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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.

rs1921565

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:184198691 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.496267 (131357/264690, TOPMED)
A=0.07980 (2255/28258, 14KJPN)
G=0.43094 (8611/19982, ALFA) (+ 16 more)
A=0.07757 (1300/16760, 8.3KJPN)
A=0.4530 (2901/6404, 1000G_30x)
A=0.4431 (2219/5008, 1000G)
A=0.4480 (2007/4480, Estonian)
A=0.4660 (1796/3854, ALSPAC)
A=0.4798 (1779/3708, TWINSUK)
A=0.0382 (112/2930, KOREAN)
A=0.4707 (885/1880, HapMap)
A=0.0371 (68/1832, Korea1K)
A=0.455 (454/998, GoNL)
A=0.405 (243/600, NorthernSweden)
A=0.183 (84/460, SGDP_PRJ)
G=0.333 (72/216, Qatari)
A=0.037 (8/216, Vietnamese)
A=0.19 (9/48, Siberian)
G=0.45 (18/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ENPP6 : Intron Variant
Publications
0 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 20076 A=0.56924 C=0.00000, G=0.43076
European Sub 16374 A=0.52877 C=0.00000, G=0.47123
African Sub 2566 A=0.8262 C=0.0000, G=0.1738
African Others Sub 96 A=0.93 C=0.00, G=0.07
African American Sub 2470 A=0.8223 C=0.0000, G=0.1777
Asian Sub 16 A=0.06 C=0.00, G=0.94
East Asian Sub 12 A=0.00 C=0.00, G=1.00
Other Asian Sub 4 A=0.2 C=0.0, G=0.8
Latin American 1 Sub 58 A=0.83 C=0.00, G=0.17
Latin American 2 Sub 120 A=0.633 C=0.000, G=0.367
South Asian Sub 30 A=0.93 C=0.00, G=0.07
Other Sub 912 A=0.545 C=0.000, G=0.455


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 A=0.496267 G=0.503733
14KJPN JAPANESE Study-wide 28258 A=0.07980 G=0.92020
Allele Frequency Aggregator Total Global 19982 A=0.56906 C=0.00000, G=0.43094
Allele Frequency Aggregator European Sub 16298 A=0.52847 C=0.00000, G=0.47153
Allele Frequency Aggregator African Sub 2566 A=0.8262 C=0.0000, G=0.1738
Allele Frequency Aggregator Other Sub 894 A=0.543 C=0.000, G=0.457
Allele Frequency Aggregator Latin American 2 Sub 120 A=0.633 C=0.000, G=0.367
Allele Frequency Aggregator Latin American 1 Sub 58 A=0.83 C=0.00, G=0.17
Allele Frequency Aggregator South Asian Sub 30 A=0.93 C=0.00, G=0.07
Allele Frequency Aggregator Asian Sub 16 A=0.06 C=0.00, G=0.94
8.3KJPN JAPANESE Study-wide 16760 A=0.07757 G=0.92243
1000Genomes_30x Global Study-wide 6404 A=0.4530 G=0.5470
1000Genomes_30x African Sub 1786 A=0.6797 G=0.3203
1000Genomes_30x Europe Sub 1266 A=0.4905 G=0.5095
1000Genomes_30x South Asian Sub 1202 A=0.5807 G=0.4193
1000Genomes_30x East Asian Sub 1170 A=0.0470 G=0.9530
1000Genomes_30x American Sub 980 A=0.319 G=0.681
1000Genomes Global Study-wide 5008 A=0.4431 G=0.5569
1000Genomes African Sub 1322 A=0.6778 G=0.3222
1000Genomes East Asian Sub 1008 A=0.0466 G=0.9534
1000Genomes Europe Sub 1006 A=0.4811 G=0.5189
1000Genomes South Asian Sub 978 A=0.578 G=0.422
1000Genomes American Sub 694 A=0.327 G=0.673
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4480 G=0.5520
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4660 G=0.5340
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.4798 G=0.5202
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0382 C=0.0000, G=0.9618, T=0.0000
HapMap Global Study-wide 1880 A=0.4707 G=0.5293
HapMap American Sub 766 A=0.406 G=0.594
HapMap African Sub 690 A=0.680 G=0.320
HapMap Asian Sub 252 A=0.071 G=0.929
HapMap Europe Sub 172 A=0.506 G=0.494
Korean Genome Project KOREAN Study-wide 1832 A=0.0371 G=0.9629
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.455 G=0.545
Northern Sweden ACPOP Study-wide 600 A=0.405 G=0.595
SGDP_PRJ Global Study-wide 460 A=0.183 G=0.817
Qatari Global Study-wide 216 A=0.667 G=0.333
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.037 G=0.963
Siberian Global Study-wide 48 A=0.19 G=0.81
The Danish reference pan genome Danish Study-wide 40 A=0.55 G=0.45
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 4 NC_000004.12:g.184198691A>C
GRCh38.p14 chr 4 NC_000004.12:g.184198691A>G
GRCh38.p14 chr 4 NC_000004.12:g.184198691A>T
GRCh37.p13 chr 4 NC_000004.11:g.185119844A>C
GRCh37.p13 chr 4 NC_000004.11:g.185119844A>G
GRCh37.p13 chr 4 NC_000004.11:g.185119844A>T
Gene: ENPP6, ectonucleotide pyrophosphatase/phosphodiesterase 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ENPP6 transcript NM_153343.4:c.241+18888T>G 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

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= C G T
GRCh38.p14 chr 4 NC_000004.12:g.184198691= NC_000004.12:g.184198691A>C NC_000004.12:g.184198691A>G NC_000004.12:g.184198691A>T
GRCh37.p13 chr 4 NC_000004.11:g.185119844= NC_000004.11:g.185119844A>C NC_000004.11:g.185119844A>G NC_000004.11:g.185119844A>T
ENPP6 transcript NM_153343.3:c.241+18888= NM_153343.3:c.241+18888T>G NM_153343.3:c.241+18888T>C NM_153343.3:c.241+18888T>A
ENPP6 transcript NM_153343.4:c.241+18888= NM_153343.4:c.241+18888T>G NM_153343.4:c.241+18888T>C NM_153343.4:c.241+18888T>A
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#.

92 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2808010 Jan 12, 2001 (92)
2 WI_SSAHASNP ss6717729 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss10136699 Jul 11, 2003 (116)
4 CSHL-HAPMAP ss19576534 Feb 27, 2004 (120)
5 ABI ss44582653 Mar 15, 2006 (126)
6 ILLUMINA ss65717100 Oct 14, 2006 (127)
7 ILLUMINA ss74884278 Dec 07, 2007 (129)
8 HGSV ss77668630 Dec 07, 2007 (129)
9 HGSV ss78547855 Dec 07, 2007 (129)
10 HUMANGENOME_JCVI ss99057410 Feb 04, 2009 (130)
11 BGI ss105894991 Feb 04, 2009 (130)
12 1000GENOMES ss108677054 Jan 23, 2009 (130)
13 1000GENOMES ss111180443 Jan 25, 2009 (130)
14 ILLUMINA-UK ss117333429 Feb 14, 2009 (130)
15 KRIBB_YJKIM ss119408540 Dec 01, 2009 (131)
16 ILLUMINA ss120240086 Dec 01, 2009 (131)
17 ENSEMBL ss134801491 Dec 01, 2009 (131)
18 ENSEMBL ss142659392 Dec 01, 2009 (131)
19 GMI ss154761662 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss162896054 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss165338007 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss167500099 Jul 04, 2010 (132)
23 ILLUMINA ss172987401 Jul 04, 2010 (132)
24 BUSHMAN ss199662667 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss206267532 Jul 04, 2010 (132)
26 1000GENOMES ss221429958 Jul 14, 2010 (132)
27 1000GENOMES ss232761956 Jul 14, 2010 (132)
28 1000GENOMES ss239974653 Jul 15, 2010 (132)
29 ILLUMINA ss244256880 Jul 04, 2010 (132)
30 BL ss253824695 May 09, 2011 (134)
31 GMI ss278094610 May 04, 2012 (137)
32 GMI ss285083462 Apr 25, 2013 (138)
33 PJP ss293277773 May 09, 2011 (134)
34 ILLUMINA ss537008645 Sep 08, 2015 (146)
35 TISHKOFF ss558103729 Apr 25, 2013 (138)
36 SSMP ss651940615 Apr 25, 2013 (138)
37 EVA-GONL ss981097994 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1072279755 Aug 21, 2014 (142)
39 1000GENOMES ss1313368679 Aug 21, 2014 (142)
40 DDI ss1430187184 Apr 01, 2015 (144)
41 EVA_GENOME_DK ss1580948274 Apr 01, 2015 (144)
42 EVA_DECODE ss1590618189 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1611996177 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1654990210 Apr 01, 2015 (144)
45 EVA_SVP ss1712733016 Apr 01, 2015 (144)
46 HAMMER_LAB ss1802766362 Sep 08, 2015 (146)
47 WEILL_CORNELL_DGM ss1924343735 Feb 12, 2016 (147)
48 GENOMED ss1969973744 Jul 19, 2016 (147)
49 JJLAB ss2022766959 Sep 14, 2016 (149)
50 USC_VALOUEV ss2150901207 Dec 20, 2016 (150)
51 HUMAN_LONGEVITY ss2270342444 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2625876942 Nov 08, 2017 (151)
53 GRF ss2706409618 Nov 08, 2017 (151)
54 GNOMAD ss2819659823 Nov 08, 2017 (151)
55 AFFY ss2985311386 Nov 08, 2017 (151)
56 AFFY ss2985939655 Nov 08, 2017 (151)
57 SWEGEN ss2996191787 Nov 08, 2017 (151)
58 BIOINF_KMB_FNS_UNIBA ss3025164151 Nov 08, 2017 (151)
59 CSHL ss3346154172 Nov 08, 2017 (151)
60 ILLUMINA ss3629144925 Oct 12, 2018 (152)
61 ILLUMINA ss3638530728 Oct 12, 2018 (152)
62 ILLUMINA ss3643478559 Oct 12, 2018 (152)
63 URBANLAB ss3647946046 Oct 12, 2018 (152)
64 ILLUMINA ss3654083950 Oct 12, 2018 (152)
65 EGCUT_WGS ss3664112396 Jul 13, 2019 (153)
66 EVA_DECODE ss3713831152 Jul 13, 2019 (153)
67 ACPOP ss3731959121 Jul 13, 2019 (153)
68 EVA ss3762890262 Jul 13, 2019 (153)
69 PACBIO ss3784977339 Jul 13, 2019 (153)
70 PACBIO ss3790398478 Jul 13, 2019 (153)
71 PACBIO ss3795274218 Jul 13, 2019 (153)
72 KHV_HUMAN_GENOMES ss3806058631 Jul 13, 2019 (153)
73 EVA ss3829017420 Apr 26, 2020 (154)
74 EVA ss3837964602 Apr 26, 2020 (154)
75 EVA ss3843406775 Apr 26, 2020 (154)
76 SGDP_PRJ ss3860883771 Apr 26, 2020 (154)
77 KRGDB ss3907268799 Apr 26, 2020 (154)
78 KOGIC ss3955847040 Apr 26, 2020 (154)
79 TOPMED ss4645375973 Apr 27, 2021 (155)
80 TOMMO_GENOMICS ss5169751969 Apr 27, 2021 (155)
81 1000G_HIGH_COVERAGE ss5262391084 Oct 13, 2022 (156)
82 EVA ss5354777889 Oct 13, 2022 (156)
83 HUGCELL_USP ss5460802783 Oct 13, 2022 (156)
84 EVA ss5507875042 Oct 13, 2022 (156)
85 1000G_HIGH_COVERAGE ss5545215119 Oct 13, 2022 (156)
86 SANFORD_IMAGENETICS ss5636896269 Oct 13, 2022 (156)
87 TOMMO_GENOMICS ss5705222784 Oct 13, 2022 (156)
88 YY_MCH ss5805886561 Oct 13, 2022 (156)
89 EVA ss5845259821 Oct 13, 2022 (156)
90 EVA ss5854617610 Oct 13, 2022 (156)
91 EVA ss5867058313 Oct 13, 2022 (156)
92 EVA ss5965313694 Oct 13, 2022 (156)
93 1000Genomes NC_000004.11 - 185119844 Oct 12, 2018 (152)
94 1000Genomes_30x NC_000004.12 - 184198691 Oct 13, 2022 (156)
95 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 185119844 Oct 12, 2018 (152)
96 Genetic variation in the Estonian population NC_000004.11 - 185119844 Oct 12, 2018 (152)
97 The Danish reference pan genome NC_000004.11 - 185119844 Apr 26, 2020 (154)
98 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 176214094 (NC_000004.12:184198690:A:C 4/140120)
Row 176214095 (NC_000004.12:184198690:A:G 67956/140054)

- Apr 27, 2021 (155)
99 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 176214094 (NC_000004.12:184198690:A:C 4/140120)
Row 176214095 (NC_000004.12:184198690:A:G 67956/140054)

- Apr 27, 2021 (155)
100 Genome of the Netherlands Release 5 NC_000004.11 - 185119844 Apr 26, 2020 (154)
101 HapMap NC_000004.12 - 184198691 Apr 26, 2020 (154)
102 KOREAN population from KRGDB NC_000004.11 - 185119844 Apr 26, 2020 (154)
103 Korean Genome Project NC_000004.12 - 184198691 Apr 26, 2020 (154)
104 Northern Sweden NC_000004.11 - 185119844 Jul 13, 2019 (153)
105 Qatari NC_000004.11 - 185119844 Apr 26, 2020 (154)
106 SGDP_PRJ NC_000004.11 - 185119844 Apr 26, 2020 (154)
107 Siberian NC_000004.11 - 185119844 Apr 26, 2020 (154)
108 8.3KJPN NC_000004.11 - 185119844 Apr 27, 2021 (155)
109 14KJPN NC_000004.12 - 184198691 Oct 13, 2022 (156)
110 TopMed NC_000004.12 - 184198691 Apr 27, 2021 (155)
111 UK 10K study - Twins NC_000004.11 - 185119844 Oct 12, 2018 (152)
112 A Vietnamese Genetic Variation Database NC_000004.11 - 185119844 Jul 13, 2019 (153)
113 ALFA NC_000004.12 - 184198691 Apr 27, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
14446193, ss2819659823, ss3907268799 NC_000004.11:185119843:A:C NC_000004.12:184198690:A:C (self)
146054788, ss5805886561 NC_000004.12:184198690:A:C NC_000004.12:184198690:A:C (self)
ss77668630, ss78547855 NC_000004.9:185494992:A:G NC_000004.12:184198690:A:G (self)
ss108677054, ss111180443, ss117333429, ss162896054, ss165338007, ss167500099, ss199662667, ss206267532, ss244256880, ss253824695, ss278094610, ss285083462, ss293277773, ss1590618189, ss1712733016, ss3643478559 NC_000004.10:185356837:A:G NC_000004.12:184198690:A:G (self)
24904264, 13859309, 9850644, 7113213, 6145205, 14446193, 5243986, 6385665, 12900751, 3417561, 27721276, 13859309, 3070782, ss221429958, ss232761956, ss239974653, ss537008645, ss558103729, ss651940615, ss981097994, ss1072279755, ss1313368679, ss1430187184, ss1580948274, ss1611996177, ss1654990210, ss1802766362, ss1924343735, ss1969973744, ss2022766959, ss2150901207, ss2625876942, ss2706409618, ss2819659823, ss2985311386, ss2985939655, ss2996191787, ss3346154172, ss3629144925, ss3638530728, ss3654083950, ss3664112396, ss3731959121, ss3762890262, ss3784977339, ss3790398478, ss3795274218, ss3829017420, ss3837964602, ss3860883771, ss3907268799, ss5169751969, ss5354777889, ss5507875042, ss5636896269, ss5845259821, ss5965313694 NC_000004.11:185119843:A:G NC_000004.12:184198690:A:G (self)
32741054, 2780640, 12225041, 39059888, 482753529, 146054788, ss2270342444, ss3025164151, ss3647946046, ss3713831152, ss3806058631, ss3843406775, ss3955847040, ss4645375973, ss5262391084, ss5460802783, ss5545215119, ss5705222784, ss5805886561, ss5854617610, ss5867058313 NC_000004.12:184198690:A:G NC_000004.12:184198690:A:G (self)
ss2808010, ss6717729, ss44582653, ss65717100, ss74884278, ss99057410, ss105894991, ss119408540, ss120240086, ss134801491, ss142659392, ss154761662, ss172987401 NT_016354.19:109667564:A:G NC_000004.12:184198690:A:G (self)
ss10136699 NT_022792.15:17531364:A:G NC_000004.12:184198690:A:G (self)
ss19576534 NT_022792.16:17531364:A:G NC_000004.12:184198690:A:G (self)
14446193, ss3907268799 NC_000004.11:185119843:A:T NC_000004.12:184198690:A:T (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 rs1921565

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