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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.

rs9550381

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:28630180 (GRCh38.p13) 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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.238033 (63005/264690, TOPMED)
A=0.241199 (33749/139922, GnomAD)
A=0.25273 (4774/18890, ALFA) (+ 13 more)
A=0.2326 (1165/5008, 1000G)
A=0.2647 (1186/4480, Estonian)
A=0.2732 (1053/3854, ALSPAC)
A=0.2767 (1026/3708, TWINSUK)
A=0.2290 (671/2930, KOREAN)
A=0.1992 (365/1832, Korea1K)
A=0.277 (276/998, GoNL)
A=0.298 (179/600, NorthernSweden)
G=0.392 (94/240, SGDP_PRJ)
A=0.204 (44/216, Qatari)
A=0.193 (41/212, Vietnamese)
A=0.25 (10/40, GENOME_DK)
G=0.44 (7/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p13 chr 13 NC_000013.11:g.28630180G>A
GRCh38.p13 chr 13 NC_000013.11:g.28630180G>C
GRCh37.p13 chr 13 NC_000013.10:g.29204317G>A
GRCh37.p13 chr 13 NC_000013.10:g.29204317G>C
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.74727 A=0.25273
European Sub 14286 G=0.73961 A=0.26039
African Sub 2946 G=0.7733 A=0.2267
African Others Sub 114 G=0.772 A=0.228
African American Sub 2832 G=0.7733 A=0.2267
Asian Sub 112 G=0.857 A=0.143
East Asian Sub 86 G=0.88 A=0.12
Other Asian Sub 26 G=0.77 A=0.23
Latin American 1 Sub 146 G=0.801 A=0.199
Latin American 2 Sub 610 G=0.780 A=0.220
South Asian Sub 98 G=0.73 A=0.27
Other Sub 692 G=0.738 A=0.262


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 G=0.761967 A=0.238033
gnomAD - Genomes Global Study-wide 139922 G=0.758801 A=0.241199
gnomAD - Genomes European Sub 75816 G=0.73858 A=0.26142
gnomAD - Genomes African Sub 41886 G=0.77599 A=0.22401
gnomAD - Genomes American Sub 13626 G=0.78798 A=0.21202
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.8058 A=0.1942
gnomAD - Genomes East Asian Sub 3124 G=0.8278 A=0.1722
gnomAD - Genomes Other Sub 2148 G=0.7793 A=0.2207
1000Genomes Global Study-wide 5008 G=0.7674 A=0.2326
1000Genomes African Sub 1322 G=0.7648 A=0.2352
1000Genomes East Asian Sub 1008 G=0.8204 A=0.1796
1000Genomes Europe Sub 1006 G=0.7654 A=0.2346
1000Genomes South Asian Sub 978 G=0.680 A=0.320
1000Genomes American Sub 694 G=0.821 A=0.179
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7353 A=0.2647
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7268 A=0.2732
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7233 A=0.2767
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7710 A=0.2290
Korean Genome Project KOREAN Study-wide 1832 G=0.8008 A=0.1992
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.723 A=0.277
Northern Sweden ACPOP Study-wide 600 G=0.702 A=0.298
SGDP_PRJ Global Study-wide 240 G=0.392 A=0.608
Qatari Global Study-wide 216 G=0.796 A=0.204
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.807 A=0.193
The Danish reference pan genome Danish Study-wide 40 G=0.75 A=0.25
Siberian Global Study-wide 16 G=0.44 A=0.56
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= A C
GRCh38.p13 chr 13 NC_000013.11:g.28630180= NC_000013.11:g.28630180G>A NC_000013.11:g.28630180G>C
GRCh37.p13 chr 13 NC_000013.10:g.29204317= NC_000013.10:g.29204317G>A NC_000013.10:g.29204317G>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#.

43 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13254276 Dec 05, 2003 (119)
2 1000GENOMES ss112647417 Jan 25, 2009 (130)
3 COMPLETE_GENOMICS ss170932016 Jul 04, 2010 (132)
4 BCM-HGSC-SUB ss208740611 Jul 04, 2010 (132)
5 1000GENOMES ss226099295 Jul 14, 2010 (132)
6 1000GENOMES ss236190573 Jul 15, 2010 (132)
7 1000GENOMES ss242698075 Jul 15, 2010 (132)
8 GMI ss281653076 May 04, 2012 (137)
9 TISHKOFF ss563571635 Apr 25, 2013 (138)
10 SSMP ss659167422 Apr 25, 2013 (138)
11 EVA-GONL ss990228462 Aug 21, 2014 (142)
12 JMKIDD_LAB ss1078963754 Aug 21, 2014 (142)
13 1000GENOMES ss1347619956 Aug 21, 2014 (142)
14 DDI ss1427140528 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1576695100 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1629957339 Apr 01, 2015 (144)
17 EVA_DECODE ss1642333034 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1672951372 Apr 01, 2015 (144)
19 WEILL_CORNELL_DGM ss1933597423 Feb 12, 2016 (147)
20 JJLAB ss2027554387 Sep 14, 2016 (149)
21 USC_VALOUEV ss2155919119 Dec 20, 2016 (150)
22 HUMAN_LONGEVITY ss2195103057 Dec 20, 2016 (150)
23 TOPMED ss2359203185 Dec 20, 2016 (150)
24 GRF ss2700291270 Nov 08, 2017 (151)
25 GNOMAD ss2917944701 Nov 08, 2017 (151)
26 SWEGEN ss3010774406 Nov 08, 2017 (151)
27 BIOINF_KMB_FNS_UNIBA ss3027592736 Nov 08, 2017 (151)
28 TOPMED ss3188783530 Nov 08, 2017 (151)
29 CSHL ss3350381992 Nov 08, 2017 (151)
30 EGCUT_WGS ss3678035148 Jul 13, 2019 (153)
31 EVA_DECODE ss3694991647 Jul 13, 2019 (153)
32 ACPOP ss3739612546 Jul 13, 2019 (153)
33 EVA ss3751275955 Jul 13, 2019 (153)
34 KHV_HUMAN_GENOMES ss3816606947 Jul 13, 2019 (153)
35 EVA ss3833466958 Apr 27, 2020 (154)
36 EVA ss3840310681 Apr 27, 2020 (154)
37 EVA ss3845795423 Apr 27, 2020 (154)
38 SGDP_PRJ ss3879660942 Apr 27, 2020 (154)
39 KRGDB ss3928482401 Apr 27, 2020 (154)
40 KOGIC ss3973268423 Apr 27, 2020 (154)
41 TOPMED ss4940999497 Apr 26, 2021 (155)
42 TOMMO_GENOMICS ss5209316994 Apr 26, 2021 (155)
43 TOMMO_GENOMICS ss5209316995 Apr 26, 2021 (155)
44 1000Genomes NC_000013.10 - 29204317 Oct 12, 2018 (152)
45 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 29204317 Oct 12, 2018 (152)
46 Genetic variation in the Estonian population NC_000013.10 - 29204317 Oct 12, 2018 (152)
47 The Danish reference pan genome NC_000013.10 - 29204317 Apr 27, 2020 (154)
48 gnomAD - Genomes NC_000013.11 - 28630180 Apr 26, 2021 (155)
49 Genome of the Netherlands Release 5 NC_000013.10 - 29204317 Apr 27, 2020 (154)
50 KOREAN population from KRGDB NC_000013.10 - 29204317 Apr 27, 2020 (154)
51 Korean Genome Project NC_000013.11 - 28630180 Apr 27, 2020 (154)
52 Northern Sweden NC_000013.10 - 29204317 Jul 13, 2019 (153)
53 Qatari NC_000013.10 - 29204317 Apr 27, 2020 (154)
54 SGDP_PRJ NC_000013.10 - 29204317 Apr 27, 2020 (154)
55 Siberian NC_000013.10 - 29204317 Apr 27, 2020 (154)
56 8.3KJPN

Submission ignored due to conflicting rows:
Row 67286301 (NC_000013.10:29204316:G:A 3997/16760)
Row 67286302 (NC_000013.10:29204316:G:C 2/16760)

- Apr 26, 2021 (155)
57 8.3KJPN

Submission ignored due to conflicting rows:
Row 67286301 (NC_000013.10:29204316:G:A 3997/16760)
Row 67286302 (NC_000013.10:29204316:G:C 2/16760)

- Apr 26, 2021 (155)
58 TopMed NC_000013.11 - 28630180 Apr 26, 2021 (155)
59 UK 10K study - Twins NC_000013.10 - 29204317 Oct 12, 2018 (152)
60 A Vietnamese Genetic Variation Database NC_000013.10 - 29204317 Jul 13, 2019 (153)
61 ALFA NC_000013.11 - 28630180 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss112647417, ss170932016, ss208740611, ss281653076, ss1642333034 NC_000013.9:28102316:G:A NC_000013.11:28630179:G:A (self)
60468379, 33584193, 23773396, 3234486, 14984942, 35659795, 12897411, 15639353, 31677922, 8435473, 33584193, 7449631, ss226099295, ss236190573, ss242698075, ss563571635, ss659167422, ss990228462, ss1078963754, ss1347619956, ss1427140528, ss1576695100, ss1629957339, ss1672951372, ss1933597423, ss2027554387, ss2155919119, ss2359203185, ss2700291270, ss2917944701, ss3010774406, ss3350381992, ss3678035148, ss3739612546, ss3751275955, ss3833466958, ss3840310681, ss3879660942, ss3928482401, ss5209316994 NC_000013.10:29204316:G:A NC_000013.11:28630179:G:A (self)
426387668, 29646424, 97892932, 156545155, 6245928412, ss2195103057, ss3027592736, ss3188783530, ss3694991647, ss3816606947, ss3845795423, ss3973268423, ss4940999497 NC_000013.11:28630179:G:A NC_000013.11:28630179:G:A (self)
ss13254276 NT_009799.12:10184316:G:A NC_000013.11:28630179:G:A (self)
ss5209316995 NC_000013.10:29204316:G:C NC_000013.11:28630179:G:C
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 rs9550381

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.post596+ae089ad