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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs17160824

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:1125228 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.109388 (28954/264690, TOPMED)
A=0.098564 (13824/140254, GnomAD)
A=0.20116 (5684/28256, 14KJPN) (+ 17 more)
A=0.10361 (2523/24350, ALFA)
A=0.20343 (3409/16758, 8.3KJPN)
A=0.1315 (842/6404, 1000G_30x)
A=0.1364 (683/5008, 1000G)
A=0.0804 (360/4480, Estonian)
A=0.1007 (388/3854, ALSPAC)
A=0.1184 (439/3708, TWINSUK)
A=0.2258 (661/2928, KOREAN)
A=0.1237 (234/1892, HapMap)
A=0.2240 (410/1830, Korea1K)
A=0.107 (107/998, GoNL)
A=0.103 (62/600, NorthernSweden)
A=0.171 (37/216, Qatari)
A=0.157 (34/216, Vietnamese)
G=0.442 (61/138, SGDP_PRJ)
A=0.12 (5/40, GENOME_DK)
G=0.29 (4/14, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC124903819 : Non Coding Transcript 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 24350 G=0.89639 A=0.10361
European Sub 18126 G=0.89214 A=0.10786
African Sub 4114 G=0.9327 A=0.0673
African Others Sub 148 G=0.946 A=0.054
African American Sub 3966 G=0.9322 A=0.0678
Asian Sub 124 G=0.839 A=0.161
East Asian Sub 96 G=0.86 A=0.14
Other Asian Sub 28 G=0.75 A=0.25
Latin American 1 Sub 168 G=0.911 A=0.089
Latin American 2 Sub 670 G=0.858 A=0.142
South Asian Sub 98 G=0.89 A=0.11
Other Sub 1050 G=0.8571 A=0.1429


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=0.890612 A=0.109388
gnomAD - Genomes Global Study-wide 140254 G=0.901436 A=0.098564
gnomAD - Genomes European Sub 75952 G=0.89572 A=0.10428
gnomAD - Genomes African Sub 42048 G=0.93752 A=0.06248
gnomAD - Genomes American Sub 13660 G=0.86999 A=0.13001
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.8226 A=0.1774
gnomAD - Genomes East Asian Sub 3126 G=0.7949 A=0.2051
gnomAD - Genomes Other Sub 2148 G=0.8738 A=0.1262
14KJPN JAPANESE Study-wide 28256 G=0.79884 A=0.20116
Allele Frequency Aggregator Total Global 24350 G=0.89639 A=0.10361
Allele Frequency Aggregator European Sub 18126 G=0.89214 A=0.10786
Allele Frequency Aggregator African Sub 4114 G=0.9327 A=0.0673
Allele Frequency Aggregator Other Sub 1050 G=0.8571 A=0.1429
Allele Frequency Aggregator Latin American 2 Sub 670 G=0.858 A=0.142
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.911 A=0.089
Allele Frequency Aggregator Asian Sub 124 G=0.839 A=0.161
Allele Frequency Aggregator South Asian Sub 98 G=0.89 A=0.11
8.3KJPN JAPANESE Study-wide 16758 G=0.79657 A=0.20343
1000Genomes_30x Global Study-wide 6404 G=0.8685 A=0.1315
1000Genomes_30x African Sub 1786 G=0.9378 A=0.0622
1000Genomes_30x Europe Sub 1266 G=0.9021 A=0.0979
1000Genomes_30x South Asian Sub 1202 G=0.7962 A=0.2038
1000Genomes_30x East Asian Sub 1170 G=0.7803 A=0.2197
1000Genomes_30x American Sub 980 G=0.893 A=0.107
1000Genomes Global Study-wide 5008 G=0.8636 A=0.1364
1000Genomes African Sub 1322 G=0.9395 A=0.0605
1000Genomes East Asian Sub 1008 G=0.7778 A=0.2222
1000Genomes Europe Sub 1006 G=0.8966 A=0.1034
1000Genomes South Asian Sub 978 G=0.798 A=0.202
1000Genomes American Sub 694 G=0.889 A=0.111
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9196 A=0.0804
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8993 A=0.1007
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8816 A=0.1184
KOREAN population from KRGDB KOREAN Study-wide 2928 G=0.7742 A=0.2258
HapMap Global Study-wide 1892 G=0.8763 A=0.1237
HapMap American Sub 770 G=0.862 A=0.138
HapMap African Sub 692 G=0.942 A=0.058
HapMap Asian Sub 254 G=0.740 A=0.260
HapMap Europe Sub 176 G=0.875 A=0.125
Korean Genome Project KOREAN Study-wide 1830 G=0.7760 A=0.2240
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.893 A=0.107
Northern Sweden ACPOP Study-wide 600 G=0.897 A=0.103
Qatari Global Study-wide 216 G=0.829 A=0.171
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.843 A=0.157
SGDP_PRJ Global Study-wide 138 G=0.442 A=0.558
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 14 G=0.29 A=0.71
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 1 NC_000001.11:g.1125228G>A
GRCh37.p13 chr 1 NC_000001.10:g.1060608G>A
Gene: LOC124903819, uncharacterized LOC124903819 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124903819 transcript XR_007065349.1:n.2699C>T N/A Non Coding 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 G= A
GRCh38.p14 chr 1 NC_000001.11:g.1125228= NC_000001.11:g.1125228G>A
GRCh37.p13 chr 1 NC_000001.10:g.1060608= NC_000001.10:g.1060608G>A
LOC124903819 transcript XR_007065349.1:n.2699= XR_007065349.1:n.2699C>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#.

64 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23837018 Sep 20, 2004 (123)
2 ABI ss43972556 Mar 15, 2006 (126)
3 PERLEGEN ss68756317 May 16, 2007 (127)
4 ILLUMINA ss75123344 Dec 06, 2007 (129)
5 BGI ss102713627 Dec 01, 2009 (131)
6 KRIBB_YJKIM ss119879786 Dec 01, 2009 (131)
7 GMI ss154528086 Dec 01, 2009 (131)
8 ENSEMBL ss161154822 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss165982724 Jul 04, 2010 (132)
10 ILLUMINA ss172772065 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss205389974 Jul 04, 2010 (132)
12 1000GENOMES ss210449588 Jul 14, 2010 (132)
13 1000GENOMES ss218191952 Jul 14, 2010 (132)
14 1000GENOMES ss230396459 Jul 14, 2010 (132)
15 1000GENOMES ss238116011 Jul 15, 2010 (132)
16 GMI ss275682481 May 04, 2012 (137)
17 ILLUMINA ss536955287 Sep 08, 2015 (146)
18 TISHKOFF ss553713686 Apr 25, 2013 (138)
19 SSMP ss647518461 Apr 25, 2013 (138)
20 EVA-GONL ss974772076 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067613732 Aug 21, 2014 (142)
22 1000GENOMES ss1289350611 Aug 21, 2014 (142)
23 DDI ss1425685880 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1573852044 Apr 01, 2015 (144)
25 EVA_DECODE ss1584131990 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1599382721 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1642376754 Apr 01, 2015 (144)
28 EVA_SVP ss1712305551 Apr 01, 2015 (144)
29 WEILL_CORNELL_DGM ss1917963983 Feb 12, 2016 (147)
30 JJLAB ss2019499867 Sep 14, 2016 (149)
31 USC_VALOUEV ss2147486648 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2159386796 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2624265555 Nov 08, 2017 (151)
34 GRF ss2697377577 Nov 08, 2017 (151)
35 GNOMAD ss2750672698 Nov 08, 2017 (151)
36 SWEGEN ss2986154485 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3023514314 Nov 08, 2017 (151)
38 CSHL ss3343274325 Nov 08, 2017 (151)
39 ILLUMINA ss3626007107 Oct 11, 2018 (152)
40 ILLUMINA ss3637732503 Oct 11, 2018 (152)
41 ILLUMINA ss3642746779 Oct 11, 2018 (152)
42 EGCUT_WGS ss3654265576 Jul 12, 2019 (153)
43 EVA_DECODE ss3685998125 Jul 12, 2019 (153)
44 ACPOP ss3726718764 Jul 12, 2019 (153)
45 EVA ss3745724398 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3798747006 Jul 12, 2019 (153)
47 EVA ss3825982645 Apr 25, 2020 (154)
48 SGDP_PRJ ss3848004151 Apr 25, 2020 (154)
49 KRGDB ss3892846968 Apr 25, 2020 (154)
50 KOGIC ss3943636487 Apr 25, 2020 (154)
51 EVA ss4016889121 Apr 25, 2021 (155)
52 TOPMED ss4436522451 Apr 25, 2021 (155)
53 TOMMO_GENOMICS ss5142067280 Apr 25, 2021 (155)
54 1000G_HIGH_COVERAGE ss5240873850 Oct 12, 2022 (156)
55 EVA ss5316200484 Oct 12, 2022 (156)
56 HUGCELL_USP ss5442120572 Oct 12, 2022 (156)
57 1000G_HIGH_COVERAGE ss5512502690 Oct 12, 2022 (156)
58 SANFORD_IMAGENETICS ss5624755521 Oct 12, 2022 (156)
59 TOMMO_GENOMICS ss5666211956 Oct 12, 2022 (156)
60 YY_MCH ss5800246403 Oct 12, 2022 (156)
61 EVA ss5831422980 Oct 12, 2022 (156)
62 EVA ss5848749789 Oct 12, 2022 (156)
63 EVA ss5906715264 Oct 12, 2022 (156)
64 EVA ss5936587775 Oct 12, 2022 (156)
65 1000Genomes NC_000001.10 - 1060608 Oct 11, 2018 (152)
66 1000Genomes_30x NC_000001.11 - 1125228 Oct 12, 2022 (156)
67 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1060608 Oct 11, 2018 (152)
68 Genetic variation in the Estonian population NC_000001.10 - 1060608 Oct 11, 2018 (152)
69 The Danish reference pan genome NC_000001.10 - 1060608 Apr 25, 2020 (154)
70 gnomAD - Genomes NC_000001.11 - 1125228 Apr 25, 2021 (155)
71 Genome of the Netherlands Release 5 NC_000001.10 - 1060608 Apr 25, 2020 (154)
72 HapMap NC_000001.11 - 1125228 Apr 25, 2020 (154)
73 KOREAN population from KRGDB NC_000001.10 - 1060608 Apr 25, 2020 (154)
74 Korean Genome Project NC_000001.11 - 1125228 Apr 25, 2020 (154)
75 Northern Sweden NC_000001.10 - 1060608 Jul 12, 2019 (153)
76 Qatari NC_000001.10 - 1060608 Apr 25, 2020 (154)
77 SGDP_PRJ NC_000001.10 - 1060608 Apr 25, 2020 (154)
78 Siberian NC_000001.10 - 1060608 Apr 25, 2020 (154)
79 8.3KJPN NC_000001.10 - 1060608 Apr 25, 2021 (155)
80 14KJPN NC_000001.11 - 1125228 Oct 12, 2022 (156)
81 TopMed NC_000001.11 - 1125228 Apr 25, 2021 (155)
82 UK 10K study - Twins NC_000001.10 - 1060608 Oct 11, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000001.10 - 1060608 Jul 12, 2019 (153)
84 ALFA NC_000001.11 - 1125228 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)
rs386542771 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss165982724, ss205389974, ss210449588, ss275682481, ss1584131990, ss1712305551, ss3642746779 NC_000001.9:1050470:G:A NC_000001.11:1125227:G:A (self)
15746, 5117, 3824, 1359278, 2378, 24362, 3629, 5913, 21131, 3002, 36587, 5117, 1139, ss218191952, ss230396459, ss238116011, ss536955287, ss553713686, ss647518461, ss974772076, ss1067613732, ss1289350611, ss1425685880, ss1573852044, ss1599382721, ss1642376754, ss1917963983, ss2019499867, ss2147486648, ss2624265555, ss2697377577, ss2750672698, ss2986154485, ss3343274325, ss3626007107, ss3637732503, ss3654265576, ss3726718764, ss3745724398, ss3825982645, ss3848004151, ss3892846968, ss4016889121, ss5142067280, ss5316200484, ss5624755521, ss5831422980, ss5936587775 NC_000001.10:1060607:G:A NC_000001.11:1125227:G:A (self)
28625, 143941, 222, 14488, 49060, 128786, 5558471959, ss2159386796, ss3023514314, ss3685998125, ss3798747006, ss3943636487, ss4436522451, ss5240873850, ss5442120572, ss5512502690, ss5666211956, ss5800246403, ss5848749789, ss5906715264 NC_000001.11:1125227:G:A NC_000001.11:1125227:G:A (self)
ss23837018, ss43972556, ss68756317, ss75123344, ss102713627, ss119879786, ss154528086, ss161154822, ss172772065 NT_004350.19:539239:G:A NC_000001.11:1125227:G:A (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 rs17160824

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