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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.

rs9549598

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:112885990 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00092 (26/28258, 14KJPN)
T=0.03676 (623/16948, ALFA)
T=0.00137 (23/16760, 8.3KJPN) (+ 12 more)
T=0.0401 (257/6404, 1000G_30x)
T=0.0403 (202/5008, 1000G)
T=0.1362 (610/4480, Estonian)
T=0.0618 (238/3854, ALSPAC)
T=0.0696 (258/3708, TWINSUK)
T=0.0003 (1/2920, KOREAN)
T=0.0011 (2/1832, Korea1K)
T=0.064 (64/998, GoNL)
T=0.148 (89/600, NorthernSweden)
T=0.009 (2/216, Qatari)
T=0.47 (42/90, SGDP_PRJ)
C=0.46 (11/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATP11A : 3 Prime UTR 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 16948 C=0.96324 G=0.00000, T=0.03676
European Sub 12878 C=0.95224 G=0.00000, T=0.04776
African Sub 2664 C=0.9992 G=0.0000, T=0.0008
African Others Sub 108 C=1.000 G=0.000, T=0.000
African American Sub 2556 C=0.9992 G=0.0000, T=0.0008
Asian Sub 112 C=1.000 G=0.000, T=0.000
East Asian Sub 86 C=1.00 G=0.00, T=0.00
Other Asian Sub 26 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 130 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 450 C=1.000 G=0.000, T=0.000
South Asian Sub 96 C=1.00 G=0.00, T=0.00
Other Sub 618 C=0.990 G=0.000, T=0.010


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
14KJPN JAPANESE Study-wide 28258 C=0.99908 T=0.00092
Allele Frequency Aggregator Total Global 16948 C=0.96324 G=0.00000, T=0.03676
Allele Frequency Aggregator European Sub 12878 C=0.95224 G=0.00000, T=0.04776
Allele Frequency Aggregator African Sub 2664 C=0.9992 G=0.0000, T=0.0008
Allele Frequency Aggregator Other Sub 618 C=0.990 G=0.000, T=0.010
Allele Frequency Aggregator Latin American 2 Sub 450 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 130 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 96 C=1.00 G=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16760 C=0.99863 T=0.00137
1000Genomes_30x Global Study-wide 6404 C=0.9486 G=0.0112, T=0.0401
1000Genomes_30x African Sub 1786 C=0.9574 G=0.0386, T=0.0039
1000Genomes_30x Europe Sub 1266 C=0.9258 G=0.0000, T=0.0742
1000Genomes_30x South Asian Sub 1202 C=0.9800 G=0.0000, T=0.0200
1000Genomes_30x East Asian Sub 1170 C=0.9991 G=0.0000, T=0.0009
1000Genomes_30x American Sub 980 C=0.863 G=0.003, T=0.134
1000Genomes Global Study-wide 5008 C=0.9489 G=0.0108, T=0.0403
1000Genomes African Sub 1322 C=0.9569 G=0.0386, T=0.0045
1000Genomes East Asian Sub 1008 C=0.9980 G=0.0000, T=0.0020
1000Genomes Europe Sub 1006 C=0.9195 G=0.0000, T=0.0805
1000Genomes South Asian Sub 978 C=0.982 G=0.000, T=0.018
1000Genomes American Sub 694 C=0.859 G=0.004, T=0.137
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8638 T=0.1362
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9382 T=0.0618
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9304 T=0.0696
KOREAN population from KRGDB KOREAN Study-wide 2920 C=0.9997 T=0.0003
Korean Genome Project KOREAN Study-wide 1832 C=0.9989 T=0.0011
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.936 T=0.064
Northern Sweden ACPOP Study-wide 600 C=0.852 T=0.148
Qatari Global Study-wide 216 C=0.991 T=0.009
SGDP_PRJ Global Study-wide 90 C=0.48 G=0.06, T=0.47
Siberian Global Study-wide 24 C=0.46 T=0.54
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 13 NC_000013.11:g.112885990C>G
GRCh38.p14 chr 13 NC_000013.11:g.112885990C>T
GRCh37.p13 chr 13 NC_000013.10:g.113540304C>G
GRCh37.p13 chr 13 NC_000013.10:g.113540304C>T
Gene: ATP11A, ATPase phospholipid transporting 11A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ATP11A transcript variant 1 NM_015205.3:c.*4124= N/A 3 Prime UTR Variant
ATP11A transcript variant 2 NM_032189.4:c.*3926= N/A 3 Prime UTR Variant
ATP11A transcript variant X1 XM_005268299.5:c.*3926= N/A 3 Prime UTR Variant
ATP11A transcript variant X2 XM_005268300.5:c.*3926= N/A 3 Prime UTR Variant
ATP11A transcript variant X3 XM_011537480.3:c.*4186= N/A 3 Prime UTR Variant
ATP11A transcript variant X8 XM_047430218.1:c.*3926= N/A 3 Prime UTR Variant
ATP11A transcript variant X4 XM_005268303.5:c. N/A Genic Downstream Transcript Variant
ATP11A transcript variant X5 XM_005268305.5:c. N/A Genic Downstream Transcript Variant
ATP11A transcript variant X1 XM_017020490.2:c. N/A Genic Downstream Transcript Variant
ATP11A transcript variant X2 XM_017020491.2:c. N/A Genic Downstream Transcript Variant
ATP11A transcript variant X7 XM_017020492.2:c. N/A Genic Downstream Transcript Variant
ATP11A transcript variant X6 XM_047430219.1:c. 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 C= G T
GRCh38.p14 chr 13 NC_000013.11:g.112885990= NC_000013.11:g.112885990C>G NC_000013.11:g.112885990C>T
GRCh37.p13 chr 13 NC_000013.10:g.113540304= NC_000013.10:g.113540304C>G NC_000013.10:g.113540304C>T
ATP11A transcript variant X1 XM_005268299.5:c.*3926= XM_005268299.5:c.*3926C>G XM_005268299.5:c.*3926C>T
ATP11A transcript variant X2 XM_005268300.5:c.*3926= XM_005268300.5:c.*3926C>G XM_005268300.5:c.*3926C>T
ATP11A transcript variant 2 NM_032189.4:c.*3926= NM_032189.4:c.*3926C>G NM_032189.4:c.*3926C>T
ATP11A transcript variant 2 NM_032189.3:c.*3926= NM_032189.3:c.*3926C>G NM_032189.3:c.*3926C>T
ATP11A transcript variant X3 XM_011537480.3:c.*4186= XM_011537480.3:c.*4186C>G XM_011537480.3:c.*4186C>T
ATP11A transcript variant 1 NM_015205.3:c.*4124= NM_015205.3:c.*4124C>G NM_015205.3:c.*4124C>T
ATP11A transcript variant 1 NM_015205.2:c.*4124= NM_015205.2:c.*4124C>G NM_015205.2:c.*4124C>T
ATP11A transcript variant X8 XM_047430218.1:c.*3926= XM_047430218.1:c.*3926C>G XM_047430218.1:c.*3926C>T
ATP11A transcript variant 5 NM_001405663.1:c.*4126= NM_001405663.1:c.*4126C>G NM_001405663.1:c.*4126C>T
ATP11A transcript variant 3 NM_001405661.1:c.*3926= NM_001405661.1:c.*3926C>G NM_001405661.1:c.*3926C>T
ATP11A transcript variant 4 NM_001405662.1:c.*3926= NM_001405662.1:c.*3926C>G NM_001405662.1:c.*3926C>T
FLJ21858 transcript NM_032210.1:c.*330= NM_032210.1:c.*330C>G NM_032210.1:c.*330C>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#.

47 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13252721 Dec 05, 2003 (119)
2 BCMHGSC_JDW ss89856668 Mar 24, 2008 (129)
3 ENSEMBL ss133844072 Dec 01, 2009 (131)
4 BCM-HGSC-SUB ss206797142 Jul 04, 2010 (132)
5 1000GENOMES ss236443903 Jul 15, 2010 (132)
6 ILLUMINA ss482626645 May 04, 2012 (137)
7 ILLUMINA ss483157460 May 04, 2012 (137)
8 SSMP ss659591657 Apr 25, 2013 (138)
9 ILLUMINA ss781824022 Sep 08, 2015 (146)
10 EVA-GONL ss990879993 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1079458805 Aug 21, 2014 (142)
12 1000GENOMES ss1350006146 Aug 21, 2014 (142)
13 1000GENOMES ss1350006147 Aug 21, 2014 (142)
14 EVA_UK10K_ALSPAC ss1631226862 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1674220895 Apr 01, 2015 (144)
16 EVA_DECODE ss1694873883 Apr 01, 2015 (144)
17 WEILL_CORNELL_DGM ss1934245281 Feb 12, 2016 (147)
18 JJLAB ss2027898280 Sep 14, 2016 (149)
19 USC_VALOUEV ss2156267036 Dec 20, 2016 (150)
20 HUMAN_LONGEVITY ss2199992705 Dec 20, 2016 (150)
21 GNOMAD ss2924725626 Nov 08, 2017 (151)
22 SWEGEN ss3011756743 Nov 08, 2017 (151)
23 BIOINF_KMB_FNS_UNIBA ss3027772915 Nov 08, 2017 (151)
24 CSHL ss3350679086 Nov 08, 2017 (151)
25 EGCUT_WGS ss3679045087 Jul 13, 2019 (153)
26 EVA_DECODE ss3696183322 Jul 13, 2019 (153)
27 ACPOP ss3740156912 Jul 13, 2019 (153)
28 EVA ss3752019446 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3817351769 Jul 13, 2019 (153)
30 KHV_HUMAN_GENOMES ss3817351770 Jul 13, 2019 (153)
31 EVA ss3833787541 Apr 27, 2020 (154)
32 SGDP_PRJ ss3880930955 Apr 27, 2020 (154)
33 KRGDB ss3929871155 Apr 27, 2020 (154)
34 KOGIC ss3974409409 Apr 27, 2020 (154)
35 TOPMED ss4962178302 Apr 27, 2021 (155)
36 TOPMED ss4962178303 Apr 27, 2021 (155)
37 TOMMO_GENOMICS ss5212021186 Apr 27, 2021 (155)
38 1000G_HIGH_COVERAGE ss5295301962 Oct 16, 2022 (156)
39 1000G_HIGH_COVERAGE ss5295301963 Oct 16, 2022 (156)
40 HUGCELL_USP ss5489504916 Oct 16, 2022 (156)
41 HUGCELL_USP ss5489504917 Oct 16, 2022 (156)
42 1000G_HIGH_COVERAGE ss5595117514 Oct 16, 2022 (156)
43 SANFORD_IMAGENETICS ss5655688542 Oct 16, 2022 (156)
44 TOMMO_GENOMICS ss5764457603 Oct 16, 2022 (156)
45 EVA ss5840102365 Oct 16, 2022 (156)
46 EVA ss5947136423 Oct 16, 2022 (156)
47 EVA ss5947136424 Oct 16, 2022 (156)
48 1000Genomes NC_000013.10 - 113540304 Oct 12, 2018 (152)
49 1000Genomes_30x NC_000013.11 - 112885990 Oct 16, 2022 (156)
50 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 113540304 Oct 12, 2018 (152)
51 Genetic variation in the Estonian population NC_000013.10 - 113540304 Oct 12, 2018 (152)
52 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 443802502 (NC_000013.11:112885989:C:G 1254/140280)
Row 443802503 (NC_000013.11:112885989:C:T 10122/140272)

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

Submission ignored due to conflicting rows:
Row 443802502 (NC_000013.11:112885989:C:G 1254/140280)
Row 443802503 (NC_000013.11:112885989:C:T 10122/140272)

- Apr 27, 2021 (155)
54 Genome of the Netherlands Release 5 NC_000013.10 - 113540304 Apr 27, 2020 (154)
55 KOREAN population from KRGDB NC_000013.10 - 113540304 Apr 27, 2020 (154)
56 Korean Genome Project NC_000013.11 - 112885990 Apr 27, 2020 (154)
57 Northern Sweden NC_000013.10 - 113540304 Jul 13, 2019 (153)
58 Qatari NC_000013.10 - 113540304 Apr 27, 2020 (154)
59 SGDP_PRJ NC_000013.10 - 113540304 Apr 27, 2020 (154)
60 Siberian NC_000013.10 - 113540304 Apr 27, 2020 (154)
61 8.3KJPN NC_000013.10 - 113540304 Apr 27, 2021 (155)
62 14KJPN NC_000013.11 - 112885990 Oct 16, 2022 (156)
63 TopMed

Submission ignored due to conflicting rows:
Row 177723960 (NC_000013.11:112885989:C:G 2578/264690)
Row 177723961 (NC_000013.11:112885989:C:T 15668/264690)

- Apr 27, 2021 (155)
64 TopMed

Submission ignored due to conflicting rows:
Row 177723960 (NC_000013.11:112885989:C:G 2578/264690)
Row 177723961 (NC_000013.11:112885989:C:T 15668/264690)

- Apr 27, 2021 (155)
65 UK 10K study - Twins NC_000013.10 - 113540304 Oct 12, 2018 (152)
66 ALFA NC_000013.11 - 112885990 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
62948443, 32947935, ss236443903, ss1350006146, ss2924725626, ss3880930955, ss5655688542, ss5947136423 NC_000013.10:113540303:C:G NC_000013.11:112885989:C:G (self)
82643449, 7608043085, ss2199992705, ss3817351770, ss4962178302, ss5295301962, ss5489504917, ss5595117514 NC_000013.11:112885989:C:G NC_000013.11:112885989:C:G (self)
ss89856668, ss206797142, ss483157460, ss1694873883 NC_000013.9:112588304:C:T NC_000013.11:112885989:C:T (self)
62948443, 34982994, 24783335, 15620300, 37048549, 13441777, 16287211, 32947935, 8783390, 69990493, 34982994, ss236443903, ss482626645, ss659591657, ss781824022, ss990879993, ss1079458805, ss1350006147, ss1631226862, ss1674220895, ss1934245281, ss2027898280, ss2156267036, ss2924725626, ss3011756743, ss3350679086, ss3679045087, ss3740156912, ss3752019446, ss3833787541, ss3880930955, ss3929871155, ss5212021186, ss5655688542, ss5840102365, ss5947136424 NC_000013.10:113540303:C:T NC_000013.11:112885989:C:T (self)
82643449, 30787410, 98294707, 7608043085, ss2199992705, ss3027772915, ss3696183322, ss3817351769, ss3974409409, ss4962178303, ss5295301963, ss5489504916, ss5595117514, ss5764457603 NC_000013.11:112885989:C:T NC_000013.11:112885989:C:T (self)
ss13252721 NT_027140.5:1036309:C:T NC_000013.11:112885989:C:T (self)
ss133844072 NT_027140.6:1036309:C:T NC_000013.11:112885989: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 rs9549598

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