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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.

rs17099070

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83122698 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.04359 (1056/24226, ALFA)
T=0.0226 (113/5008, 1000G)
T=0.1308 (586/4480, Estonian) (+ 9 more)
T=0.0003 (1/2922, KOREAN)
T=0.0352 (40/1136, Daghestan)
T=0.048 (48/998, GoNL)
T=0.103 (62/600, NorthernSweden)
T=0.014 (3/216, Qatari)
T=0.05 (2/40, GENOME_DK)
C=0.44 (15/34, SGDP_PRJ)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, 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.83122698C>A
GRCh38.p13 chr 1 NC_000001.11:g.83122698C>T
GRCh37.p13 chr 1 NC_000001.10:g.83588381C>A
GRCh37.p13 chr 1 NC_000001.10:g.83588381C>T
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 24226 C=0.95641 A=0.00000, T=0.04359
European Sub 19238 C=0.94636 A=0.00000, T=0.05364
African Sub 2908 C=1.0000 A=0.0000, T=0.0000
African Others Sub 114 C=1.000 A=0.000, T=0.000
African American Sub 2794 C=1.0000 A=0.0000, T=0.0000
Asian Sub 118 C=1.000 A=0.000, T=0.000
East Asian Sub 90 C=1.00 A=0.00, T=0.00
Other Asian Sub 28 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 142 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 540 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 1182 C=0.9797 A=0.0000, T=0.0203


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").

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Study Population Group Sample Size Ref Allele Alt Allele
1000Genomes Global Study-wide 5008 C=0.9774 T=0.0226
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9215 T=0.0785
1000Genomes South Asian Sub 978 C=0.995 T=0.005
1000Genomes American Sub 694 C=0.960 T=0.040
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8692 T=0.1308
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9997 T=0.0003
Genome-wide autozygosity in Daghestan Global Study-wide 1136 C=0.9648 T=0.0352
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.962 T=0.038
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.993 T=0.007
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.967 T=0.033
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.935 T=0.065
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.98 T=0.02
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.94 T=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.952 T=0.048
Northern Sweden ACPOP Study-wide 600 C=0.897 T=0.103
Qatari Global Study-wide 216 C=0.986 T=0.014
The Danish reference pan genome Danish Study-wide 40 C=0.95 T=0.05
SGDP_PRJ Global Study-wide 34 C=0.44 T=0.56
Siberian Global Study-wide 12 C=0.50 T=0.50
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 C= A T
GRCh38.p13 chr 1 NC_000001.11:g.83122698= NC_000001.11:g.83122698C>A NC_000001.11:g.83122698C>T
GRCh37.p13 chr 1 NC_000001.10:g.83588381= NC_000001.10:g.83588381C>A NC_000001.10:g.83588381C>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#.

33 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23145054 Sep 20, 2004 (123)
2 1000GENOMES ss108367081 Jan 23, 2009 (130)
3 1000GENOMES ss230612943 Jul 14, 2010 (132)
4 ILLUMINA ss536345538 Sep 08, 2015 (146)
5 EVA-GONL ss975365999 Aug 21, 2014 (142)
6 JMKIDD_LAB ss1068043891 Aug 21, 2014 (142)
7 1000GENOMES ss1291670384 Aug 21, 2014 (142)
8 HAMMER_LAB ss1397251765 Sep 08, 2015 (146)
9 EVA_GENOME_DK ss1574191899 Apr 01, 2015 (144)
10 EVA_DECODE ss1584739938 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1918568896 Feb 12, 2016 (147)
12 JJLAB ss2019805115 Sep 14, 2016 (149)
13 USC_VALOUEV ss2147822222 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2164133093 Dec 20, 2016 (150)
15 TOPMED ss2326425309 Dec 20, 2016 (150)
16 GNOMAD ss2757365979 Nov 08, 2017 (151)
17 AFFY ss2984865702 Nov 08, 2017 (151)
18 AFFY ss2985518178 Nov 08, 2017 (151)
19 SWEGEN ss2987126009 Nov 08, 2017 (151)
20 BIOINF_KMB_FNS_UNIBA ss3023665364 Nov 08, 2017 (151)
21 TOPMED ss3081740778 Nov 08, 2017 (151)
22 TOPMED ss3081740779 Nov 08, 2017 (151)
23 CSHL ss3343543932 Nov 08, 2017 (151)
24 ILLUMINA ss3626140376 Oct 11, 2018 (152)
25 ILLUMINA ss3653637281 Oct 11, 2018 (152)
26 EGCUT_WGS ss3655206596 Jul 12, 2019 (153)
27 EVA_DECODE ss3687151762 Jul 12, 2019 (153)
28 ACPOP ss3727217447 Jul 12, 2019 (153)
29 EVA ss3826271610 Apr 25, 2020 (154)
30 SGDP_PRJ ss3849251093 Apr 25, 2020 (154)
31 KRGDB ss3894302492 Apr 25, 2020 (154)
32 TOPMED ss4456702799 Apr 25, 2021 (155)
33 TOPMED ss4456702800 Apr 25, 2021 (155)
34 1000Genomes NC_000001.10 - 83588381 Oct 11, 2018 (152)
35 Genome-wide autozygosity in Daghestan NC_000001.9 - 83360969 Apr 25, 2020 (154)
36 Genetic variation in the Estonian population NC_000001.10 - 83588381 Oct 11, 2018 (152)
37 The Danish reference pan genome NC_000001.10 - 83588381 Apr 25, 2020 (154)
38 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 17063350 (NC_000001.11:83122697:C:A 1/140126)
Row 17063351 (NC_000001.11:83122697:C:T 7968/140118)

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

Submission ignored due to conflicting rows:
Row 17063350 (NC_000001.11:83122697:C:A 1/140126)
Row 17063351 (NC_000001.11:83122697:C:T 7968/140118)

- Apr 25, 2021 (155)
40 Genome of the Netherlands Release 5 NC_000001.10 - 83588381 Apr 25, 2020 (154)
41 KOREAN population from KRGDB NC_000001.10 - 83588381 Apr 25, 2020 (154)
42 Northern Sweden NC_000001.10 - 83588381 Jul 12, 2019 (153)
43 Qatari NC_000001.10 - 83588381 Apr 25, 2020 (154)
44 SGDP_PRJ NC_000001.10 - 83588381 Apr 25, 2020 (154)
45 Siberian NC_000001.10 - 83588381 Apr 25, 2020 (154)
46 TopMed

Submission ignored due to conflicting rows:
Row 20309134 (NC_000001.11:83122697:C:A 1/264690)
Row 20309135 (NC_000001.11:83122697:C:T 12235/264690)

- Apr 25, 2021 (155)
47 TopMed

Submission ignored due to conflicting rows:
Row 20309134 (NC_000001.11:83122697:C:A 1/264690)
Row 20309135 (NC_000001.11:83122697:C:T 12235/264690)

- Apr 25, 2021 (155)
48 ALFA NC_000001.11 - 83122698 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
12792390, 3242857683, ss3081740778, ss4456702799 NC_000001.11:83122697:C:A NC_000001.11:83122697:C:A (self)
13104, ss108367081, ss1397251765, ss1584739938 NC_000001.9:83360968:C:T NC_000001.11:83122697:C:T (self)
2417645, 944844, 1583271, 572993, 1479886, 502312, 610826, 1268073, 338576, ss230612943, ss536345538, ss975365999, ss1068043891, ss1291670384, ss1574191899, ss1918568896, ss2019805115, ss2147822222, ss2326425309, ss2757365979, ss2984865702, ss2985518178, ss2987126009, ss3343543932, ss3626140376, ss3653637281, ss3655206596, ss3727217447, ss3826271610, ss3849251093, ss3894302492 NC_000001.10:83588380:C:T NC_000001.11:83122697:C:T (self)
12792390, 3242857683, ss2164133093, ss3023665364, ss3081740779, ss3687151762, ss4456702800 NC_000001.11:83122697:C:T NC_000001.11:83122697:C:T (self)
ss23145054 NT_032977.9:53560298:C:T NC_000001.11:83122697:C:T (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 rs17099070

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