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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.

rs140837427

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:180197055 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000364 (51/140270, GnomAD)
T=0.000826 (86/104138, ExAC)
T=0.00258 (73/28256, 14KJPN) (+ 8 more)
T=0.00286 (48/16760, 8.3KJPN)
A=0.00000 (0/14418, ALFA)
G=0.00000 (0/14418, ALFA)
T=0.00000 (0/14418, ALFA)
T=0.0017 (11/6404, 1000G_30x)
T=0.0016 (8/5008, 1000G)
T=0.0065 (19/2920, KOREAN)
T=0.0109 (20/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
QSOX1 : 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 14418 C=1.00000 A=0.00000, G=0.00000, T=0.00000
European Sub 9824 C=1.0000 A=0.0000, G=0.0000, T=0.0000
African Sub 2946 C=1.0000 A=0.0000, G=0.0000, T=0.0000
African Others Sub 114 C=1.000 A=0.000, G=0.000, T=0.000
African American Sub 2832 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Asian Sub 110 C=1.000 A=0.000, G=0.000, T=0.000
East Asian Sub 84 C=1.00 A=0.00, G=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, G=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, G=0.00, T=0.00
Other Sub 684 C=1.000 A=0.000, G=0.000, T=0.000


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
gnomAD - Genomes Global Study-wide 140270 C=0.999636 T=0.000364
gnomAD - Genomes European Sub 75952 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42052 C=0.99998 T=0.00002
gnomAD - Genomes American Sub 13664 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3126 C=0.9840 T=0.0160
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 104138 C=0.999174 T=0.000826
ExAC Europe Sub 64674 C=0.99998 T=0.00002
ExAC Asian Sub 19522 C=0.99570 T=0.00430
ExAC American Sub 10430 C=1.00000 T=0.00000
ExAC African Sub 8774 C=0.9999 T=0.0001
ExAC Other Sub 738 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28256 C=0.99742 T=0.00258
8.3KJPN JAPANESE Study-wide 16760 C=0.99714 T=0.00286
Allele Frequency Aggregator Total Global 14418 C=1.00000 A=0.00000, G=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 9824 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2946 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 684 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 110 C=1.000 A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, G=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9983 T=0.0017
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9906 T=0.0094
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9984 T=0.0016
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9921 T=0.0079
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
KOREAN population from KRGDB KOREAN Study-wide 2920 C=0.9935 T=0.0065
Korean Genome Project KOREAN Study-wide 1832 C=0.9891 T=0.0109
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 1 NC_000001.11:g.180197055C>A
GRCh38.p14 chr 1 NC_000001.11:g.180197055C>G
GRCh38.p14 chr 1 NC_000001.11:g.180197055C>T
GRCh37.p13 chr 1 NC_000001.10:g.180166190C>A
GRCh37.p13 chr 1 NC_000001.10:g.180166190C>G
GRCh37.p13 chr 1 NC_000001.10:g.180166190C>T
Gene: QSOX1, quiescin sulfhydryl oxidase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
QSOX1 transcript variant 2 NM_001004128.3:c.1807-278…

NM_001004128.3:c.1807-278C>A

N/A Intron Variant
QSOX1 transcript variant 1 NM_002826.5:c.*18= N/A 3 Prime UTR Variant
QSOX1 transcript variant X1 XM_047426230.1:c.2097+165…

XM_047426230.1:c.2097+165C>A

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 C= A G T
GRCh38.p14 chr 1 NC_000001.11:g.180197055= NC_000001.11:g.180197055C>A NC_000001.11:g.180197055C>G NC_000001.11:g.180197055C>T
GRCh37.p13 chr 1 NC_000001.10:g.180166190= NC_000001.10:g.180166190C>A NC_000001.10:g.180166190C>G NC_000001.10:g.180166190C>T
QSOX1 transcript variant 1 NM_002826.5:c.*18= NM_002826.5:c.*18C>A NM_002826.5:c.*18C>G NM_002826.5:c.*18C>T
QSOX1 transcript variant 1 NM_002826.4:c.*18= NM_002826.4:c.*18C>A NM_002826.4:c.*18C>G NM_002826.4:c.*18C>T
QSOX1 transcript variant 2 NM_001004128.2:c.1807-278= NM_001004128.2:c.1807-278C>A NM_001004128.2:c.1807-278C>G NM_001004128.2:c.1807-278C>T
QSOX1 transcript variant 2 NM_001004128.3:c.1807-278= NM_001004128.3:c.1807-278C>A NM_001004128.3:c.1807-278C>G NM_001004128.3:c.1807-278C>T
QSOX1 transcript variant X1 XM_005245375.1:c.2097+165= XM_005245375.1:c.2097+165C>A XM_005245375.1:c.2097+165C>G XM_005245375.1:c.2097+165C>T
QSOX1 transcript variant X1 XM_047426230.1:c.2097+165= XM_047426230.1:c.2097+165C>A XM_047426230.1:c.2097+165C>G XM_047426230.1:c.2097+165C>T
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#.

25 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss329063536 May 09, 2011 (134)
2 1000GENOMES ss489780246 May 04, 2012 (137)
3 ILLUMINA ss534950709 Sep 08, 2015 (146)
4 1000GENOMES ss1293634380 Aug 21, 2014 (142)
5 EVA_EXAC ss1685938438 Apr 01, 2015 (144)
6 HUMAN_LONGEVITY ss2167989412 Dec 20, 2016 (150)
7 GNOMAD ss2732096414 Nov 08, 2017 (151)
8 GNOMAD ss2746509700 Nov 08, 2017 (151)
9 GNOMAD ss2763324905 Nov 08, 2017 (151)
10 ILLUMINA ss3626252257 Oct 11, 2018 (152)
11 EVA ss3747024841 Jul 12, 2019 (153)
12 KRGDB ss3895626733 Apr 25, 2020 (154)
13 KOGIC ss3946001509 Apr 25, 2020 (154)
14 TOPMED ss4474557301 Apr 25, 2021 (155)
15 TOPMED ss4474557302 Apr 25, 2021 (155)
16 TOPMED ss4474557303 Apr 25, 2021 (155)
17 TOMMO_GENOMICS ss5147283180 Apr 25, 2021 (155)
18 1000G_HIGH_COVERAGE ss5244906678 Oct 17, 2022 (156)
19 EVA ss5323172888 Oct 17, 2022 (156)
20 1000G_HIGH_COVERAGE ss5518544749 Oct 17, 2022 (156)
21 SANFORD_IMAGENETICS ss5626941723 Oct 17, 2022 (156)
22 TOMMO_GENOMICS ss5674712858 Oct 17, 2022 (156)
23 YY_MCH ss5801413831 Oct 17, 2022 (156)
24 EVA ss5910951548 Oct 17, 2022 (156)
25 EVA ss5938753510 Oct 17, 2022 (156)
26 1000Genomes NC_000001.10 - 180166190 Oct 11, 2018 (152)
27 1000Genomes_30x NC_000001.11 - 180197055 Oct 17, 2022 (156)
28 ExAC NC_000001.10 - 180166190 Oct 11, 2018 (152)
29 gnomAD - Genomes NC_000001.11 - 180197055 Apr 25, 2021 (155)
30 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 1126131 (NC_000001.10:180166189:C:C 224111/224112, NC_000001.10:180166189:C:G 1/224112)
Row 1126132 (NC_000001.10:180166189:C:C 223919/224112, NC_000001.10:180166189:C:T 193/224112)

- Jul 12, 2019 (153)
31 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 1126131 (NC_000001.10:180166189:C:C 224111/224112, NC_000001.10:180166189:C:G 1/224112)
Row 1126132 (NC_000001.10:180166189:C:C 223919/224112, NC_000001.10:180166189:C:T 193/224112)

- Jul 12, 2019 (153)
32 KOREAN population from KRGDB NC_000001.10 - 180166190 Apr 25, 2020 (154)
33 Korean Genome Project NC_000001.11 - 180197055 Apr 25, 2020 (154)
34 8.3KJPN NC_000001.10 - 180166190 Apr 25, 2021 (155)
35 14KJPN NC_000001.11 - 180197055 Oct 17, 2022 (156)
36 TopMed

Submission ignored due to conflicting rows:
Row 38163636 (NC_000001.11:180197054:C:A 1/264690)
Row 38163637 (NC_000001.11:180197054:C:G 1/264690)
Row 38163638 (NC_000001.11:180197054:C:T 196/264690)

- Apr 25, 2021 (155)
37 TopMed

Submission ignored due to conflicting rows:
Row 38163636 (NC_000001.11:180197054:C:A 1/264690)
Row 38163637 (NC_000001.11:180197054:C:G 1/264690)
Row 38163638 (NC_000001.11:180197054:C:T 196/264690)

- Apr 25, 2021 (155)
38 TopMed

Submission ignored due to conflicting rows:
Row 38163636 (NC_000001.11:180197054:C:A 1/264690)
Row 38163637 (NC_000001.11:180197054:C:G 1/264690)
Row 38163638 (NC_000001.11:180197054:C:T 196/264690)

- Apr 25, 2021 (155)
39 ALFA NC_000001.11 - 180197055 Apr 25, 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
13781011934, ss4474557301 NC_000001.11:180197054:C:A NC_000001.11:180197054:C:A (self)
ss2732096414 NC_000001.10:180166189:C:G NC_000001.11:180197054:C:G (self)
13781011934, ss4474557302 NC_000001.11:180197054:C:G NC_000001.11:180197054:C:G (self)
4451212, 5166468, 2804127, 5252487, ss329063536, ss489780246, ss534950709, ss1293634380, ss1685938438, ss2732096414, ss2746509700, ss2763324905, ss3626252257, ss3747024841, ss3895626733, ss5147283180, ss5323172888, ss5626941723, ss5938753510 NC_000001.10:180166189:C:T NC_000001.11:180197054:C:T (self)
6070684, 32164184, 2379510, 8549962, 13781011934, ss2167989412, ss3946001509, ss4474557303, ss5244906678, ss5518544749, ss5674712858, ss5801413831, ss5910951548 NC_000001.11:180197054:C:T NC_000001.11:180197054:C: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 rs140837427

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