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dbSNP Short Genetic Variations

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.


Current Build 152

Released October 2, 2018

Homo sapiens
chr11:61890194 (GRCh38.p12) 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.

Variation Type
SNV Single Nucleotide Variation
A=0.17067 (21431/125568, TOPMED)
A=0.1465 (4474/30540, GnomAD)
A=0.231 (1158/5008, 1000G) (+ 3 more)
A=0.147 (659/4478, Estonian)
A=0.169 (652/3854, ALSPAC)
A=0.172 (639/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FADS3 : Intron Variant
0 citations
Genomic View
See rs on genome

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.p12 chr 11 NC_000011.10:g.61890194G>A
GRCh37.p13 chr 11 NC_000011.9:g.61657666G>A
Gene: FADS3, fatty acid desaturase 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FADS3 transcript NM_021727.4:c. N/A Intron Variant
FADS3 transcript variant X3 XM_011545023.2:c. N/A Intron Variant
FADS3 transcript variant X1 XM_017017723.1:c. N/A Intron Variant
FADS3 transcript variant X2 XM_017017724.1:c. N/A Intron Variant
FADS3 transcript variant X4 XR_001747866.1:n. N/A Intron Variant
FADS3 transcript variant X5 XR_001747867.1:n. N/A Intron Variant
FADS3 transcript variant X6 XR_001747868.1:n. N/A Intron Variant
FADS3 transcript variant X7 XR_001747869.1:n. N/A Intron Variant

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

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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.82933 A=0.17067
gnomAD - Genomes Global Study-wide 30540 G=0.8535 A=0.1465
gnomAD - Genomes European Sub 18170 G=0.8527 A=0.1473
gnomAD - Genomes African Sub 8656 G=0.918 A=0.082
gnomAD - Genomes East Asian Sub 1616 G=0.693 A=0.307
gnomAD - Genomes Other Sub 964 G=0.83 A=0.17
gnomAD - Genomes American Sub 832 G=0.53 A=0.47
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=0.87 A=0.13
1000Genomes Global Study-wide 5008 G=0.769 A=0.231
1000Genomes African Sub 1322 G=0.924 A=0.076
1000Genomes East Asian Sub 1008 G=0.692 A=0.308
1000Genomes Europe Sub 1006 G=0.831 A=0.169
1000Genomes South Asian Sub 978 G=0.74 A=0.26
1000Genomes American Sub 694 G=0.54 A=0.46
Genetic variation in the Estonian population Estonian Study-wide 4478 G=0.853 A=0.147
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.831 A=0.169
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.828 A=0.172

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 Note
GRCh38.p12 chr 11 NC_000011.10:g.61890194G= NC_000011.10:g.61890194G>A
GRCh37.p13 chr 11 NC_000011.9:g.61657666G= NC_000011.9:g.61657666G>A

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#.

44 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss232278 Jul 12, 2000 (79)
2 SC_JCM ss552341 Jul 16, 2000 (80)
3 KWOK ss1272140 Oct 04, 2000 (86)
4 KWOK ss2050000 Oct 18, 2000 (87)
5 KWOK ss2050132 Oct 18, 2000 (87)
6 ABI ss38741907 Mar 15, 2006 (126)
7 GMI ss156385058 Dec 01, 2009 (131)
8 1000GENOMES ss225274727 Jul 14, 2010 (132)
9 1000GENOMES ss235585113 Jul 15, 2010 (132)
10 1000GENOMES ss242211553 Jul 15, 2010 (132)
11 GMI ss281034719 May 04, 2012 (137)
12 ILLUMINA ss410793907 Sep 17, 2011 (135)
13 ILLUMINA ss482863319 May 04, 2012 (137)
14 ILLUMINA ss483045838 May 04, 2012 (137)
15 ILLUMINA ss535111157 Sep 08, 2015 (146)
16 TISHKOFF ss562598673 Apr 25, 2013 (138)
17 SSMP ss658109411 Apr 25, 2013 (138)
18 ILLUMINA ss780130918 Sep 08, 2015 (146)
19 ILLUMINA ss781966445 Sep 08, 2015 (146)
20 ILLUMINA ss835614085 Sep 08, 2015 (146)
21 EVA-GONL ss988588015 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1077777873 Aug 21, 2014 (142)
23 1000GENOMES ss1341527005 Aug 21, 2014 (142)
24 EVA_GENOME_DK ss1575748989 Apr 01, 2015 (144)
25 EVA_DECODE ss1598250592 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1626722433 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1669716466 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1931947001 Feb 12, 2016 (147)
29 GENOMED ss1967377023 Jul 19, 2016 (147)
30 JJLAB ss2026720224 Sep 14, 2016 (149)
31 USC_VALOUEV ss2155022833 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2182849189 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2627833272 Nov 08, 2017 (151)
34 ILLUMINA ss2632840822 Nov 08, 2017 (151)
35 ILLUMINA ss2632840823 Nov 08, 2017 (151)
36 GRF ss2699312485 Nov 08, 2017 (151)
37 GNOMAD ss2900369190 Nov 08, 2017 (151)
38 SWEGEN ss3008197955 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3027158808 Nov 08, 2017 (151)
40 TOPMED ss3147001996 Nov 08, 2017 (151)
41 CSHL ss3349629819 Nov 08, 2017 (151)
42 ILLUMINA ss3626670684 Oct 12, 2018 (152)
43 ILLUMINA ss3630857796 Oct 12, 2018 (152)
44 ILLUMINA ss3641737264 Oct 12, 2018 (152)
45 1000Genomes NC_000011.9 - 61657666 Oct 12, 2018 (152)
46 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 61657666 Oct 12, 2018 (152)
47 Genetic variation in the Estonian population NC_000011.9 - 61657666 Oct 12, 2018 (152)
48 gnomAD - Genomes NC_000011.9 - 61657666 Oct 12, 2018 (152)
49 TopMed NC_000011.10 - 61890194 Oct 12, 2018 (152)
50 UK 10K study - Twins NC_000011.9 - 61657666 Oct 12, 2018 (152)

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
ss281034719, ss482863319, ss1598250592 NC_000011.8:61414241:G:A NC_000011.10:61890193:G:A (self)
54058180, 30019347, 21274536, 34070712, 30019347, ss225274727, ss235585113, ss242211553, ss483045838, ss535111157, ss562598673, ss658109411, ss780130918, ss781966445, ss835614085, ss988588015, ss1077777873, ss1341527005, ss1575748989, ss1626722433, ss1669716466, ss1931947001, ss1967377023, ss2026720224, ss2155022833, ss2627833272, ss2632840822, ss2632840823, ss2699312485, ss2900369190, ss3008197955, ss3349629819, ss3626670684, ss3630857796, ss3641737264 NC_000011.9:61657665:G:A NC_000011.10:61890193:G:A (self)
64650637, ss2182849189, ss3027158808, ss3147001996 NC_000011.10:61890193:G:A NC_000011.10:61890193:G:A (self)
ss232278, ss552341, ss1272140, ss2050000, ss2050132, ss38741907, ss156385058, ss410793907 NT_167190.1:6963460:G:A NC_000011.10:61890193:G:A (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs174462

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.post104+4a6ee9c