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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.

rs2486758

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr10:102837723 (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.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.17057 (21418/125568, TOPMED)
C=0.1712 (13470/78698, PAGE_STUDY)
C=0.1860 (5817/31280, GnomAD) (+ 6 more)
C=0.177 (888/5008, 1000G)
C=0.218 (977/4480, Estonian)
C=0.208 (803/3854, ALSPAC)
C=0.218 (808/3708, TWINSUK)
C=0.21 (128/600, NorthernSweden)
C=0.10 (22/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP17A1 : 2KB Upstream Variant
Publications
18 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.p12 chr 10 NC_000010.11:g.102837723T>C
GRCh37.p13 chr 10 NC_000010.10:g.104597480T>C
CYP17A1 RefSeqGene NG_007955.1:g.4811A>G
LOC110408762 genomic region NG_055002.1:g.451T>C
Gene: CYP17A1, cytochrome P450 family 17 subfamily A member 1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CYP17A1 transcript NM_000102.4:c. N/A Upstream Transcript 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
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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
TopMed Global Study-wide 125568 T=0.82943 C=0.17057
The PAGE Study Global Study-wide 78698 T=0.8288 C=0.1712
The PAGE Study AfricanAmerican Sub 32516 T=0.9239 C=0.0761
The PAGE Study Mexican Sub 10808 T=0.6935 C=0.3065
The PAGE Study Asian Sub 8318 T=0.705 C=0.295
The PAGE Study PuertoRican Sub 7918 T=0.805 C=0.195
The PAGE Study NativeHawaiian Sub 4532 T=0.849 C=0.151
The PAGE Study Cuban Sub 4230 T=0.822 C=0.178
The PAGE Study Dominican Sub 3828 T=0.865 C=0.135
The PAGE Study CentralAmerican Sub 2450 T=0.723 C=0.277
The PAGE Study SouthAmerican Sub 1982 T=0.725 C=0.275
The PAGE Study NativeAmerican Sub 1260 T=0.779 C=0.221
The PAGE Study SouthAsian Sub 856 T=0.73 C=0.27
gnomAD - Genomes Global Study-wide 31280 T=0.8140 C=0.1860
gnomAD - Genomes European Sub 18820 T=0.7665 C=0.2335
gnomAD - Genomes African Sub 8688 T=0.933 C=0.067
gnomAD - Genomes East Asian Sub 1552 T=0.819 C=0.181
gnomAD - Genomes Other Sub 1084 T=0.749 C=0.251
gnomAD - Genomes American Sub 846 T=0.72 C=0.28
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.82 C=0.18
1000Genomes Global Study-wide 5008 T=0.823 C=0.177
1000Genomes African Sub 1322 T=0.955 C=0.045
1000Genomes East Asian Sub 1008 T=0.813 C=0.187
1000Genomes Europe Sub 1006 T=0.774 C=0.226
1000Genomes South Asian Sub 978 T=0.75 C=0.25
1000Genomes American Sub 694 T=0.76 C=0.24
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.782 C=0.218
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.792 C=0.208
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.782 C=0.218
Northern Sweden ACPOP Study-wide 600 T=0.79 C=0.21
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.90 C=0.10
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.p12 chr 10 NC_000010.11:g.102837723= NC_000010.11:g.10283772...

NC_000010.11:g.102837723T>C

GRCh37.p13 chr 10 NC_000010.10:g.104597480= NC_000010.10:g.10459748...

NC_000010.10:g.104597480T>C

CYP17A1 RefSeqGene NG_007955.1:g.4811= NG_007955.1:g.4811A>G
LOC110408762 genomic region NG_055002.1:g.451= NG_055002.1:g.451T>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#.

102 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3488235 Sep 28, 2001 (100)
2 SC_SNP ss12974912 Dec 05, 2003 (119)
3 PERLEGEN ss24497159 Sep 20, 2004 (123)
4 KYUGEN ss28459159 Sep 20, 2004 (123)
5 SNP500CANCER ss48293527 Mar 14, 2006 (126)
6 ILLUMINA ss66613682 Nov 30, 2006 (127)
7 ILLUMINA ss67257158 Nov 30, 2006 (127)
8 ILLUMINA ss67655692 Nov 30, 2006 (127)
9 EGP_SNPS ss70457527 May 17, 2007 (127)
10 ILLUMINA ss70735515 May 24, 2008 (130)
11 ILLUMINA ss71305617 May 17, 2007 (127)
12 SI_EXO ss71647910 May 17, 2007 (127)
13 ILLUMINA ss75837129 Dec 07, 2007 (129)
14 AFFY ss76565040 Dec 07, 2007 (129)
15 ILLUMINA ss79136868 Dec 15, 2007 (130)
16 KRIBB_YJKIM ss84053261 Dec 15, 2007 (130)
17 PHARMGKB_PPII ss84171795 Dec 15, 2007 (130)
18 RSG_UW ss86211520 Mar 23, 2008 (129)
19 BCMHGSC_JDW ss88336632 Mar 23, 2008 (129)
20 BGI ss102907440 Dec 01, 2009 (131)
21 1000GENOMES ss109706925 Jan 24, 2009 (130)
22 ILLUMINA ss122046012 Dec 01, 2009 (131)
23 ENSEMBL ss132050569 Dec 01, 2009 (131)
24 ILLUMINA ss153915489 Dec 01, 2009 (131)
25 GMI ss155476302 Dec 01, 2009 (131)
26 ILLUMINA ss159393297 Dec 01, 2009 (131)
27 ILLUMINA ss160552049 Dec 01, 2009 (131)
28 ILLUMINA ss171276110 Jul 04, 2010 (132)
29 ILLUMINA ss173367374 Jul 04, 2010 (132)
30 COMPLETE_GENOMICS ss174728300 Jul 04, 2010 (132)
31 1000GENOMES ss224909288 Jul 14, 2010 (132)
32 1000GENOMES ss235311790 Jul 15, 2010 (132)
33 1000GENOMES ss241991300 Jul 15, 2010 (132)
34 ILLUMINA ss244290773 Jul 04, 2010 (132)
35 GMI ss280751628 May 04, 2012 (137)
36 GMI ss286253165 Apr 25, 2013 (138)
37 ILLUMINA ss410778277 Sep 17, 2011 (135)
38 ILLUMINA ss480583345 May 04, 2012 (137)
39 ILLUMINA ss480597843 May 04, 2012 (137)
40 ILLUMINA ss481422507 Sep 08, 2015 (146)
41 ILLUMINA ss485087135 May 04, 2012 (137)
42 ILLUMINA ss537096273 Sep 08, 2015 (146)
43 TISHKOFF ss562173244 Apr 25, 2013 (138)
44 SSMP ss657259308 Apr 25, 2013 (138)
45 ILLUMINA ss778870629 Sep 08, 2015 (146)
46 ILLUMINA ss782989842 Sep 08, 2015 (146)
47 ILLUMINA ss783950656 Sep 08, 2015 (146)
48 ILLUMINA ss825467386 Apr 01, 2015 (144)
49 ILLUMINA ss832246635 Sep 08, 2015 (146)
50 ILLUMINA ss832905038 Jul 13, 2019 (153)
51 ILLUMINA ss834331521 Sep 08, 2015 (146)
52 EVA-GONL ss987860573 Aug 21, 2014 (142)
53 JMKIDD_LAB ss1077252761 Aug 21, 2014 (142)
54 1000GENOMES ss1338836833 Aug 21, 2014 (142)
55 DDI ss1426427306 Apr 01, 2015 (144)
56 EVA_GENOME_DK ss1575324742 Apr 01, 2015 (144)
57 EVA_DECODE ss1597535489 Apr 01, 2015 (144)
58 EVA_UK10K_ALSPAC ss1625310490 Apr 01, 2015 (144)
59 EVA_UK10K_TWINSUK ss1668304523 Apr 01, 2015 (144)
60 EVA_SVP ss1713206896 Apr 01, 2015 (144)
61 ILLUMINA ss1751943953 Sep 08, 2015 (146)
62 HAMMER_LAB ss1806543273 Sep 08, 2015 (146)
63 WEILL_CORNELL_DGM ss1931223974 Feb 12, 2016 (147)
64 ILLUMINA ss1959290388 Feb 12, 2016 (147)
65 GENOMED ss1967211157 Jul 19, 2016 (147)
66 JJLAB ss2026342349 Sep 14, 2016 (149)
67 USC_VALOUEV ss2154621068 Nov 08, 2017 (151)
68 HUMAN_LONGEVITY ss2177596492 Dec 20, 2016 (150)
69 TOPMED ss2340719144 Dec 20, 2016 (150)
70 SYSTEMSBIOZJU ss2627639245 Nov 08, 2017 (151)
71 ILLUMINA ss2632755349 Nov 08, 2017 (151)
72 ILLUMINA ss2635018511 Nov 08, 2017 (151)
73 GRF ss2698874777 Nov 08, 2017 (151)
74 GNOMAD ss2892755198 Nov 08, 2017 (151)
75 SWEGEN ss3007056481 Nov 08, 2017 (151)
76 ILLUMINA ss3021270489 Nov 08, 2017 (151)
77 BIOINF_KMB_FNS_UNIBA ss3026960859 Nov 08, 2017 (151)
78 TOPMED ss3128966583 Nov 08, 2017 (151)
79 CSHL ss3349285072 Nov 08, 2017 (151)
80 ILLUMINA ss3626522496 Oct 12, 2018 (152)
81 ILLUMINA ss3630778013 Oct 12, 2018 (152)
82 ILLUMINA ss3632962497 Oct 12, 2018 (152)
83 ILLUMINA ss3633660254 Oct 12, 2018 (152)
84 ILLUMINA ss3634421382 Oct 12, 2018 (152)
85 ILLUMINA ss3635352465 Oct 12, 2018 (152)
86 ILLUMINA ss3636105812 Oct 12, 2018 (152)
87 ILLUMINA ss3637103193 Oct 12, 2018 (152)
88 ILLUMINA ss3637871008 Oct 12, 2018 (152)
89 ILLUMINA ss3638950828 Oct 12, 2018 (152)
90 ILLUMINA ss3639475597 Oct 12, 2018 (152)
91 ILLUMINA ss3640128723 Oct 12, 2018 (152)
92 ILLUMINA ss3642872714 Oct 12, 2018 (152)
93 ILLUMINA ss3651629448 Oct 12, 2018 (152)
94 EGCUT_WGS ss3674467551 Jul 13, 2019 (153)
95 EVA_DECODE ss3690571673 Jul 13, 2019 (153)
96 ILLUMINA ss3725184546 Jul 13, 2019 (153)
97 ACPOP ss3737631488 Jul 13, 2019 (153)
98 ILLUMINA ss3744722329 Jul 13, 2019 (153)
99 EVA ss3748533353 Jul 13, 2019 (153)
100 PAGE_CC ss3771579895 Jul 13, 2019 (153)
101 ILLUMINA ss3772222650 Jul 13, 2019 (153)
102 KHV_HUMAN_GENOMES ss3813895480 Jul 13, 2019 (153)
103 1000Genomes NC_000010.10 - 104597480 Oct 12, 2018 (152)
104 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 104597480 Oct 12, 2018 (152)
105 Genetic variation in the Estonian population NC_000010.10 - 104597480 Oct 12, 2018 (152)
106 gnomAD - Genomes NC_000010.10 - 104597480 Jul 13, 2019 (153)
107 Northern Sweden NC_000010.10 - 104597480 Jul 13, 2019 (153)
108 The PAGE Study NC_000010.11 - 102837723 Jul 13, 2019 (153)
109 TopMed NC_000010.11 - 102837723 Oct 12, 2018 (152)
110 UK 10K study - Twins NC_000010.10 - 104597480 Oct 12, 2018 (152)
111 A Vietnamese Genetic Variation Database NC_000010.10 - 104597480 Jul 13, 2019 (153)
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)
rs17786415 Oct 08, 2004 (123)
rs58578453 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638950828, ss3639475597 NC_000010.8:104587469:T:C NC_000010.11:102837722:T:C (self)
ss88336632, ss109706925, ss174728300, ss280751628, ss286253165, ss480583345, ss825467386, ss1597535489, ss1713206896, ss2635018511, ss3642872714 NC_000010.9:104587469:T:C NC_000010.11:102837722:T:C (self)
51275971, 28472162, 20205799, 140103164, 10916353, 28472162, 6320196, ss224909288, ss235311790, ss241991300, ss480597843, ss481422507, ss485087135, ss537096273, ss562173244, ss657259308, ss778870629, ss782989842, ss783950656, ss832246635, ss832905038, ss834331521, ss987860573, ss1077252761, ss1338836833, ss1426427306, ss1575324742, ss1625310490, ss1668304523, ss1751943953, ss1806543273, ss1931223974, ss1959290388, ss1967211157, ss2026342349, ss2154621068, ss2340719144, ss2627639245, ss2632755349, ss2698874777, ss2892755198, ss3007056481, ss3021270489, ss3349285072, ss3626522496, ss3630778013, ss3632962497, ss3633660254, ss3634421382, ss3635352465, ss3636105812, ss3637103193, ss3637871008, ss3640128723, ss3651629448, ss3674467551, ss3737631488, ss3744722329, ss3748533353, ss3772222650 NC_000010.10:104597479:T:C NC_000010.11:102837722:T:C (self)
801364, 50345321, ss2177596492, ss3026960859, ss3128966583, ss3690571673, ss3725184546, ss3771579895, ss3813895480 NC_000010.11:102837722:T:C NC_000010.11:102837722:T:C (self)
ss12974912 NT_030059.10:23036037:T:C NC_000010.11:102837722:T:C (self)
ss3488235, ss24497159, ss28459159, ss48293527, ss66613682, ss67257158, ss67655692, ss70457527, ss70735515, ss71305617, ss71647910, ss75837129, ss76565040, ss79136868, ss84053261, ss84171795, ss86211520, ss102907440, ss122046012, ss132050569, ss153915489, ss155476302, ss159393297, ss160552049, ss171276110, ss173367374, ss244290773, ss410778277 NT_030059.13:55401943:T:C NC_000010.11:102837722: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.

18 citations for rs2486758
PMID Title Author Year Journal
17975119 Association of gene variants with incident myocardial infarction in the Cardiovascular Health Study. Shiffman D et al. 2008 Arteriosclerosis, thrombosis, and vascular biology
18006912 CYP17 genetic variation and risk of breast and prostate cancer from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3). Setiawan VW et al. 2007 Cancer epidemiology, biomarkers & prevention
18505952 Genetic susceptibility to cancer: the role of polymorphisms in candidate genes. Dong LM et al. 2008 JAMA
19015200 Polymorphisms in estrogen- and androgen-metabolizing genes and the risk of gastric cancer. Freedman ND et al. 2009 Carcinogenesis
19567509 Genetic variants and prostate cancer risk: candidate replication and exploration of viral restriction genes. Breyer JP et al. 2009 Cancer epidemiology, biomarkers & prevention
20411041 Common Variation in the CYP17A1 and IFIT1 Genes on Chromosome 10 Does Not Contribute to the Risk of Endometriosis. Zhao ZZ et al. 2008 The open reproductive science journal
21229561
21656827 CYP17 gene polymorphisms and prostate cancer risk: a meta-analysis based on 38 independent studies. Wang F et al. 2011 The Prostate
22006096 Genomics of ADME gene expression: mapping expression quantitative trait loci relevant for absorption, distribution, metabolism and excretion of drugs in human liver. Schröder A et al. 2013 The pharmacogenomics journal
22057025 Variants in CYP17 and CYP19 cytochrome P450 genes are associated with onset of Alzheimer's disease in women with down syndrome. Chace C et al. 2012 Journal of Alzheimer's disease
22969879 Association between cytochrome P450 promoter polymorphisms and ischemic stroke. Kim SK et al. 2012 Experimental and therapeutic medicine
24687554 CYP17 polymorphism (rs743572) is associated with increased risk of gallbladder cancer in tobacco users. Rai R et al. 2014 Tumour biology
25592814 Haplotype analyses of CYP17A1 genetic polymorphisms and coronary artery disease in a Uygur population. Dai CF et al. 2015 Journal of the renin-angiotensin-aldosterone system
26602921 A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations. Rai R et al. 2015 International journal of molecular sciences
26902494 Common Polymorphisms at the CYP17A1 Locus Associate With Steroid Phenotype: Support for Blood Pressure Genome-Wide Association Study Signals at This Locus. Diver LA et al. 2016 Hypertension (Dallas, Tex.
27409606 Common Genetic Variation in CYP17A1 and Response to Abiraterone Acetate in Patients with Metastatic Castration-Resistant Prostate Cancer. Binder M et al. 2016 International journal of molecular sciences
27717337 Polymorphisms in the estrogen receptor alpha gene (ESR1), daily cycling estrogen and mammographic density phenotypes. Fjeldheim FN et al. 2016 BMC cancer
30013390 <i>CYP17</i> polymorphisms are associated with decreased risk of breast cancer in Chinese Han women: a case-control study. Yang P et al. 2018 Cancer management and research

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.post246+3cda961