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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.

rs2353398

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:144601606 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.337448 (89319/264690, TOPMED)
T=0.345094 (47605/137948, GnomAD)
T=0.23685 (18640/78698, PAGE_STUDY) (+ 19 more)
T=0.22109 (6247/28256, 14KJPN)
T=0.22405 (3755/16760, 8.3KJPN)
A=0.4892 (4862/9938, ALFA)
T=0.2380 (1524/6404, 1000G_30x)
T=0.2398 (1201/5008, 1000G)
T=0.4105 (1838/4478, Estonian)
T=0.4894 (1886/3854, ALSPAC)
T=0.4868 (1805/3708, TWINSUK)
T=0.2695 (789/2928, KOREAN)
T=0.2467 (452/1832, Korea1K)
T=0.461 (460/998, GoNL)
T=0.290 (230/792, PRJEB37584)
T=0.435 (261/600, NorthernSweden)
T=0.208 (105/504, SGDP_PRJ)
T=0.274 (90/328, HapMap)
T=0.338 (73/216, Qatari)
T=0.26 (13/50, Siberian)
A=0.47 (19/40, GENOME_DK)
T=0.0 (0/4, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 9938 T=0.5108 A=0.4892, C=0.0000 0.317971 0.296438 0.385591 32
European Sub 8868 T=0.5326 A=0.4674, C=0.0000 0.331078 0.2659 0.403022 32
African Sub 674 T=0.162 A=0.838, C=0.000 0.050445 0.727003 0.222552 6
African Others Sub 32 T=0.16 A=0.84, C=0.00 0.0625 0.75 0.1875 1
African American Sub 642 T=0.162 A=0.838, C=0.000 0.049844 0.725857 0.224299 6
Asian Sub 10 T=0.7 A=0.3, C=0.0 0.6 0.2 0.2 1
East Asian Sub 6 T=0.8 A=0.2, C=0.0 0.666667 0.0 0.333333 0
Other Asian Sub 4 T=0.5 A=0.5, C=0.0 0.5 0.5 0.0 1
Latin American 1 Sub 32 T=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Latin American 2 Sub 58 T=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
South Asian Sub 16 T=0.75 A=0.25, C=0.00 0.75 0.25 0.0 5
Other Sub 280 T=0.482 A=0.518, C=0.000 0.292857 0.328571 0.378571 5


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 T=0.337448 A=0.662552
gnomAD - Genomes Global Study-wide 137948 T=0.345094 A=0.654906
gnomAD - Genomes European Sub 75068 T=0.45396 A=0.54604
gnomAD - Genomes African Sub 40874 T=0.12529 A=0.87471
gnomAD - Genomes American Sub 13440 T=0.39866 A=0.60134
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.4424 A=0.5576
gnomAD - Genomes East Asian Sub 3118 T=0.2537 A=0.7463
gnomAD - Genomes Other Sub 2130 T=0.3704 A=0.6296
The PAGE Study Global Study-wide 78698 T=0.23685 A=0.76315
The PAGE Study AfricanAmerican Sub 32512 T=0.13398 A=0.86602
The PAGE Study Mexican Sub 10810 T=0.32183 A=0.67817
The PAGE Study Asian Sub 8318 T=0.2245 A=0.7755
The PAGE Study PuertoRican Sub 7918 T=0.3532 A=0.6468
The PAGE Study NativeHawaiian Sub 4534 T=0.2435 A=0.7565
The PAGE Study Cuban Sub 4230 T=0.4499 A=0.5501
The PAGE Study Dominican Sub 3828 T=0.2780 A=0.7220
The PAGE Study CentralAmerican Sub 2450 T=0.3265 A=0.6735
The PAGE Study SouthAmerican Sub 1982 T=0.3345 A=0.6655
The PAGE Study NativeAmerican Sub 1260 T=0.3587 A=0.6413
The PAGE Study SouthAsian Sub 856 T=0.181 A=0.819
14KJPN JAPANESE Study-wide 28256 T=0.22109 A=0.77891
8.3KJPN JAPANESE Study-wide 16760 T=0.22405 A=0.77595
Allele Frequency Aggregator Total Global 9938 T=0.5108 A=0.4892, C=0.0000
Allele Frequency Aggregator European Sub 8868 T=0.5326 A=0.4674, C=0.0000
Allele Frequency Aggregator African Sub 674 T=0.162 A=0.838, C=0.000
Allele Frequency Aggregator Other Sub 280 T=0.482 A=0.518, C=0.000
Allele Frequency Aggregator Latin American 2 Sub 58 T=1.00 A=0.00, C=0.00
Allele Frequency Aggregator Latin American 1 Sub 32 T=1.00 A=0.00, C=0.00
Allele Frequency Aggregator South Asian Sub 16 T=0.75 A=0.25, C=0.00
Allele Frequency Aggregator Asian Sub 10 T=0.7 A=0.3, C=0.0
1000Genomes_30x Global Study-wide 6404 T=0.2380 A=0.7620
1000Genomes_30x African Sub 1786 T=0.0594 A=0.9406
1000Genomes_30x Europe Sub 1266 T=0.4834 A=0.5166
1000Genomes_30x South Asian Sub 1202 T=0.1639 A=0.8361
1000Genomes_30x East Asian Sub 1170 T=0.2299 A=0.7701
1000Genomes_30x American Sub 980 T=0.347 A=0.653
1000Genomes Global Study-wide 5008 T=0.2398 A=0.7602
1000Genomes African Sub 1322 T=0.0658 A=0.9342
1000Genomes East Asian Sub 1008 T=0.2222 A=0.7778
1000Genomes Europe Sub 1006 T=0.4781 A=0.5219
1000Genomes South Asian Sub 978 T=0.173 A=0.827
1000Genomes American Sub 694 T=0.346 A=0.654
Genetic variation in the Estonian population Estonian Study-wide 4478 T=0.4105 A=0.5895
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.4894 A=0.5106
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.4868 A=0.5132
KOREAN population from KRGDB KOREAN Study-wide 2928 T=0.2695 A=0.7305, C=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.2467 A=0.7533
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.461 A=0.539
CNV burdens in cranial meningiomas Global Study-wide 792 T=0.290 A=0.710
CNV burdens in cranial meningiomas CRM Sub 792 T=0.290 A=0.710
Northern Sweden ACPOP Study-wide 600 T=0.435 A=0.565
SGDP_PRJ Global Study-wide 504 T=0.208 A=0.792
HapMap Global Study-wide 328 T=0.274 A=0.726
HapMap African Sub 120 T=0.075 A=0.925
HapMap American Sub 120 T=0.533 A=0.467
HapMap Asian Sub 88 T=0.19 A=0.81
Qatari Global Study-wide 216 T=0.338 A=0.662
Siberian Global Study-wide 50 T=0.26 A=0.74
The Danish reference pan genome Danish Study-wide 40 T=0.53 A=0.47
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 4 T=0.0 A=1.0
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.144601606T>A
GRCh38.p14 chr 4 NC_000004.12:g.144601606T>C
GRCh37.p13 chr 4 NC_000004.11:g.145522758T>A
GRCh37.p13 chr 4 NC_000004.11:g.145522758T>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
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 T= A C
GRCh38.p14 chr 4 NC_000004.12:g.144601606= NC_000004.12:g.144601606T>A NC_000004.12:g.144601606T>C
GRCh37.p13 chr 4 NC_000004.11:g.145522758= NC_000004.11:g.145522758T>A NC_000004.11:g.145522758T>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#.

88 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3308737 Sep 28, 2001 (100)
2 SC_JCM ss6025836 Feb 20, 2003 (111)
3 SC_JCM ss11233059 Jul 11, 2003 (117)
4 WI_SSAHASNP ss11634426 Jul 11, 2003 (117)
5 WI_SSAHASNP ss14601197 Dec 05, 2003 (123)
6 SSAHASNP ss22138100 Apr 05, 2004 (121)
7 ABI ss42392767 Mar 13, 2006 (126)
8 HGSV ss78256457 Dec 07, 2007 (129)
9 BCMHGSC_JDW ss92816411 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss98871769 Feb 04, 2009 (130)
11 BGI ss105872059 Feb 04, 2009 (130)
12 1000GENOMES ss108426721 Jan 23, 2009 (130)
13 1000GENOMES ss110746932 Jan 25, 2009 (130)
14 ILLUMINA-UK ss117224759 Dec 01, 2009 (131)
15 ENSEMBL ss135104635 Dec 01, 2009 (131)
16 ENSEMBL ss139940195 Dec 01, 2009 (131)
17 GMI ss158022935 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss162631616 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss164616394 Jul 04, 2010 (132)
20 BUSHMAN ss199301091 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss206414401 Jul 04, 2010 (132)
22 1000GENOMES ss221269241 Jul 14, 2010 (132)
23 1000GENOMES ss232640621 Jul 14, 2010 (132)
24 1000GENOMES ss239878791 Jul 15, 2010 (132)
25 BL ss253596896 May 09, 2011 (134)
26 GMI ss277975534 May 04, 2012 (137)
27 GMI ss285025648 Apr 25, 2013 (138)
28 PJP ss293218269 May 09, 2011 (134)
29 SSMP ss651740664 Apr 25, 2013 (138)
30 EVA-GONL ss980790443 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1072041224 Aug 21, 2014 (142)
32 1000GENOMES ss1312233606 Aug 21, 2014 (142)
33 DDI ss1430085693 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1580821634 Apr 01, 2015 (144)
35 EVA_DECODE ss1590303080 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1611389559 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1654383592 Apr 01, 2015 (144)
38 HAMMER_LAB ss1802343421 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1924032713 Feb 12, 2016 (147)
40 ILLUMINA ss1958727168 Feb 12, 2016 (147)
41 GENOMED ss1969897607 Jul 19, 2016 (147)
42 JJLAB ss2022602961 Sep 14, 2016 (149)
43 USC_VALOUEV ss2150734259 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2267986490 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2625797917 Nov 08, 2017 (151)
46 GRF ss2706228575 Nov 08, 2017 (151)
47 GNOMAD ss2816460826 Nov 08, 2017 (151)
48 AFFY ss2985932384 Nov 08, 2017 (151)
49 SWEGEN ss2995727546 Nov 08, 2017 (151)
50 ILLUMINA ss3022423201 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3025078717 Nov 08, 2017 (151)
52 CSHL ss3346011958 Nov 08, 2017 (151)
53 URBANLAB ss3647875267 Oct 12, 2018 (152)
54 ILLUMINA ss3652913298 Oct 12, 2018 (152)
55 EGCUT_WGS ss3663632019 Jul 13, 2019 (153)
56 EVA_DECODE ss3713263953 Jul 13, 2019 (153)
57 ILLUMINA ss3726177924 Jul 13, 2019 (153)
58 ACPOP ss3731700682 Jul 13, 2019 (153)
59 EVA ss3762538651 Jul 13, 2019 (153)
60 PAGE_CC ss3771159032 Jul 13, 2019 (153)
61 PACBIO ss3784892511 Jul 13, 2019 (153)
62 PACBIO ss3790324563 Jul 13, 2019 (153)
63 PACBIO ss3795200106 Jul 13, 2019 (153)
64 KHV_HUMAN_GENOMES ss3805700637 Jul 13, 2019 (153)
65 EVA ss3828863424 Apr 26, 2020 (154)
66 EVA ss3837882101 Apr 26, 2020 (154)
67 EVA ss3843322129 Apr 26, 2020 (154)
68 SGDP_PRJ ss3860279110 Apr 26, 2020 (154)
69 KRGDB ss3906611991 Apr 26, 2020 (154)
70 KOGIC ss3955317272 Apr 26, 2020 (154)
71 EVA ss3984536384 Apr 26, 2021 (155)
72 EVA ss3985100712 Apr 26, 2021 (155)
73 TOPMED ss4635648606 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5168477628 Apr 26, 2021 (155)
75 1000G_HIGH_COVERAGE ss5261389585 Oct 13, 2022 (156)
76 HUGCELL_USP ss5459904419 Oct 13, 2022 (156)
77 EVA ss5507771262 Oct 13, 2022 (156)
78 1000G_HIGH_COVERAGE ss5543679334 Oct 13, 2022 (156)
79 SANFORD_IMAGENETICS ss5624569898 Oct 13, 2022 (156)
80 SANFORD_IMAGENETICS ss5636311785 Oct 13, 2022 (156)
81 TOMMO_GENOMICS ss5703599101 Oct 13, 2022 (156)
82 YY_MCH ss5805630234 Oct 13, 2022 (156)
83 EVA ss5844858309 Oct 13, 2022 (156)
84 EVA ss5847252582 Oct 13, 2022 (156)
85 EVA ss5854490541 Oct 13, 2022 (156)
86 EVA ss5865919046 Oct 13, 2022 (156)
87 EVA ss5964713931 Oct 13, 2022 (156)
88 EVA ss5979717287 Oct 13, 2022 (156)
89 1000Genomes NC_000004.11 - 145522758 Oct 12, 2018 (152)
90 1000Genomes_30x NC_000004.12 - 144601606 Oct 13, 2022 (156)
91 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 145522758 Oct 12, 2018 (152)
92 Genetic variation in the Estonian population NC_000004.11 - 145522758 Oct 12, 2018 (152)
93 The Danish reference pan genome NC_000004.11 - 145522758 Apr 26, 2020 (154)
94 gnomAD - Genomes NC_000004.12 - 144601606 Apr 26, 2021 (155)
95 Genome of the Netherlands Release 5 NC_000004.11 - 145522758 Apr 26, 2020 (154)
96 HapMap NC_000004.12 - 144601606 Apr 26, 2020 (154)
97 KOREAN population from KRGDB NC_000004.11 - 145522758 Apr 26, 2020 (154)
98 Korean Genome Project NC_000004.12 - 144601606 Apr 26, 2020 (154)
99 Northern Sweden NC_000004.11 - 145522758 Jul 13, 2019 (153)
100 The PAGE Study NC_000004.12 - 144601606 Jul 13, 2019 (153)
101 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000004.11 - 145522758 Apr 26, 2021 (155)
102 CNV burdens in cranial meningiomas NC_000004.11 - 145522758 Apr 26, 2021 (155)
103 Qatari NC_000004.11 - 145522758 Apr 26, 2020 (154)
104 SGDP_PRJ NC_000004.11 - 145522758 Apr 26, 2020 (154)
105 Siberian NC_000004.11 - 145522758 Apr 26, 2020 (154)
106 8.3KJPN NC_000004.11 - 145522758 Apr 26, 2021 (155)
107 14KJPN NC_000004.12 - 144601606 Oct 13, 2022 (156)
108 TopMed NC_000004.12 - 144601606 Apr 26, 2021 (155)
109 UK 10K study - Twins NC_000004.11 - 145522758 Oct 12, 2018 (152)
110 ALFA NC_000004.12 - 144601606 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).

Associated ID History Updated (Build)
rs6537299 Aug 27, 2003 (117)
rs10388539 Sep 24, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78256457 NC_000004.9:145880362:T:A NC_000004.12:144601605:T:A (self)
ss92816411, ss108426721, ss110746932, ss117224759, ss162631616, ss164616394, ss199301091, ss206414401, ss253596896, ss277975534, ss285025648, ss293218269, ss1590303080 NC_000004.10:145742207:T:A NC_000004.12:144601605:T:A (self)
23724795, 13190833, 9370267, 6986573, 5845409, 13789385, 4985547, 326639, 85746, 6074643, 12296090, 3250613, 26446935, 13190833, ss221269241, ss232640621, ss239878791, ss651740664, ss980790443, ss1072041224, ss1312233606, ss1430085693, ss1580821634, ss1611389559, ss1654383592, ss1802343421, ss1924032713, ss1958727168, ss1969897607, ss2022602961, ss2150734259, ss2625797917, ss2706228575, ss2816460826, ss2985932384, ss2995727546, ss3022423201, ss3346011958, ss3652913298, ss3663632019, ss3731700682, ss3762538651, ss3784892511, ss3790324563, ss3795200106, ss3828863424, ss3837882101, ss3860279110, ss3906611991, ss3984536384, ss3985100712, ss5168477628, ss5507771262, ss5624569898, ss5636311785, ss5844858309, ss5847252582, ss5964713931, ss5979717287 NC_000004.11:145522757:T:A NC_000004.12:144601605:T:A (self)
31205269, 168034925, 2728150, 11695273, 380501, 37436205, 473026162, 6551316023, ss2267986490, ss3025078717, ss3647875267, ss3713263953, ss3726177924, ss3771159032, ss3805700637, ss3843322129, ss3955317272, ss4635648606, ss5261389585, ss5459904419, ss5543679334, ss5703599101, ss5805630234, ss5854490541, ss5865919046 NC_000004.12:144601605:T:A NC_000004.12:144601605:T:A (self)
ss3308737, ss6025836, ss42392767, ss98871769, ss105872059, ss135104635, ss139940195, ss158022935 NT_016354.19:70070478:T:A NC_000004.12:144601605:T:A (self)
ss11233059, ss11634426 NT_016606.15:7042422:T:A NC_000004.12:144601605:T:A (self)
ss14601197, ss22138100 NT_016606.16:7070813:T:A NC_000004.12:144601605:T:A (self)
13789385, ss3906611991 NC_000004.11:145522757:T:C NC_000004.12:144601605:T:C (self)
6551316023 NC_000004.12:144601605:T:C NC_000004.12:144601605:T:C (self)
Help

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

1 citation for rs2353398
PMID Title Author Year Journal
20881960 Hundreds of variants clustered in genomic loci and biological pathways affect human height. Lango Allen H et al. 2010 Nature
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.post820+afb47a3d