A>G NG_008725.1:g.32509A>C
PON2 transcript variant 1 NM_000305.2:c.696-496= NM_000305.2:c.696-496A>T NM_000305.2:c.696-496A>G NM_000305.2:c.696-496A>C
PON2 transcript variant 1 NM_000305.3:c.696-496= NM_000305.3:c.696-496A>T NM_000305.3:c.696-496A>G NM_000305.3:c.696-496A>C
PON2 transcript variant 2 NM_001018161.1:c.660-496= NM_001018161.1:c.660-496A>T NM_001018161.1:c.660-496A>G NM_001018161.1:c.660-496A>C
PON2 transcript variant 2 NM_001018161.2:c.660-496= NM_001018161.2:c.660-496A>T NM_001018161.2:c.660-496A>G NM_001018161.2:c.660-496A>C
PON2 transcript variant X1 XM_005250453.1:c.492-496= XM_005250453.1:c.492-496A>T XM_005250453.1:c.492-496A>G XM_005250453.1:c.492-496A>C
PON2 transcript variant X1 XM_005250453.2:c.492-496= XM_005250453.2:c.492-496A>T XM_005250453.2:c.492-496A>G XM_005250453.2:c.492-496A>C
PON2 transcript variant X2 XM_005250454.1:c.486-496= XM_005250454.1:c.486-496A>T XM_005250454.1:c.486-496A>G XM_005250454.1:c.486-496A>C
PON2 transcript variant X2 XM_017012357.3:c.486-496= XM_017012357.3:c.486-496A>T XM_017012357.3:c.486-496A>G XM_017012357.3:c.486-496A>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#.

80 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3334163 Sep 28, 2001 (100)
2 SC_SNP ss13420386 Dec 05, 2003 (120)
3 CSHL-HAPMAP ss19733030 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss20326362 Feb 27, 2004 (120)
5 PERLEGEN ss24681997 Sep 20, 2004 (123)
6 PGA-UW-FHCRC ss28526118 Dec 02, 2004 (126)
7 ABI ss44784957 Mar 10, 2006 (126)
8 PERLEGEN ss69022675 May 17, 2007 (127)
9 KRIBB_YJKIM ss80763845 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss93729848 Mar 25, 2008 (129)
11 HUMANGENOME_JCVI ss98319770 Feb 05, 2009 (130)
12 BGI ss104451603 Dec 01, 2009 (131)
13 1000GENOMES ss112370937 Jan 25, 2009 (130)
14 1000GENOMES ss114119548 Jan 25, 2009 (130)
15 ILLUMINA-UK ss116203629 Feb 14, 2009 (130)
16 ENSEMBL ss142695969 Dec 01, 2009 (131)
17 ENSEMBL ss143446796 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss162541887 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss164888772 Jul 04, 2010 (132)
20 ILLUMINA ss173314438 Jul 04, 2010 (132)
21 BUSHMAN ss197935857 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss207993567 Jul 04, 2010 (132)
23 1000GENOMES ss223213609 Jul 14, 2010 (132)
24 1000GENOMES ss234082251 Jul 15, 2010 (132)
25 1000GENOMES ss241016840 Jul 15, 2010 (132)
26 ILLUMINA ss244290298 Jul 04, 2010 (132)
27 BL ss254525194 May 09, 2011 (134)
28 GMI ss279445274 May 04, 2012 (137)
29 GMI ss285679300 Apr 25, 2013 (138)
30 PJP ss293919231 May 09, 2011 (134)
31 ILLUMINA ss537083654 Sep 08, 2015 (146)
32 TISHKOFF ss560165267 Apr 25, 2013 (138)
33 SSMP ss654567346 Apr 25, 2013 (138)
34 EVA-GONL ss984560062 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1074810247 Aug 21, 2014 (142)
36 1000GENOMES ss1326221574 Aug 21, 2014 (142)
37 DDI ss1431213541 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1582313236 Apr 01, 2015 (144)
39 EVA_DECODE ss1594138243 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1618739151 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1661733184 Apr 01, 2015 (144)
42 HAMMER_LAB ss1805120095 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1927819681 Feb 12, 2016 (147)
44 GENOMED ss1970764983 Jul 19, 2016 (147)
45 JJLAB ss2024592970 Sep 14, 2016 (149)
46 USC_VALOUEV ss2152814318 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2295968858 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2626788622 Nov 08, 2017 (151)
49 GRF ss2708522945 Nov 08, 2017 (151)
50 GNOMAD ss2856424990 Nov 08, 2017 (151)
51 SWEGEN ss3001658572 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3026089291 Nov 08, 2017 (151)
53 CSHL ss3347738761 Nov 08, 2017 (151)
54 ILLUMINA ss3629867028 Oct 12, 2018 (152)
55 ILLUMINA ss3638711397 Oct 12, 2018 (152)
56 URBANLAB ss3648704958 Oct 12, 2018 (152)
57 EGCUT_WGS ss3669417390 Jul 13, 2019 (153)
58 EVA_DECODE ss3720242299 Jul 13, 2019 (153)
59 ACPOP ss3734876903 Jul 13, 2019 (153)
60 EVA ss3766889953 Jul 13, 2019 (153)
61 KHV_HUMAN_GENOMES ss3810062252 Jul 13, 2019 (153)
62 EVA ss3830708058 Apr 26, 2020 (154)
63 EVA ss3838852677 Apr 26, 2020 (154)
64 EVA ss3844307657 Apr 26, 2020 (154)
65 SGDP_PRJ ss3867921100 Apr 26, 2020 (154)
66 KRGDB ss3915198436 Apr 26, 2020 (154)
67 EVA ss4017348358 Apr 26, 2021 (155)
68 TOPMED ss4755541735 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5184523598 Apr 26, 2021 (155)
70 1000G_HIGH_COVERAGE ss5273926262 Oct 13, 2022 (156)
71 EVA ss5375312714 Oct 13, 2022 (156)
72 HUGCELL_USP ss5470909405 Oct 13, 2022 (156)
73 1000G_HIGH_COVERAGE ss5562655796 Oct 13, 2022 (156)
74 SANFORD_IMAGENETICS ss5643528976 Oct 13, 2022 (156)
75 TOMMO_GENOMICS ss5725190125 Oct 13, 2022 (156)
76 YY_MCH ss5808899877 Oct 13, 2022 (156)
77 EVA ss5823215009 Oct 13, 2022 (156)
78 EVA ss5856010296 Oct 13, 2022 (156)
79 EVA ss5859969736 Oct 13, 2022 (156)
80 EVA ss5972711180 Oct 13, 2022 (156)
81 1000Genomes NC_000007.13 - 95036876 Oct 12, 2018 (152)
82 1000Genomes_30x NC_000007.14 - 95407564 Oct 13, 2022 (156)
83 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 95036876 Oct 12, 2018 (152)
84 Genetic variation in the Estonian population NC_000007.13 - 95036876 Oct 12, 2018 (152)
85 The Danish reference pan genome NC_000007.13 - 95036876 Apr 26, 2020 (154)
86 gnomAD - Genomes NC_000007.14 - 95407564 Apr 26, 2021 (155)
87 Genome of the Netherlands Release 5 NC_000007.13 - 95036876 Apr 26, 2020 (154)
88 HapMap NC_000007.14 - 95407564 Apr 26, 2020 (154)
89 KOREAN population from KRGDB NC_000007.13 - 95036876 Apr 26, 2020 (154)
90 Northern Sweden NC_000007.13 - 95036876 Jul 13, 2019 (153)
91 Qatari NC_000007.13 - 95036876 Apr 26, 2020 (154)
92 SGDP_PRJ NC_000007.13 - 95036876 Apr 26, 2020 (154)
93 Siberian NC_000007.13 - 95036876 Apr 26, 2020 (154)
94 8.3KJPN NC_000007.13 - 95036876 Apr 26, 2021 (155)
95 14KJPN NC_000007.14 - 95407564 Oct 13, 2022 (156)
96 TopMed NC_000007.14 - 95407564 Apr 26, 2021 (155)
97 UK 10K study - Twins NC_000007.13 - 95036876 Oct 12, 2018 (152)
98 A Vietnamese Genetic Variation Database NC_000007.13 - 95036876 Jul 13, 2019 (153)
99 ALFA NC_000007.14 - 95407564 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)
rs9641165 Feb 27, 2004 (120)
rs11552927 Apr 05, 2004 (121)
rs17703560 Oct 08, 2004 (123)
rs17876161 Mar 10, 2006 (126)
rs59035044 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93729848, ss112370937, ss114119548, ss116203629, ss162541887, ss164888772, ss197935857, ss207993567, ss254525194, ss279445274, ss285679300, ss293919231, ss1594138243 NC_000007.12:94874811:T:A NC_000007.14:95407563:T:A (self)
38231188, 21274332, 15155638, 8478175, 9497993, 22375830, 8161768, 9861611, 19938080, 5330672, 42492905, 21274332, 4744959, ss223213609, ss234082251, ss241016840, ss537083654, ss560165267, ss654567346, ss984560062, ss1074810247, ss1326221574, ss1431213541, ss1582313236, ss1618739151, ss1661733184, ss1805120095, ss1927819681, ss1970764983, ss2024592970, ss2152814318, ss2626788622, ss2708522945, ss2856424990, ss3001658572, ss3347738761, ss3629867028, ss3638711397, ss3669417390, ss3734876903, ss3766889953, ss3830708058, ss3838852677, ss3867921100, ss3915198436, ss4017348358, ss5184523598, ss5375312714, ss5643528976, ss5823215009, ss5972711180 NC_000007.13:95036875:T:A NC_000007.14:95407563:T:A (self)
50181731, 269768834, 3450222, 59027229, 592919294, 7027035537, ss2295968858, ss3026089291, ss3648704958, ss3720242299, ss3810062252, ss3844307657, ss4755541735, ss5273926262, ss5470909405, ss5562655796, ss5725190125, ss5808899877, ss5856010296, ss5859969736 NC_000007.14:95407563:T:A NC_000007.14:95407563:T:A (self)
ss13420386 NT_007933.12:20271091:T:A NC_000007.14:95407563:T:A (self)
ss19733030, ss20326362 NT_007933.13:20271091:T:A NC_000007.14:95407563:T:A (self)
ss3334163, ss24681997, ss28526118, ss44784957, ss69022675, ss80763845, ss98319770, ss104451603, ss142695969, ss143446796, ss173314438, ss244290298 NT_007933.15:33069718:T:A NC_000007.14:95407563:T:A (self)
22375830, ss3915198436 NC_000007.13:95036875:T:C NC_000007.14:95407563:T:C (self)
22375830, ss3915198436 NC_000007.13:95036875:T:G NC_000007.14:95407563:T:G (self)
Help

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

2 citations for rs2375005
PMID Title Author Year Journal
20980077 Serum paraoxonase activity is associated with variants in the PON gene cluster and risk of Alzheimer disease. Erlich PM et al. 2012 Neurobiology of aging
22685667 Additional Common Polymorphisms in the PON Gene Cluster Predict PON1 Activity but Not Vascular Disease. Kim DS et al. 2012 Journal of lipids
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
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: 2.0.1.post761+d5e8e07