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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1799762

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chr7:101126426-101126429 (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
dupG
Variation Type
Indel Insertion and Deletion
Frequency
(G)4=0.425656 (112667/264690, TOPMED)
(G)4=0.441014 (65637/148832, GnomAD_genomes)
dupG=0.36692 (28416/77444, 38KJPN) (+ 10 more)
(G)4=0.48510 (8984/18520, ALFA)
dupG=0.4198 (3037/7234, Korea4K)
(G)4=0.4202 (2691/6404, 1000G_30X)
(G)4=0.4315 (2161/5008, 1000G)
dupG=0.4578 (2051/4480, Estonian)
dupG=0.4639 (1788/3854, ALSPAC)
dupG=0.4471 (1658/3708, TWINSUK)
dupG=0.460 (459/998, GoNL)
dupG=0.402 (241/600, NorthernSweden)
dupG=0.45 (18/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SERPINE1 : 2KB Upstream Variant
Publications
6 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 18520 GGGG=0.48510 GGGGG=0.51490 0.248488 0.278294 0.473218 14
European Sub 14152 GGGG=0.53999 GGGGG=0.46001 0.29381 0.213821 0.492369 0
African Sub 2898 GGGG=0.2640 GGGGG=0.7360 0.066943 0.538992 0.394065 0
African Others Sub 114 GGGG=0.193 GGGGG=0.807 0.070175 0.684211 0.245614 2
African American Sub 2784 GGGG=0.2669 GGGGG=0.7331 0.06681 0.533046 0.400144 0
Asian Sub 112 GGGG=0.482 GGGGG=0.518 0.25 0.285714 0.464286 0
East Asian Sub 86 GGGG=0.52 GGGGG=0.48 0.302326 0.255814 0.44186 0
Other Asian Sub 26 GGGG=0.35 GGGGG=0.65 0.076923 0.384615 0.538462 0
Latin American 1 Sub 146 GGGG=0.445 GGGGG=0.555 0.191781 0.30137 0.506849 0
Latin American 2 Sub 610 GGGG=0.321 GGGGG=0.679 0.121311 0.478689 0.4 1
South Asian Sub 98 GGGG=0.54 GGGGG=0.46 0.326531 0.244898 0.428571 1
Other Sub 504 GGGG=0.415 GGGGG=0.585 0.174603 0.345238 0.480159 0


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 -

No frequency provided

 dupG=0.574344
gnomAD v4 - Genomes Global Study-wide 148832 -

No frequency provided

 dupG=0.558986
gnomAD v4 - Genomes European Sub 78508 -

No frequency provided

 dupG=0.46520
gnomAD v4 - Genomes African Sub 41474 -

No frequency provided

 dupG=0.73875
gnomAD v4 - Genomes American Sub 15256 -

No frequency provided

 dupG=0.63542
gnomAD v4 - Genomes East Asian Sub 5144 -

No frequency provided

 dupG=0.4230
gnomAD v4 - Genomes South Asian Sub 4686 -

No frequency provided

 dupG=0.4979
gnomAD v4 - Genomes Ashkenazi Jewish Sub 3470 -

No frequency provided

 dupG=0.4729
gnomAD v4 - Genomes Middle Eastern sub 294 -

No frequency provided

 dupG=0.646
38KJPN JAPANESE Study-wide 77444 -

No frequency provided

 dupG=0.36692
Allele Frequency Aggregator Total Global 18520 (G)4=0.48510 dupG=0.51490
Allele Frequency Aggregator European Sub 14152 (G)4=0.53999 dupG=0.46001
Allele Frequency Aggregator African Sub 2898 (G)4=0.2640 dupG=0.7360
Allele Frequency Aggregator Latin American 2 Sub 610 (G)4=0.321 dupG=0.679
Allele Frequency Aggregator Other Sub 504 (G)4=0.415 dupG=0.585
Allele Frequency Aggregator Latin American 1 Sub 146 (G)4=0.445 dupG=0.555
Allele Frequency Aggregator Asian Sub 112 (G)4=0.482 dupG=0.518
Allele Frequency Aggregator South Asian Sub 98 (G)4=0.54 dupG=0.46
Korean Genome Project 4K KOREAN Study-wide 7234 -

No frequency provided

 dupG=0.4198
1000Genomes_30X Global Study-wide 6404 -

No frequency provided

 dupG=0.5798
1000Genomes_30X African Sub 1786 -

No frequency provided

 dupG=0.7581
1000Genomes_30X Europe Sub 1266 -

No frequency provided

 dupG=0.4684
1000Genomes_30X South Asian Sub 1202 -

No frequency provided

 dupG=0.5100
1000Genomes_30X East Asian Sub 1170 -

No frequency provided

 dupG=0.4444
1000Genomes_30X American Sub 980 -

No frequency provided

 dupG=0.646
1000Genomes Global Study-wide 5008 -

No frequency provided

 dupG=0.5685
1000Genomes African Sub 1322 -

No frequency provided

 dupG=0.7564
1000Genomes East Asian Sub 1008 -

No frequency provided

 dupG=0.4365
1000Genomes Europe Sub 1006 -

No frequency provided

 dupG=0.4622
1000Genomes South Asian Sub 978 -

No frequency provided

 dupG=0.504
1000Genomes American Sub 694 -

No frequency provided

 dupG=0.647
Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

 dupG=0.4578
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

 dupG=0.4639
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

 dupG=0.4471
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 -

No frequency provided

 dupG=0.460
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

 dupG=0.402
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

 dupG=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 7 NC_000007.14:g.101126429dup
GRCh37.p13 chr 7 NC_000007.13:g.100769710dup
SERPINE1 RefSeqGene (LRG_597) NG_013213.1:g.4332dup
LOC127457188 genomic region NG_111962.1:g.550dup
Gene: SERPINE1, serpin family E member 1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SERPINE1 transcript variant 2 NM_000602.5:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 3 NM_001386456.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 4 NM_001386457.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 5 NM_001386458.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 6 NM_001386459.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 1 NM_001386460.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 7 NM_001386461.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 8 NM_001386462.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 9 NM_001386463.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 10 NM_001386464.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 11 NM_001386465.1:c. N/A Upstream Transcript Variant
SERPINE1 transcript variant 12 NM_001386466.1:c. N/A Upstream 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.

Allele: dupG (allele ID: 28611 )
ClinVar Accession Disease Names Clinical Significance
RCV000014540.25 Transcription level of plasminogen activator inhibitor 1 Pathogenic,Other
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)4= dupG
GRCh38.p14 chr 7 NC_000007.14:g.101126426_101126429= NC_000007.14:g.101126429dup
GRCh37.p13 chr 7 NC_000007.13:g.100769707_100769710= NC_000007.13:g.100769710dup
SERPINE1 RefSeqGene (LRG_597) NG_013213.1:g.4329_4332= NG_013213.1:g.4332dup
LOC127457188 genomic region NG_111962.1:g.547_550= NG_111962.1:g.550dup
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#.

69 SubSNP, 13 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2419772 Dec 03, 2013 (138)
2 HGBASE ss2419778 Nov 14, 2000 (89)
3 PGA-UW-FHCRC ss3172207 Apr 25, 2013 (138)
4 ABI ss43011992 Apr 25, 2013 (138)
5 STEJUSTINE-REGGEN ss51854403 Dec 03, 2013 (138)
6 HGSV ss83059001 Dec 05, 2013 (138)
7 PHARMGKB_CREATE ss84173070 Apr 25, 2013 (138)
8 HUMANGENOME_JCVI ss98211963 Dec 05, 2013 (138)
9 BGI ss104778884 Feb 13, 2009 (137)
10 BGI ss105537504 Feb 13, 2009 (137)
11 BUSHMAN ss193936430 Jul 04, 2010 (132)
12 BL ss256080932 May 09, 2011 (135)
13 GMI ss288861517 May 04, 2012 (137)
14 PJP ss295348629 May 09, 2011 (137)
15 PJP ss295348630 May 09, 2011 (137)
16 1000GENOMES ss326969150 May 09, 2011 (135)
17 1000GENOMES ss327023652 May 09, 2011 (135)
18 1000GENOMES ss327319484 May 09, 2011 (135)
19 PAGE_STUDY ss469996548 May 04, 2012 (137)
20 1000GENOMES ss499959982 May 04, 2012 (137)
21 LUNTER ss551766794 Apr 25, 2013 (138)
22 LUNTER ss551971750 Apr 25, 2013 (138)
23 LUNTER ss553310325 Apr 25, 2013 (138)
24 TISHKOFF ss559289256 Apr 25, 2013 (138)
25 SSMP ss663729219 Apr 01, 2015 (144)
26 EVA-GONL ss984599249 Aug 21, 2014 (142)
27 1000GENOMES ss1377445597 Aug 21, 2014 (142)
28 OMIM-CURATED-RECORDS ss1399966301 Oct 14, 2014 (142)
29 DDI ss1536557495 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1577053940 Apr 01, 2015 (144)
31 EVA_DECODE ss1594178485 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1705753237 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1705753282 Apr 01, 2015 (144)
34 HAMMER_LAB ss1805136295 Sep 08, 2015 (146)
35 GENOMED ss1970772842 Jul 19, 2016 (147)
36 CLINVAR ss2019497273 Aug 17, 2016 (147)
37 JJLAB ss2030859769 Sep 14, 2016 (149)
38 SYSTEMSBIOZJU ss2626798247 Nov 08, 2017 (151)
39 GNOMAD ss2856891925 Nov 08, 2017 (151)
40 SWEGEN ss3001726090 Nov 08, 2017 (151)
41 MCHAISSO ss3066160203 Nov 08, 2017 (151)
42 BEROUKHIMLAB ss3644244798 Oct 12, 2018 (152)
43 BIOINF_KMB_FNS_UNIBA ss3646047137 Oct 12, 2018 (152)
44 URBANLAB ss3648713700 Oct 12, 2018 (152)
45 EGCUT_WGS ss3669476422 Jul 13, 2019 (153)
46 EVA_DECODE ss3720321414 Jul 13, 2019 (153)
47 ACPOP ss3734909983 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3810106534 Jul 13, 2019 (153)
49 EVA ss3830726520 Apr 26, 2020 (154)
50 EVA ss3838861880 Apr 26, 2020 (154)
51 EVA ss3844317126 Apr 26, 2020 (154)
52 TOPMED ss4756917486 Apr 26, 2021 (155)
53 TOMMO_GENOMICS ss6081326555 Oct 31, 2024 (157)
54 EVA ss6322316680 Oct 31, 2024 (157)
55 EVA ss6325526513 Oct 31, 2024 (157)
56 YEGNASUBRAMANIAN_LAB ss6340804281 Oct 31, 2024 (157)
57 KOGIC ss6374359045 Oct 31, 2024 (157)
58 GNOMAD ss6764196593 Oct 31, 2024 (157)
59 TOMMO_GENOMICS ss8184715112 Oct 31, 2024 (157)
60 1000G_HIGH_COVERAGE ss8274068670 Oct 31, 2024 (157)
61 HUGCELL_USP ss8471032489 Oct 31, 2024 (157)
62 1000G_HIGH_COVERAGE ss8562868885 Oct 31, 2024 (157)
63 SANFORD_IMAGENETICS ss8643606194 Oct 31, 2024 (157)
64 TOMMO_GENOMICS ss8725449675 Oct 31, 2024 (157)
65 YY_MCH ss8808934056 Oct 31, 2024 (157)
66 EVA ss8823269270 Oct 31, 2024 (157)
67 EVA ss8856024790 Oct 31, 2024 (157)
68 EVA ss8860126598 Oct 31, 2024 (157)
69 EVA ss8972789969 Oct 31, 2024 (157)
70 1000Genomes NC_000007.13 - 100769707 Oct 12, 2018 (152)
71 1000Genomes_30X NC_000007.14 - 101126426 Oct 31, 2024 (157)
72 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 100769707 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000007.13 - 100769707 Oct 12, 2018 (152)
74 The Danish reference pan genome NC_000007.13 - 100769707 Apr 26, 2020 (154)
75 gnomAD v4 - Genomes NC_000007.14 - 101126426 Oct 31, 2024 (157)
76 Genome of the Netherlands Release 5 NC_000007.13 - 100769707 Apr 26, 2020 (154)
77 Korean Genome Project 4K NC_000007.14 - 101126426 Oct 31, 2024 (157)
78 Northern Sweden NC_000007.13 - 100769707 Jul 13, 2019 (153)
79 38KJPN NC_000007.14 - 101126426 Oct 31, 2024 (157)
80 TopMed NC_000007.14 - 101126426 Apr 26, 2021 (155)
81 UK 10K study - Twins NC_000007.13 - 100769707 Oct 12, 2018 (152)
82 ALFA NC_000007.14 - 101126426 Oct 31, 2024 (157)
83 ClinVar RCV000014540.25 Oct 13, 2022 (156)
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)
rs11406947 Apr 05, 2004 (121)
rs139304273 Sep 17, 2011 (135)
rs34857375 Jan 15, 2013 (137)
rs72310593 May 11, 2012 (137)
rs72578597 Jan 15, 2013 (137)
rs72594212 Feb 26, 2009 (130)
rs145125635 Sep 17, 2011 (135)
rs147166758 May 11, 2012 (137)
rs368372116 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss256080932, ss326969150, ss327023652, ss327319484, ss551766794, ss551971750, ss553310325, ss1594178485 NC_000007.12:100556426::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss295348629 NC_000007.12:100556427::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss288861517, ss295348630 NC_000007.12:100556430::G NC_000007.14:101126425:GGGG:GGGGG (self)
38393823, 21360975, 15214670, 1171774, 9535300, 8194848, 21360975, ss499959982, ss663729219, ss984599249, ss1377445597, ss1536557495, ss1577053940, ss1705753237, ss1705753282, ss1805136295, ss1970772842, ss2030859769, ss2626798247, ss2856891925, ss3001726090, ss3644244798, ss3669476422, ss3734909983, ss3830726520, ss3838861880, ss6322316680, ss6325526513, ss6340804281, ss8184715112, ss8643606194, ss8823269270, ss8972789969 NC_000007.13:100769706::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss559289256 NC_000007.13:100769710::G NC_000007.14:101126425:GGGG:GGGGG (self)
50394820, 291099135, 24210943, 98702375, 594295045, ss3066160203, ss3646047137, ss3648713700, ss3720321414, ss3810106534, ss3844317126, ss4756917486, ss6081326555, ss6374359045, ss6764196593, ss8274068670, ss8471032489, ss8562868885, ss8725449675, ss8808934056, ss8856024790, ss8860126598 NC_000007.14:101126425::G NC_000007.14:101126425:GGGG:GGGGG (self)
323424903, ss1399966301, ss2019497273 NC_000007.14:101126425:GGGG:GGGGG NC_000007.14:101126425:GGGG:GGGGG (self)
RCV000014540.25 NG_013213.1:4332::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss2419778, ss469996548 NT_007933.15:38802549::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss2419772 NT_007933.15:38802551::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss104778884, ss105537504 NT_007933.15:38802552::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss3172207, ss43011992, ss51854403, ss83059001, ss84173070, ss98211963 NT_007933.15:38802553::G NC_000007.14:101126425:GGGG:GGGGG (self)
ss193936430 NT_007933.16:38619646::G NC_000007.14:101126425:GGGG:GGGGG (self)
Help

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

6 citations for rs1799762
PMID Title Author Year Journal
18603647 Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. Simoni M et al. 2008 Human reproduction update
18805939 Functional genetic polymorphisms and female reproductive disorders: part II--endometriosis. Tempfer CB et al. 2009 Human reproduction update
18936436 Prevalence in the United States of selected candidate gene variants: Third National Health and Nutrition Examination Survey, 1991-1994. Chang MH et al. 2009 American journal of epidemiology
21054877 Inflammation gene variants and susceptibility to albuminuria in the U.S. population: analysis in the Third National Health and Nutrition Examination Survey (NHANES III), 1991-1994. Ned RM et al. 2010 BMC medical genetics
23274712 Genetic polymorphisms and the risk of myocardial infarction in patients under 45 years of age. Sakowicz A et al. 2013 Biochemical genetics
30515004 Association Between - 675 ID, 4G/5G PAI-1 Gene Polymorphism and Pregnancy Loss: A Systematic Review. Adler G et al. 2018 Acta informatica medica
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.post825+45319f0