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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.

rs17109640

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83061289 (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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00179 (30/16760, 8.3KJPN)
A=0.04080 (631/15464, ALFA)
A=0.1226 (614/5008, 1000G) (+ 14 more)
A=0.1333 (597/4480, Estonian)
A=0.1492 (575/3854, ALSPAC)
A=0.1340 (497/3708, TWINSUK)
A=0.0034 (10/2922, KOREAN)
A=0.0066 (12/1832, Korea1K)
A=0.168 (168/998, GoNL)
A=0.103 (62/600, NorthernSweden)
A=0.119 (38/320, HapMap)
A=0.181 (39/216, Qatari)
A=0.005 (1/214, Vietnamese)
T=0.425 (45/106, SGDP_PRJ)
A=0.12 (5/40, GENOME_DK)
T=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01362 : Intron Variant
LOC107985037 : Intron Variant
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.83061289T>A
GRCh38.p13 chr 1 NC_000001.11:g.83061289T>C
GRCh37.p13 chr 1 NC_000001.10:g.83526972T>A
GRCh37.p13 chr 1 NC_000001.10:g.83526972T>C
Gene: LINC01362, long intergenic non-protein coding RNA 1362 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01362 transcript NR_147074.1:n. N/A Intron Variant
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1:n. N/A Intron 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

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 15464 T=0.95920 A=0.04080, C=0.00000
European Sub 11692 T=0.94860 A=0.05140, C=0.00000
African Sub 2374 T=0.9979 A=0.0021, C=0.0000
African Others Sub 94 T=1.00 A=0.00, C=0.00
African American Sub 2280 T=0.9978 A=0.0022, C=0.0000
Asian Sub 112 T=1.000 A=0.000, C=0.000
East Asian Sub 86 T=1.00 A=0.00, C=0.00
Other Asian Sub 26 T=1.00 A=0.00, C=0.00
Latin American 1 Sub 118 T=1.000 A=0.000, C=0.000
Latin American 2 Sub 528 T=1.000 A=0.000, C=0.000
South Asian Sub 46 T=1.00 A=0.00, C=0.00
Other Sub 594 T=0.958 A=0.042, C=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
8.3KJPN JAPANESE Study-wide 16760 T=0.99821 A=0.00179
1000Genomes Global Study-wide 5008 T=0.8774 A=0.1226
1000Genomes African Sub 1322 T=0.8979 A=0.1021
1000Genomes East Asian Sub 1008 T=0.9990 A=0.0010
1000Genomes Europe Sub 1006 T=0.8658 A=0.1342
1000Genomes South Asian Sub 978 T=0.734 A=0.266
1000Genomes American Sub 694 T=0.880 A=0.120
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8667 A=0.1333
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8508 A=0.1492
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8660 A=0.1340
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9966 A=0.0034
Korean Genome Project KOREAN Study-wide 1832 T=0.9934 A=0.0066
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.832 A=0.168
Northern Sweden ACPOP Study-wide 600 T=0.897 A=0.103
HapMap Global Study-wide 320 T=0.881 A=0.119
HapMap African Sub 116 T=0.853 A=0.147
HapMap American Sub 114 T=0.816 A=0.184
HapMap Asian Sub 90 T=1.00 A=0.00
Qatari Global Study-wide 216 T=0.819 A=0.181
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.995 A=0.005
SGDP_PRJ Global Study-wide 106 T=0.425 A=0.575
The Danish reference pan genome Danish Study-wide 40 T=0.88 A=0.12
Siberian Global Study-wide 2 T=0.5 A=0.5
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.p13 chr 1 NC_000001.11:g.83061289= NC_000001.11:g.83061289T>A NC_000001.11:g.83061289T>C
GRCh37.p13 chr 1 NC_000001.10:g.83526972= NC_000001.10:g.83526972T>A NC_000001.10:g.83526972T>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#.

48 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23145048 Sep 20, 2004 (123)
2 ABI ss43936497 Mar 15, 2006 (126)
3 HUMANGENOME_JCVI ss99223111 Feb 05, 2009 (130)
4 1000GENOMES ss108366626 Jan 23, 2009 (130)
5 1000GENOMES ss110735441 Jan 25, 2009 (130)
6 ENSEMBL ss131818788 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss163588506 Jul 04, 2010 (132)
8 1000GENOMES ss218491803 Jul 14, 2010 (132)
9 1000GENOMES ss230612780 Jul 14, 2010 (132)
10 1000GENOMES ss238290899 Jul 15, 2010 (132)
11 TISHKOFF ss554362104 Apr 25, 2013 (138)
12 SSMP ss648176148 Apr 25, 2013 (138)
13 EVA-GONL ss975365580 Aug 21, 2014 (142)
14 JMKIDD_LAB ss1068043606 Aug 21, 2014 (142)
15 1000GENOMES ss1291668910 Aug 21, 2014 (142)
16 EVA_GENOME_DK ss1574191735 Apr 01, 2015 (144)
17 EVA_DECODE ss1584739517 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1600582813 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1643576846 Apr 01, 2015 (144)
20 HAMMER_LAB ss1794651286 Sep 08, 2015 (146)
21 WEILL_CORNELL_DGM ss1918568524 Feb 12, 2016 (147)
22 GENOMED ss1966794077 Jul 19, 2016 (147)
23 JJLAB ss2019804921 Sep 14, 2016 (149)
24 USC_VALOUEV ss2147822014 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2164129661 Dec 20, 2016 (150)
26 TOPMED ss2326421888 Dec 20, 2016 (150)
27 GRF ss2697744187 Nov 08, 2017 (151)
28 GNOMAD ss2757361695 Nov 08, 2017 (151)
29 SWEGEN ss2987125408 Nov 08, 2017 (151)
30 BIOINF_KMB_FNS_UNIBA ss3023665249 Nov 08, 2017 (151)
31 TOPMED ss3081730049 Nov 08, 2017 (151)
32 TOPMED ss3081730050 Nov 08, 2017 (151)
33 CSHL ss3343543760 Nov 08, 2017 (151)
34 URBANLAB ss3646705725 Oct 11, 2018 (152)
35 EGCUT_WGS ss3655205950 Jul 12, 2019 (153)
36 EVA_DECODE ss3687150953 Jul 12, 2019 (153)
37 ACPOP ss3727217085 Jul 12, 2019 (153)
38 EVA ss3746440445 Jul 12, 2019 (153)
39 KHV_HUMAN_GENOMES ss3799446492 Jul 12, 2019 (153)
40 EVA ss3826271386 Apr 25, 2020 (154)
41 EVA ss3836524626 Apr 25, 2020 (154)
42 EVA ss3841931831 Apr 25, 2020 (154)
43 SGDP_PRJ ss3849250348 Apr 25, 2020 (154)
44 KRGDB ss3894301692 Apr 25, 2020 (154)
45 KOGIC ss3944881441 Apr 25, 2020 (154)
46 TOPMED ss4456688374 Apr 25, 2021 (155)
47 TOPMED ss4456688375 Apr 25, 2021 (155)
48 TOMMO_GENOMICS ss5144811614 Apr 25, 2021 (155)
49 1000Genomes NC_000001.10 - 83526972 Oct 11, 2018 (152)
50 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 83526972 Oct 11, 2018 (152)
51 Genetic variation in the Estonian population NC_000001.10 - 83526972 Oct 11, 2018 (152)
52 The Danish reference pan genome NC_000001.10 - 83526972 Apr 25, 2020 (154)
53 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 17051304 (NC_000001.11:83061288:T:A 16898/140148)
Row 17051305 (NC_000001.11:83061288:T:C 2/140166)

- Apr 25, 2021 (155)
54 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 17051304 (NC_000001.11:83061288:T:A 16898/140148)
Row 17051305 (NC_000001.11:83061288:T:C 2/140166)

- Apr 25, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000001.10 - 83526972 Apr 25, 2020 (154)
56 HapMap NC_000001.11 - 83061289 Apr 25, 2020 (154)
57 KOREAN population from KRGDB NC_000001.10 - 83526972 Apr 25, 2020 (154)
58 Korean Genome Project NC_000001.11 - 83061289 Apr 25, 2020 (154)
59 Northern Sweden NC_000001.10 - 83526972 Jul 12, 2019 (153)
60 Qatari NC_000001.10 - 83526972 Apr 25, 2020 (154)
61 SGDP_PRJ NC_000001.10 - 83526972 Apr 25, 2020 (154)
62 Siberian NC_000001.10 - 83526972 Apr 25, 2020 (154)
63 8.3KJPN NC_000001.10 - 83526972 Apr 25, 2021 (155)
64 TopMed

Submission ignored due to conflicting rows:
Row 20294709 (NC_000001.11:83061288:T:A 30829/264690)
Row 20294710 (NC_000001.11:83061288:T:C 1/264690)

- Apr 25, 2021 (155)
65 TopMed

Submission ignored due to conflicting rows:
Row 20294709 (NC_000001.11:83061288:T:A 30829/264690)
Row 20294710 (NC_000001.11:83061288:T:C 1/264690)

- Apr 25, 2021 (155)
66 UK 10K study - Twins NC_000001.10 - 83526972 Oct 11, 2018 (152)
67 A Vietnamese Genetic Variation Database NC_000001.10 - 83526972 Jul 12, 2019 (153)
68 ALFA NC_000001.11 - 83061289 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108366626, ss110735441, ss163588506, ss1584739517 NC_000001.9:83299559:T:A NC_000001.11:83061288:T:A (self)
2416102, 1326081, 944198, 1583117, 572580, 1479086, 501950, 610454, 1267328, 338368, 2780921, 1326081, 284431, ss218491803, ss230612780, ss238290899, ss554362104, ss648176148, ss975365580, ss1068043606, ss1291668910, ss1574191735, ss1600582813, ss1643576846, ss1794651286, ss1918568524, ss1966794077, ss2019804921, ss2147822014, ss2326421888, ss2697744187, ss2757361695, ss2987125408, ss3343543760, ss3655205950, ss3727217085, ss3746440445, ss3826271386, ss3836524626, ss3849250348, ss3894301692, ss5144811614 NC_000001.10:83526971:T:A NC_000001.11:83061288:T:A (self)
112935, 1259442, 12783158, 8554065526, ss2164129661, ss3023665249, ss3081730049, ss3646705725, ss3687150953, ss3799446492, ss3841931831, ss3944881441, ss4456688374 NC_000001.11:83061288:T:A NC_000001.11:83061288:T:A (self)
ss23145048, ss43936497, ss99223111, ss131818788 NT_032977.9:53498889:T:A NC_000001.11:83061288:T:A (self)
12783158, 8554065526, ss3081730050, ss4456688375 NC_000001.11:83061288:T:C NC_000001.11:83061288: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 rs17109640

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