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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs17881144

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr3:3103687 (GRCh38.p7) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.03538 (4442/125568, TOPMED)
T=0.0435 (1347/30968, GnomAD)
T=0.047 (234/5008, 1000G) (+ 2 more)
T=0.033 (127/3854, ALSPAC)
T=0.034 (125/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IL5RA : Intron Variant
Publications
2 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.p7 chr 3 NC_000003.12:g.3103687A>T
GRCh37.p13 chr 3 NC_000003.11:g.3145371A>T
IL5RA RefSeqGene NG_029547.1:g.11688T>A
Gene: IL5RA, interleukin 5 receptor subunit alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IL5RA transcript variant 1 NM_000564.4:c. N/A Intron Variant
IL5RA transcript variant 7 NM_001243099.1:c. N/A Intron Variant
IL5RA transcript variant 2 NM_175724.2:c. N/A Intron Variant
IL5RA transcript variant 3 NM_175725.2:c. N/A Intron Variant
IL5RA transcript variant 4 NM_175726.3:c. N/A Intron Variant
IL5RA transcript variant 5 NM_175727.2:c. N/A Intron Variant
IL5RA transcript variant 6 NM_175728.2:c. N/A Intron Variant
IL5RA transcript variant X1 XM_011533677.2:c. N/A Intron Variant
IL5RA transcript variant X2 XM_011533678.2:c. 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
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
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.96462 T=0.03538
The Genome Aggregation Database Global Study-wide 30968 A=0.9565 T=0.0435
The Genome Aggregation Database European Sub 18496 A=0.9449 T=0.0551
The Genome Aggregation Database African Sub 8732 A=0.992 T=0.008
The Genome Aggregation Database East Asian Sub 1620 A=0.946 T=0.054
The Genome Aggregation Database Other Sub 982 A=0.94 T=0.06
The Genome Aggregation Database American Sub 836 A=0.88 T=0.12
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=0.98 T=0.02
1000Genomes Global Study-wide 5008 A=0.953 T=0.047
1000Genomes African Sub 1322 A=0.997 T=0.003
1000Genomes East Asian Sub 1008 A=0.933 T=0.067
1000Genomes Europe Sub 1006 A=0.961 T=0.039
1000Genomes South Asian Sub 978 A=0.97 T=0.03
1000Genomes American Sub 694 A=0.86 T=0.14
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.967 T=0.033
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.966 T=0.034
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= T Note
GRCh38.p7 chr 3 NC_000003.12:g.3103687A= NC_000003.12:g.3103687A>T
GRCh37.p13 chr 3 NC_000003.11:g.3145371A= NC_000003.11:g.3145371A>T
IL5RA RefSeqGene NG_029547.1:g.11688T= NG_029547.1:g.11688T>A
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#.

5 Frequency, 28 SubSNP submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss28527354 Dec 02, 2004 (124)
2 ABI ss44471719 Mar 13, 2006 (126)
3 HUMANGENOME_JCVI ss99162444 Feb 06, 2009 (130)
4 ENSEMBL ss135348518 Dec 01, 2009 (131)
5 ILLUMINA ss172917198 Jul 04, 2010 (132)
6 BCM-HGSC-SUB ss206171166 Jul 04, 2010 (132)
7 1000GENOMES ss231678036 Jul 14, 2010 (132)
8 1000GENOMES ss239117400 Jul 15, 2010 (132)
9 GMI ss276984127 May 04, 2012 (137)
10 PJP ss292782489 May 09, 2011 (134)
11 EVA-GONL ss978196498 Aug 21, 2014 (142)
12 JMKIDD_LAB ss1070116512 Aug 21, 2014 (142)
13 1000GENOMES ss1302525587 Aug 21, 2014 (142)
14 EVA_GENOME_DK ss1579813937 Apr 01, 2015 (144)
15 EVA_DECODE ss1587655823 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1606265205 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1649259238 Apr 01, 2015 (144)
18 GENOMED ss1969304246 Jul 19, 2016 (147)
19 JJLAB ss2021274322 Sep 14, 2016 (149)
20 USC_VALOUEV ss2149342134 Dec 20, 2016 (150)
21 HUMAN_LONGEVITY ss2248526087 Dec 20, 2016 (150)
22 TOPMED ss2415559116 Dec 20, 2016 (150)
23 GRF ss2704697805 Nov 08, 2017 (151)
24 GNOMAD ss2788781224 Nov 08, 2017 (151)
25 SWEGEN ss2991719492 Nov 08, 2017 (151)
26 CSHL ss3344849802 Nov 08, 2017 (151)
27 TOPMED ss3380960966 Nov 08, 2017 (151)
28 ILLUMINA ss3638392742 Jul 19, 2018 (151)
29 1000Genomes NC_000003.11 - 3145371 Jul 19, 2018 (151)
30 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 3145371 Jul 19, 2018 (151)
31 The Genome Aggregation Database NC_000003.11 - 3145371 Jul 19, 2018 (151)
32 Trans-Omics for Precision Medicine NC_000003.12 - 3103687 Jul 19, 2018 (151)
33 UK 10K study - Twins NC_000003.11 - 3145371 Jul 19, 2018 (151)
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
ss206171166, ss276984127, ss292782489, ss1587655823 NC_000003.10:3120370:A= NC_000003.12:3103686:A= (self)
13661638, 7569332, 129408978, 7569332, ss231678036, ss239117400, ss978196498, ss1070116512, ss1302525587, ss1579813937, ss1606265205, ss1649259238, ss1969304246, ss2021274322, ss2149342134, ss2415559116, ss2704697805, ss2788781224, ss2991719492, ss3344849802, ss3638392742 NC_000003.11:3145370:A= NC_000003.12:3103686:A= (self)
243254717, ss2248526087, ss3380960966 NC_000003.12:3103686:A= NC_000003.12:3103686:A= (self)
ss28527354, ss44471719, ss99162444, ss135348518, ss172917198 NT_022517.18:3085370:A= NC_000003.12:3103686:A= (self)
ss206171166, ss276984127, ss292782489, ss1587655823 NC_000003.10:3120370:A>T NC_000003.12:3103686:A>T (self)
13661638, 7569332, 129408978, 7569332, ss231678036, ss239117400, ss978196498, ss1070116512, ss1302525587, ss1579813937, ss1606265205, ss1649259238, ss1969304246, ss2021274322, ss2149342134, ss2415559116, ss2704697805, ss2788781224, ss2991719492, ss3344849802, ss3638392742 NC_000003.11:3145370:A>T NC_000003.12:3103686:A>T (self)
243254717, ss2248526087, ss3380960966 NC_000003.12:3103686:A>T NC_000003.12:3103686:A>T (self)
ss28527354, ss44471719, ss99162444, ss135348518, ss172917198 NT_022517.18:3085370:A>T NC_000003.12:3103686: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.

2 citations for rs17881144
PMID Title Author Year Journal
24332579 Case-control study of rhinoconjunctivitis associated with IL5RA polymorphisms in Japanese women: the Kyushu Okinawa Maternal and Child Health Study. Miyake Y et al. 2014 Cytokine
25523412 IL5RA polymorphisms, smoking and eczema in Japanese women: the Kyushu Okinawa Maternal and Child Health Study. Miyake Y et al. 2015 International journal of immunogenetics

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: 0.1.4.post833+d3ba21e