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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.

rs9442380

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1152303 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.096373 (25509/264690, TOPMED)
T=0.079790 (15952/199924, ALFA)
T=0.088880 (12458/140166, GnomAD) (+ 17 more)
T=0.39737 (6660/16760, 8.3KJPN)
T=0.1609 (806/5008, 1000G)
T=0.0857 (384/4480, Estonian)
T=0.0690 (266/3854, ALSPAC)
T=0.0704 (261/3708, TWINSUK)
T=0.3949 (1157/2930, KOREAN)
T=0.1660 (346/2084, HGDP_Stanford)
T=0.1540 (291/1890, HapMap)
T=0.3854 (706/1832, Korea1K)
T=0.089 (89/998, GoNL)
T=0.065 (39/600, NorthernSweden)
T=0.125 (67/538, SGDP_PRJ)
T=0.093 (20/216, Qatari)
T=0.397 (85/214, Vietnamese)
T=0.00 (0/54, Ancient Sardinia)
T=0.13 (7/54, Siberian)
T=0.07 (3/40, GENOME_DK)
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 1 NC_000001.11:g.1152303T>C
GRCh37.p13 chr 1 NC_000001.10:g.1087683T>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 199924 T=0.079790 C=0.920210
European Sub 172690 T=0.073490 C=0.926510
African Sub 7092 T=0.0826 C=0.9174
African Others Sub 264 T=0.080 C=0.920
African American Sub 6828 T=0.0827 C=0.9173
Asian Sub 702 T=0.433 C=0.567
East Asian Sub 556 T=0.424 C=0.576
Other Asian Sub 146 T=0.466 C=0.534
Latin American 1 Sub 844 T=0.100 C=0.900
Latin American 2 Sub 6910 T=0.1265 C=0.8735
South Asian Sub 5042 T=0.1456 C=0.8544
Other Sub 6644 T=0.1022 C=0.8978


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=0.096373 C=0.903627
gnomAD - Genomes Global Study-wide 140166 T=0.088880 C=0.911120
gnomAD - Genomes European Sub 75928 T=0.07624 C=0.92376
gnomAD - Genomes African Sub 41996 T=0.08377 C=0.91623
gnomAD - Genomes American Sub 13650 T=0.09824 C=0.90176
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.0890 C=0.9110
gnomAD - Genomes East Asian Sub 3114 T=0.4165 C=0.5835
gnomAD - Genomes Other Sub 2154 T=0.1007 C=0.8993
8.3KJPN JAPANESE Study-wide 16760 T=0.39737 C=0.60263
1000Genomes Global Study-wide 5008 T=0.1609 C=0.8391
1000Genomes African Sub 1322 T=0.0938 C=0.9062
1000Genomes East Asian Sub 1008 T=0.3978 C=0.6022
1000Genomes Europe Sub 1006 T=0.0606 C=0.9394
1000Genomes South Asian Sub 978 T=0.162 C=0.838
1000Genomes American Sub 694 T=0.089 C=0.911
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.0857 C=0.9143
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.0690 C=0.9310
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.0704 C=0.9296
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.3949 C=0.6051
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.1660 C=0.8340
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.366 C=0.634
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.118 C=0.882
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.077 C=0.923
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.109 C=0.891
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.066 C=0.934
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.171 C=0.829
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.14 C=0.86
HapMap Global Study-wide 1890 T=0.1540 C=0.8460
HapMap American Sub 768 T=0.150 C=0.850
HapMap African Sub 692 T=0.081 C=0.919
HapMap Asian Sub 254 T=0.429 C=0.571
HapMap Europe Sub 176 T=0.062 C=0.938
Korean Genome Project KOREAN Study-wide 1832 T=0.3854 C=0.6146
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.089 C=0.911
Northern Sweden ACPOP Study-wide 600 T=0.065 C=0.935
SGDP_PRJ Global Study-wide 538 T=0.125 C=0.875
Qatari Global Study-wide 216 T=0.093 C=0.907
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.397 C=0.603
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 54 T=0.00 C=1.00
Siberian Global Study-wide 54 T=0.13 C=0.87
The Danish reference pan genome Danish Study-wide 40 T=0.07 C=0.93
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= C
GRCh38.p13 chr 1 NC_000001.11:g.1152303= NC_000001.11:g.1152303T>C
GRCh37.p13 chr 1 NC_000001.10:g.1087683= NC_000001.10:g.1087683T>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#.

112 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13052183 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss16388527 Feb 27, 2004 (120)
3 SSAHASNP ss20470091 Apr 05, 2004 (121)
4 ABI ss41347639 Mar 15, 2006 (126)
5 ILLUMINA ss67918033 Dec 01, 2006 (127)
6 ILLUMINA ss68042959 Dec 01, 2006 (127)
7 ILLUMINA ss68303586 Dec 12, 2006 (127)
8 PERLEGEN ss68756322 May 17, 2007 (127)
9 ILLUMINA ss71607613 May 17, 2007 (127)
10 ILLUMINA ss75688875 Dec 07, 2007 (129)
11 HGSV ss77392018 Dec 07, 2007 (129)
12 HGSV ss83206912 Dec 15, 2007 (130)
13 KRIBB_YJKIM ss84819415 Dec 15, 2007 (130)
14 BCMHGSC_JDW ss87158367 Mar 23, 2008 (129)
15 ILLUMINA ss98259543 May 25, 2008 (130)
16 HUMANGENOME_JCVI ss99179788 Feb 05, 2009 (130)
17 BGI ss102713653 Feb 23, 2009 (131)
18 1000GENOMES ss107938597 Jan 22, 2009 (130)
19 1000GENOMES ss109941600 Jan 24, 2009 (130)
20 ILLUMINA-UK ss118440335 Feb 14, 2009 (130)
21 ENSEMBL ss131636106 Dec 01, 2009 (131)
22 ENSEMBL ss137754509 Dec 01, 2009 (131)
23 ILLUMINA ss154494076 Dec 01, 2009 (131)
24 GMI ss154528311 Dec 01, 2009 (131)
25 ILLUMINA ss159668085 Dec 01, 2009 (131)
26 ILLUMINA ss160987368 Dec 01, 2009 (131)
27 COMPLETE_GENOMICS ss162983745 Jul 04, 2010 (132)
28 COMPLETE_GENOMICS ss163707920 Jul 04, 2010 (132)
29 COMPLETE_GENOMICS ss165982923 Jul 04, 2010 (132)
30 ILLUMINA ss174842647 Jul 04, 2010 (132)
31 BUSHMAN ss197889235 Jul 04, 2010 (132)
32 BCM-HGSC-SUB ss205072967 Jul 04, 2010 (132)
33 1000GENOMES ss218192103 Jul 14, 2010 (132)
34 1000GENOMES ss230396531 Jul 14, 2010 (132)
35 1000GENOMES ss238116058 Jul 15, 2010 (132)
36 BL ss252866379 May 09, 2011 (134)
37 GMI ss275682553 May 04, 2012 (137)
38 GMI ss283988032 Apr 25, 2013 (138)
39 PJP ss290494388 May 09, 2011 (134)
40 ILLUMINA ss481900336 May 04, 2012 (137)
41 ILLUMINA ss481933450 May 04, 2012 (137)
42 ILLUMINA ss482890576 Sep 08, 2015 (146)
43 ILLUMINA ss485744155 May 04, 2012 (137)
44 ILLUMINA ss537598663 Sep 08, 2015 (146)
45 TISHKOFF ss553714049 Apr 25, 2013 (138)
46 SSMP ss647518645 Apr 25, 2013 (138)
47 ILLUMINA ss779010311 Sep 08, 2015 (146)
48 ILLUMINA ss783317857 Sep 08, 2015 (146)
49 ILLUMINA ss784269825 Sep 08, 2015 (146)
50 ILLUMINA ss832579401 Sep 08, 2015 (146)
51 ILLUMINA ss833178830 Jul 12, 2019 (153)
52 ILLUMINA ss834472773 Sep 08, 2015 (146)
53 EVA-GONL ss974772333 Aug 21, 2014 (142)
54 JMKIDD_LAB ss1067613861 Aug 21, 2014 (142)
55 1000GENOMES ss1289351680 Aug 21, 2014 (142)
56 DDI ss1425685948 Apr 01, 2015 (144)
57 EVA_GENOME_DK ss1573852124 Apr 01, 2015 (144)
58 EVA_DECODE ss1584132247 Apr 01, 2015 (144)
59 EVA_UK10K_ALSPAC ss1599383164 Apr 01, 2015 (144)
60 EVA_UK10K_TWINSUK ss1642377197 Apr 01, 2015 (144)
61 EVA_SVP ss1712305559 Apr 01, 2015 (144)
62 ILLUMINA ss1751861747 Sep 08, 2015 (146)
63 HAMMER_LAB ss1793717710 Sep 08, 2015 (146)
64 WEILL_CORNELL_DGM ss1917964327 Feb 12, 2016 (147)
65 GENOMED ss1966667764 Jul 19, 2016 (147)
66 JJLAB ss2019499998 Sep 14, 2016 (149)
67 USC_VALOUEV ss2147486842 Dec 20, 2016 (150)
68 HUMAN_LONGEVITY ss2159389006 Dec 20, 2016 (150)
69 TOPMED ss2321528311 Dec 20, 2016 (150)
70 SYSTEMSBIOZJU ss2624265605 Nov 08, 2017 (151)
71 ILLUMINA ss2632465786 Nov 08, 2017 (151)
72 GRF ss2697377716 Nov 08, 2017 (151)
73 GNOMAD ss2750675804 Nov 08, 2017 (151)
74 SWEGEN ss2986154936 Nov 08, 2017 (151)
75 BIOINF_KMB_FNS_UNIBA ss3023514370 Nov 08, 2017 (151)
76 TOPMED ss3066480946 Nov 08, 2017 (151)
77 CSHL ss3343274477 Nov 08, 2017 (151)
78 ILLUMINA ss3626007153 Oct 11, 2018 (152)
79 ILLUMINA ss3630505812 Oct 11, 2018 (152)
80 ILLUMINA ss3633571490 Oct 11, 2018 (152)
81 ILLUMINA ss3634302077 Oct 11, 2018 (152)
82 ILLUMINA ss3635265693 Oct 11, 2018 (152)
83 ILLUMINA ss3635978728 Oct 11, 2018 (152)
84 ILLUMINA ss3637016033 Oct 11, 2018 (152)
85 ILLUMINA ss3637732511 Oct 11, 2018 (152)
86 ILLUMINA ss3638887875 Oct 11, 2018 (152)
87 ILLUMINA ss3639756843 Oct 11, 2018 (152)
88 ILLUMINA ss3640009443 Oct 11, 2018 (152)
89 ILLUMINA ss3642746791 Oct 11, 2018 (152)
90 ILLUMINA ss3643810774 Oct 11, 2018 (152)
91 URBANLAB ss3646581995 Oct 11, 2018 (152)
92 EGCUT_WGS ss3654266007 Jul 12, 2019 (153)
93 EVA_DECODE ss3685998704 Jul 12, 2019 (153)
94 ACPOP ss3726718988 Jul 12, 2019 (153)
95 ILLUMINA ss3744603008 Jul 12, 2019 (153)
96 EVA ss3745724691 Jul 12, 2019 (153)
97 ILLUMINA ss3772104766 Jul 12, 2019 (153)
98 PACBIO ss3783303101 Jul 12, 2019 (153)
99 PACBIO ss3788980879 Jul 12, 2019 (153)
100 PACBIO ss3793853440 Jul 12, 2019 (153)
101 KHV_HUMAN_GENOMES ss3798747337 Jul 12, 2019 (153)
102 EVA ss3825982748 Apr 25, 2020 (154)
103 EVA ss3836379065 Apr 25, 2020 (154)
104 EVA ss3841783095 Apr 25, 2020 (154)
105 HGDP ss3847322126 Apr 25, 2020 (154)
106 SGDP_PRJ ss3848005080 Apr 25, 2020 (154)
107 KRGDB ss3892847947 Apr 25, 2020 (154)
108 KOGIC ss3943637114 Apr 25, 2020 (154)
109 EVA ss3984774104 Apr 25, 2021 (155)
110 EVA ss4016889128 Apr 25, 2021 (155)
111 TOPMED ss4436530599 Apr 25, 2021 (155)
112 TOMMO_GENOMICS ss5142068532 Apr 25, 2021 (155)
113 1000Genomes NC_000001.10 - 1087683 Oct 11, 2018 (152)
114 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1087683 Oct 11, 2018 (152)
115 Genetic variation in the Estonian population NC_000001.10 - 1087683 Oct 11, 2018 (152)
116 The Danish reference pan genome NC_000001.10 - 1087683 Apr 25, 2020 (154)
117 gnomAD - Genomes NC_000001.11 - 1152303 Apr 25, 2021 (155)
118 Genome of the Netherlands Release 5 NC_000001.10 - 1087683 Apr 25, 2020 (154)
119 HGDP-CEPH-db Supplement 1 NC_000001.9 - 1077546 Apr 25, 2020 (154)
120 HapMap NC_000001.11 - 1152303 Apr 25, 2020 (154)
121 KOREAN population from KRGDB NC_000001.10 - 1087683 Apr 25, 2020 (154)
122 Korean Genome Project NC_000001.11 - 1152303 Apr 25, 2020 (154)
123 Northern Sweden NC_000001.10 - 1087683 Jul 12, 2019 (153)
124 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 1087683 Apr 25, 2021 (155)
125 Qatari NC_000001.10 - 1087683 Apr 25, 2020 (154)
126 SGDP_PRJ NC_000001.10 - 1087683 Apr 25, 2020 (154)
127 Siberian NC_000001.10 - 1087683 Apr 25, 2020 (154)
128 8.3KJPN NC_000001.10 - 1087683 Apr 25, 2021 (155)
129 TopMed NC_000001.11 - 1152303 Apr 25, 2021 (155)
130 UK 10K study - Twins NC_000001.10 - 1087683 Oct 11, 2018 (152)
131 A Vietnamese Genetic Variation Database NC_000001.10 - 1087683 Jul 12, 2019 (153)
132 ALFA NC_000001.11 - 1152303 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).

Associated ID History Updated (Build)
rs59849084 May 25, 2008 (130)
rs74223863 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77392018, ss83206912, ss3638887875, ss3639756843, ss3643810774 NC_000001.8:1127605:T:C NC_000001.11:1152302:T:C (self)
18, ss87158367, ss107938597, ss109941600, ss118440335, ss162983745, ss163707920, ss165982923, ss197889235, ss205072967, ss252866379, ss275682553, ss283988032, ss290494388, ss481900336, ss1584132247, ss1712305559, ss3642746791, ss3847322126 NC_000001.9:1077545:T:C NC_000001.11:1152302:T:C (self)
16837, 5582, 4255, 1359358, 2528, 25341, 3853, 31, 6257, 22060, 3196, 37839, 5582, 1237, ss218192103, ss230396531, ss238116058, ss481933450, ss482890576, ss485744155, ss537598663, ss553714049, ss647518645, ss779010311, ss783317857, ss784269825, ss832579401, ss833178830, ss834472773, ss974772333, ss1067613861, ss1289351680, ss1425685948, ss1573852124, ss1599383164, ss1642377197, ss1751861747, ss1793717710, ss1917964327, ss1966667764, ss2019499998, ss2147486842, ss2321528311, ss2624265605, ss2632465786, ss2697377716, ss2750675804, ss2986154936, ss3343274477, ss3626007153, ss3630505812, ss3633571490, ss3634302077, ss3635265693, ss3635978728, ss3637016033, ss3637732511, ss3640009443, ss3654266007, ss3726718988, ss3744603008, ss3745724691, ss3772104766, ss3783303101, ss3788980879, ss3793853440, ss3825982748, ss3836379065, ss3848005080, ss3892847947, ss3984774104, ss4016889128, ss5142068532 NC_000001.10:1087682:T:C NC_000001.11:1152302:T:C (self)
151148, 244, 15115, 78067, 136934, 11350414845, ss2159389006, ss3023514370, ss3066480946, ss3646581995, ss3685998704, ss3798747337, ss3841783095, ss3943637114, ss4436530599 NC_000001.11:1152302:T:C NC_000001.11:1152302:T:C (self)
ss41347639, ss67918033, ss68042959, ss68303586, ss68756322, ss71607613, ss75688875, ss84819415, ss98259543, ss99179788, ss102713653, ss131636106, ss137754509, ss154494076, ss154528311, ss159668085, ss160987368, ss174842647 NT_004350.19:566314:T:C NC_000001.11:1152302:T:C (self)
ss16388527, ss20470091 NT_077913.2:91393:T:C NC_000001.11:1152302:T:C (self)
ss13052183 NT_077960.1:157123:T:C NC_000001.11:1152302: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.

No publications for rs9442380

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