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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.

rs17001659

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:76209916 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.18325 (23010/125568, TOPMED)
C=0.1702 (5266/30936, GnomAD)
C=0.250 (1251/5008, 1000G) (+ 2 more)
C=0.065 (251/3854, ALSPAC)
C=0.062 (231/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SCARB2 : 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.p7 chr 4 NC_000004.12:g.76209916T>C
GRCh37.p13 chr 4 NC_000004.11:g.77131069T>C
SCARB2 RefSeqGene NG_012054.1:g.8967A>G
Gene: SCARB2, scavenger receptor class B, member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SCARB2 transcript variant 2 NM_001204255.1:c. N/A Intron Variant
SCARB2 transcript variant 1 NM_005506.3: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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.81675 C=0.18325
The Genome Aggregation Database Global Study-wide 30936 T=0.8298 C=0.1702
The Genome Aggregation Database European Sub 18492 T=0.9194 C=0.0806
The Genome Aggregation Database African Sub 8706 T=0.659 C=0.341
The Genome Aggregation Database East Asian Sub 1616 T=0.697 C=0.303
The Genome Aggregation Database Other Sub 982 T=0.86 C=0.14
The Genome Aggregation Database American Sub 838 T=0.85 C=0.15
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.83 C=0.17
1000Genomes Global Study-wide 5008 T=0.750 C=0.250
1000Genomes African Sub 1322 T=0.599 C=0.401
1000Genomes East Asian Sub 1008 T=0.661 C=0.339
1000Genomes Europe Sub 1006 T=0.936 C=0.064
1000Genomes South Asian Sub 978 T=0.81 C=0.19
1000Genomes American Sub 694 T=0.82 C=0.18
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.935 C=0.065
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.938 C=0.062
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= C Note
GRCh38.p7 chr 4 NC_000004.12:g.76209916T= NC_000004.12:g.76209916T>C
GRCh37.p13 chr 4 NC_000004.11:g.77131069T= NC_000004.11:g.77131069T>C
SCARB2 RefSeqGene NG_012054.1:g.8967A= NG_012054.1:g.8967A>G
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, 57 SubSNP submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23274056 Sep 20, 2004 (123)
2 HGSV ss80871500 Dec 15, 2007 (130)
3 BGI ss104084358 Dec 01, 2009 (131)
4 1000GENOMES ss110047204 Jan 24, 2009 (130)
5 ILLUMINA-UK ss117054131 Feb 14, 2009 (130)
6 ILLUMINA ss160408986 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss163625774 Jul 04, 2010 (132)
8 BUSHMAN ss198719121 Jul 04, 2010 (132)
9 1000GENOMES ss221009656 Jul 14, 2010 (132)
10 1000GENOMES ss232452873 Jul 14, 2010 (132)
11 1000GENOMES ss239733429 Jul 15, 2010 (132)
12 GMI ss277784461 May 04, 2012 (137)
13 ILLUMINA ss480139337 May 04, 2012 (137)
14 ILLUMINA ss480148526 May 04, 2012 (137)
15 ILLUMINA ss480852737 Sep 08, 2015 (146)
16 ILLUMINA ss484867663 May 04, 2012 (137)
17 ILLUMINA ss536931385 Sep 08, 2015 (146)
18 TISHKOFF ss557613847 Apr 25, 2013 (138)
19 SSMP ss651423054 Apr 25, 2013 (138)
20 ILLUMINA ss778824352 Sep 08, 2015 (146)
21 ILLUMINA ss782880255 Sep 08, 2015 (146)
22 ILLUMINA ss783844043 Sep 08, 2015 (146)
23 ILLUMINA ss832134569 Sep 08, 2015 (146)
24 ILLUMINA ss834284737 Sep 08, 2015 (146)
25 EVA-GONL ss980275717 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1071659745 Aug 21, 2014 (142)
27 1000GENOMES ss1310343990 Aug 21, 2014 (142)
28 DDI ss1429932258 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1580621689 Apr 01, 2015 (144)
30 EVA_DECODE ss1589774977 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1610394147 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1653388180 Apr 01, 2015 (144)
33 ILLUMINA ss1752532152 Sep 08, 2015 (146)
34 HAMMER_LAB ss1801682492 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1923518487 Feb 12, 2016 (147)
36 GENOMED ss1969779979 Jul 19, 2016 (147)
37 JJLAB ss2022345121 Sep 14, 2016 (149)
38 USC_VALOUEV ss2150473607 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2264085253 Dec 20, 2016 (150)
40 TOPMED ss2431876026 Dec 20, 2016 (150)
41 SYSTEMSBIOZJU ss2625673221 Nov 08, 2017 (151)
42 ILLUMINA ss2634136241 Nov 08, 2017 (151)
43 GRF ss2705947584 Nov 08, 2017 (151)
44 GNOMAD ss2811024682 Nov 08, 2017 (151)
45 SWEGEN ss2994948442 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3024947135 Nov 08, 2017 (151)
47 CSHL ss3345789367 Nov 08, 2017 (151)
48 TOPMED ss3433037550 Nov 08, 2017 (151)
49 ILLUMINA ss3628993837 Jul 20, 2018 (151)
50 ILLUMINA ss3632071672 Jul 20, 2018 (151)
51 ILLUMINA ss3633338733 Jul 20, 2018 (151)
52 ILLUMINA ss3634057865 Jul 20, 2018 (151)
53 ILLUMINA ss3634957307 Jul 20, 2018 (151)
54 ILLUMINA ss3635740697 Jul 20, 2018 (151)
55 ILLUMINA ss3636661026 Jul 20, 2018 (151)
56 ILLUMINA ss3637493219 Jul 20, 2018 (151)
57 ILLUMINA ss3640664601 Jul 20, 2018 (151)
58 1000Genomes NC_000004.11 - 77131069 Jul 20, 2018 (151)
59 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 77131069 Jul 20, 2018 (151)
60 The Genome Aggregation Database NC_000004.11 - 77131069 Jul 20, 2018 (151)
61 Trans-Omics for Precision Medicine NC_000004.12 - 76209916 Jul 20, 2018 (151)
62 UK 10K study - Twins NC_000004.11 - 77131069 Jul 20, 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).

Associated ID History Updated (Build)
rs58393375 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss80871500 NC_000004.9:77488247:T= NC_000004.12:76209915:T= (self)
ss110047204, ss117054131, ss163625774, ss198719121, ss277784461, ss480139337, ss1589774977 NC_000004.10:77350092:T= NC_000004.12:76209915:T= (self)
21761226, 12096782, 151652437, 12096782, ss221009656, ss232452873, ss239733429, ss480148526, ss480852737, ss484867663, ss536931385, ss557613847, ss651423054, ss778824352, ss782880255, ss783844043, ss832134569, ss834284737, ss980275717, ss1071659745, ss1310343990, ss1429932258, ss1580621689, ss1610394147, ss1653388180, ss1752532152, ss1801682492, ss1923518487, ss1969779979, ss2022345121, ss2150473607, ss2431876026, ss2625673221, ss2634136241, ss2705947584, ss2811024682, ss2994948442, ss3345789367, ss3628993837, ss3632071672, ss3633338733, ss3634057865, ss3634957307, ss3635740697, ss3636661026, ss3637493219, ss3640664601 NC_000004.11:77131068:T= NC_000004.12:76209915:T= (self)
285294383, ss2264085253, ss3024947135, ss3433037550 NC_000004.12:76209915:T= NC_000004.12:76209915:T= (self)
ss23274056, ss104084358, ss160408986 NT_016354.19:1678789:T= NC_000004.12:76209915:T= (self)
ss80871500 NC_000004.9:77488247:T>C NC_000004.12:76209915:T>C (self)
ss110047204, ss117054131, ss163625774, ss198719121, ss277784461, ss480139337, ss1589774977 NC_000004.10:77350092:T>C NC_000004.12:76209915:T>C (self)
21761226, 12096782, 151652437, 12096782, ss221009656, ss232452873, ss239733429, ss480148526, ss480852737, ss484867663, ss536931385, ss557613847, ss651423054, ss778824352, ss782880255, ss783844043, ss832134569, ss834284737, ss980275717, ss1071659745, ss1310343990, ss1429932258, ss1580621689, ss1610394147, ss1653388180, ss1752532152, ss1801682492, ss1923518487, ss1969779979, ss2022345121, ss2150473607, ss2431876026, ss2625673221, ss2634136241, ss2705947584, ss2811024682, ss2994948442, ss3345789367, ss3628993837, ss3632071672, ss3633338733, ss3634057865, ss3634957307, ss3635740697, ss3636661026, ss3637493219, ss3640664601 NC_000004.11:77131068:T>C NC_000004.12:76209915:T>C (self)
285294383, ss2264085253, ss3024947135, ss3433037550 NC_000004.12:76209915:T>C NC_000004.12:76209915:T>C (self)
ss23274056, ss104084358, ss160408986 NT_016354.19:1678789:T>C NC_000004.12:76209915: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 rs17001659

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