Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs9419541

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:81984 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.227874 (60316/264690, TOPMED)
G=0.38091 (6384/16760, 8.3KJPN)
A=0.20700 (2891/13966, ALFA) (+ 11 more)
A=0.3183 (1594/5008, 1000G)
A=0.1713 (660/3854, ALSPAC)
A=0.1802 (668/3708, TWINSUK)
G=0.4140 (1213/2930, KOREAN)
A=0.152 (152/998, GoNL)
A=0.193 (116/600, NorthernSweden)
A=0.222 (105/472, SGDP_PRJ)
A=0.139 (30/216, Qatari)
A=0.448 (95/212, Vietnamese)
A=0.25 (12/48, Siberian)
A=0.17 (7/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 10 NC_000010.11:g.81984A>G
GRCh38.p13 chr 10 NC_000010.11:g.81984A>T
GRCh37.p13 chr 10 NC_000010.10:g.127924A>G
GRCh37.p13 chr 10 NC_000010.10:g.127924A>T
IL9RP2 pseudogene NG_009864.2:g.4362T>C
IL9RP2 pseudogene NG_009864.2:g.4362T>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.71984A>G
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.71984A>T
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 13966 A=0.20700 G=0.79300, T=0.00000
European Sub 12980 A=0.18467 G=0.81533, T=0.00000
African Sub 324 A=0.682 G=0.318, T=0.000
African Others Sub 26 A=0.81 G=0.19, T=0.00
African American Sub 298 A=0.671 G=0.329, T=0.000
Asian Sub 34 A=0.88 G=0.12, T=0.00
East Asian Sub 26 A=0.92 G=0.08, T=0.00
Other Asian Sub 8 A=0.8 G=0.2, T=0.0
Latin American 1 Sub 8 A=1.0 G=0.0, T=0.0
Latin American 2 Sub 112 A=1.000 G=0.000, T=0.000
South Asian Sub 16 A=0.88 G=0.12, T=0.00
Other Sub 492 A=0.222 G=0.778, 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
TopMed Global Study-wide 264690 A=0.227874 G=0.772126
8.3KJPN JAPANESE Study-wide 16760 A=0.61909 G=0.38091
1000Genomes Global Study-wide 5008 A=0.3183 G=0.6817
1000Genomes African Sub 1322 A=0.2428 G=0.7572
1000Genomes East Asian Sub 1008 A=0.5506 G=0.4494
1000Genomes Europe Sub 1006 A=0.1561 G=0.8439
1000Genomes South Asian Sub 978 A=0.359 G=0.641
1000Genomes American Sub 694 A=0.303 G=0.697
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.1713 G=0.8287
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.1802 G=0.8198
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.5860 G=0.4140
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.152 G=0.848
Northern Sweden ACPOP Study-wide 600 A=0.193 G=0.807
SGDP_PRJ Global Study-wide 472 A=0.222 G=0.778
Qatari Global Study-wide 216 A=0.139 G=0.861
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.448 G=0.552
Siberian Global Study-wide 48 A=0.25 G=0.75
The Danish reference pan genome Danish Study-wide 40 A=0.17 G=0.82
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 A= G T
GRCh38.p13 chr 10 NC_000010.11:g.81984= NC_000010.11:g.81984A>G NC_000010.11:g.81984A>T
GRCh37.p13 chr 10 NC_000010.10:g.127924= NC_000010.10:g.127924A>G NC_000010.10:g.127924A>T
IL9RP2 pseudogene NG_009864.2:g.4362= NG_009864.2:g.4362T>C NG_009864.2:g.4362T>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.71984= NW_003571043.1:g.71984A>G NW_003571043.1:g.71984A>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#.

66 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12973422 Dec 05, 2003 (119)
2 SC_SNP ss15789867 Feb 27, 2004 (120)
3 SSAHASNP ss20716102 Apr 05, 2004 (121)
4 ABI ss38582041 Mar 14, 2006 (126)
5 BCMHGSC_JDW ss88057414 Mar 23, 2008 (129)
6 HUMANGENOME_JCVI ss97527214 Feb 04, 2009 (130)
7 BGI ss102844553 Dec 01, 2009 (131)
8 ENSEMBL ss107935986 Feb 04, 2009 (130)
9 1000GENOMES ss109145732 Jan 23, 2009 (130)
10 1000GENOMES ss115221478 Jan 25, 2009 (130)
11 ILLUMINA-UK ss118963230 Feb 15, 2009 (130)
12 ENSEMBL ss138802648 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss167614004 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss170210004 Jul 04, 2010 (132)
15 BUSHMAN ss201023293 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss207137600 Jul 04, 2010 (132)
17 1000GENOMES ss224512351 Jul 14, 2010 (132)
18 1000GENOMES ss235012252 Jul 15, 2010 (132)
19 1000GENOMES ss241753211 Jul 15, 2010 (132)
20 BL ss253971519 May 09, 2011 (134)
21 GMI ss280440374 May 04, 2012 (137)
22 GMI ss286110756 Apr 25, 2013 (138)
23 PJP ss290815787 May 09, 2011 (134)
24 TISHKOFF ss561707911 Apr 25, 2013 (138)
25 SSMP ss656208247 Apr 25, 2013 (138)
26 EVA-GONL ss987096727 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1076687386 Aug 21, 2014 (142)
28 1000GENOMES ss1335912700 Aug 21, 2014 (142)
29 DDI ss1426189094 Apr 09, 2015 (144)
30 EVA_GENOME_DK ss1574842080 Apr 09, 2015 (144)
31 EVA_DECODE ss1596744224 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1623797520 Apr 09, 2015 (144)
33 EVA_UK10K_TWINSUK ss1666791553 Apr 09, 2015 (144)
34 HAMMER_LAB ss1806212545 Sep 11, 2015 (146)
35 WEILL_CORNELL_DGM ss1930414716 Feb 17, 2016 (147)
36 GENOMED ss1967034966 Sep 28, 2016 (149)
37 JJLAB ss2025929547 Sep 28, 2016 (149)
38 USC_VALOUEV ss2154169604 Oct 12, 2018 (152)
39 TOPMED ss2334634947 Oct 12, 2018 (152)
40 SYSTEMSBIOZJU ss2627432616 Oct 12, 2018 (152)
41 GRF ss2698388996 Oct 12, 2018 (152)
42 GNOMAD ss2884518638 Oct 12, 2018 (152)
43 AFFY ss2984902795 Oct 12, 2018 (152)
44 AFFY ss2985548028 Oct 12, 2018 (152)
45 SWEGEN ss3005784315 Oct 12, 2018 (152)
46 BIOINF_KMB_FNS_UNIBA ss3026746701 Nov 08, 2017 (151)
47 TOPMED ss3109331222 Nov 08, 2017 (151)
48 TOPMED ss3109331223 Nov 08, 2017 (151)
49 CSHL ss3348911592 Oct 12, 2018 (152)
50 URBANLAB ss3649265487 Oct 12, 2018 (152)
51 ILLUMINA ss3653672423 Oct 12, 2018 (152)
52 ACPOP ss3736974270 Jul 13, 2019 (153)
53 EVA ss3747627288 Jul 13, 2019 (153)
54 PACBIO ss3786553486 Jul 13, 2019 (153)
55 PACBIO ss3791748142 Jul 13, 2019 (153)
56 PACBIO ss3796629764 Jul 13, 2019 (153)
57 KHV_HUMAN_GENOMES ss3812993277 Jul 13, 2019 (153)
58 EVA ss3831916721 Apr 26, 2020 (154)
59 EVA ss3839487144 Apr 26, 2020 (154)
60 EVA ss3844952612 Apr 26, 2020 (154)
61 SGDP_PRJ ss3873326362 Apr 26, 2020 (154)
62 KRGDB ss3921253351 Apr 26, 2020 (154)
63 GNOMAD ss4211409491 Apr 26, 2021 (155)
64 GNOMAD ss4211409492 Apr 26, 2021 (155)
65 TOPMED ss4839522429 Apr 26, 2021 (155)
66 TOMMO_GENOMICS ss5195847891 Apr 26, 2021 (155)
67 1000Genomes NC_000010.10 - 127924 Oct 12, 2018 (152)
68 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 127924 Oct 12, 2018 (152)
69 The Danish reference pan genome NC_000010.10 - 127924 Apr 26, 2020 (154)
70 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 340932670 (NC_000010.11:81983:A:G 110847/139736)
Row 340932671 (NC_000010.11:81983:A:T 1/139922)

- Apr 26, 2021 (155)
71 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 340932670 (NC_000010.11:81983:A:G 110847/139736)
Row 340932671 (NC_000010.11:81983:A:T 1/139922)

- Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000010.10 - 127924 Apr 26, 2020 (154)
73 KOREAN population from KRGDB NC_000010.10 - 127924 Apr 26, 2020 (154)
74 Northern Sweden NC_000010.10 - 127924 Jul 13, 2019 (153)
75 Qatari NC_000010.10 - 127924 Apr 26, 2020 (154)
76 SGDP_PRJ NC_000010.10 - 127924 Apr 26, 2020 (154)
77 Siberian NC_000010.10 - 127924 Apr 26, 2020 (154)
78 8.3KJPN NC_000010.10 - 127924 Apr 26, 2021 (155)
79 TopMed NC_000010.11 - 81984 Apr 26, 2021 (155)
80 UK 10K study - Twins NC_000010.10 - 127924 Oct 12, 2018 (152)
81 A Vietnamese Genetic Variation Database NC_000010.10 - 127924 Jul 13, 2019 (153)
82 ALFA NC_000010.11 - 81984 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
ss88057414, ss109145732, ss115221478, ss118963230, ss167614004, ss170210004, ss201023293, ss207137600, ss253971519, ss280440374, ss286110756, ss290815787, ss1596744224 NC_000010.9:117923:A:G NC_000010.11:81983:A:G (self)
48246397, 26806290, 1988099, 11953854, 28430745, 10259135, 12456646, 25343342, 6685958, 53817198, 26806290, 5948659, ss224512351, ss235012252, ss241753211, ss561707911, ss656208247, ss987096727, ss1076687386, ss1335912700, ss1426189094, ss1574842080, ss1623797520, ss1666791553, ss1806212545, ss1930414716, ss1967034966, ss2025929547, ss2154169604, ss2334634947, ss2627432616, ss2698388996, ss2884518638, ss2984902795, ss2985548028, ss3005784315, ss3348911592, ss3653672423, ss3736974270, ss3747627288, ss3786553486, ss3791748142, ss3796629764, ss3831916721, ss3839487144, ss3873326362, ss3921253351, ss5195847891 NC_000010.10:127923:A:G NC_000010.11:81983:A:G (self)
34601565, 55068084, 2150341746, ss3026746701, ss3109331222, ss3649265487, ss3812993277, ss3844952612, ss4211409491, ss4839522429 NC_000010.11:81983:A:G NC_000010.11:81983:A:G (self)
ss38582041, ss97527214, ss102844553, ss107935986, ss138802648 NT_008705.16:67923:A:G NC_000010.11:81983:A:G (self)
ss12973422 NT_024115.14:67923:A:G NC_000010.11:81983:A:G (self)
ss15789867, ss20716102 NT_077567.3:67923:A:G NC_000010.11:81983:A:G (self)
2150341746, ss3109331223, ss4211409492 NC_000010.11:81983:A:T NC_000010.11:81983:A:T (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 rs9419541
PMID Title Author Year Journal
17544380 Evidence for a susceptibility locus on chromosome 10p15 in early-onset obsessive-compulsive disorder. Hanna GL et al. 2007 Biological psychiatry
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