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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.

rs10519097

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr15:60997989 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.12596 (15817/125568, TOPMED)
T=0.1268 (3923/30942, GnomAD)
T=0.128 (639/5008, 1000G) (+ 3 more)
T=0.151 (676/4480, Estonian)
T=0.145 (558/3854, ALSPAC)
T=0.145 (539/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RORA : Intron Variant
Publications
1 citation
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 15 NC_000015.10:g.60997989C>T
GRCh37.p13 chr 15 NC_000015.9:g.61290188C>T
RORA RefSeqGene NG_029246.1:g.236315G>A
Gene: RORA, RAR related orphan receptor A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RORA transcript variant 1 NM_134261.2:c. N/A Intron Variant
RORA transcript variant 3 NM_002943.3:c. N/A Genic Upstream Transcript Variant
RORA transcript variant 2 NM_134260.2:c. N/A Genic Upstream Transcript Variant
RORA transcript variant 4 NM_134262.2:c. N/A Genic Upstream Transcript Variant
RORA transcript variant X6 XM_011521878.2:c. N/A Intron Variant
RORA transcript variant X3 XM_005254584.5:c. N/A Genic Upstream Transcript Variant
RORA transcript variant X1 XM_011521874.1:c. N/A Genic Upstream Transcript Variant
RORA transcript variant X2 XM_011521875.2:c. N/A Genic Upstream Transcript Variant
RORA transcript variant X4 XM_011521877.3:c. N/A Genic Upstream Transcript Variant
RORA transcript variant X8 XM_011521879.3:c. N/A Genic Upstream Transcript Variant
RORA transcript variant X5 XM_017022466.2:c. N/A Genic Upstream Transcript Variant
RORA transcript variant X7 XM_017022467.2:c. N/A Genic 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
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
TopMed Global Study-wide 125568 C=0.87404 T=0.12596
gnomAD - Genomes Global Study-wide 30942 C=0.8732 T=0.1268
gnomAD - Genomes European Sub 18474 C=0.8577 T=0.1423
gnomAD - Genomes African Sub 8732 C=0.904 T=0.096
gnomAD - Genomes East Asian Sub 1618 C=0.861 T=0.139
gnomAD - Genomes Other Sub 982 C=0.88 T=0.12
gnomAD - Genomes American Sub 836 C=0.91 T=0.09
gnomAD - Genomes Ashkenazi Jewish Sub 300 C=0.86 T=0.14
1000Genomes Global Study-wide 5008 C=0.872 T=0.128
1000Genomes African Sub 1322 C=0.896 T=0.104
1000Genomes East Asian Sub 1008 C=0.882 T=0.118
1000Genomes Europe Sub 1006 C=0.860 T=0.140
1000Genomes South Asian Sub 978 C=0.81 T=0.19
1000Genomes American Sub 694 C=0.92 T=0.08
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.849 T=0.151
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.855 T=0.145
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.855 T=0.145
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= T Note
GRCh38.p12 chr 15 NC_000015.10:g.60997989C= NC_000015.10:g.60997989C>T
GRCh37.p13 chr 15 NC_000015.9:g.61290188C= NC_000015.9:g.61290188C>T
RORA RefSeqGene NG_029246.1:g.236315G= NG_029246.1:g.236315G>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#.

6 Frequency, 58 SubSNP submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14921271 Dec 05, 2003 (119)
2 PERLEGEN ss23812237 Sep 20, 2004 (123)
3 AFFY ss65938654 Nov 30, 2006 (127)
4 ILLUMINA ss66825280 Nov 30, 2006 (127)
5 ILLUMINA ss66895203 Nov 30, 2006 (127)
6 ILLUMINA ss67003734 Nov 30, 2006 (127)
7 PERLEGEN ss69178566 May 17, 2007 (127)
8 ILLUMINA ss70375958 May 17, 2007 (127)
9 ILLUMINA ss70491236 May 24, 2008 (130)
10 ILLUMINA ss71015816 May 17, 2007 (127)
11 ILLUMINA ss75871696 Dec 07, 2007 (129)
12 KRIBB_YJKIM ss84979977 Dec 14, 2007 (130)
13 ILLUMINA ss121366444 Dec 01, 2009 (131)
14 ILLUMINA ss152789301 Dec 01, 2009 (131)
15 ILLUMINA ss159136032 Dec 01, 2009 (131)
16 ILLUMINA ss169553291 Jul 04, 2010 (132)
17 ILLUMINA ss170354979 Jul 04, 2010 (132)
18 BUSHMAN ss200928354 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss207171214 Jul 04, 2010 (132)
20 1000GENOMES ss226929590 Jul 14, 2010 (132)
21 1000GENOMES ss236804646 Jul 15, 2010 (132)
22 1000GENOMES ss243187326 Jul 15, 2010 (132)
23 BL ss255038387 May 09, 2011 (134)
24 GMI ss282284479 May 04, 2012 (137)
25 ILLUMINA ss536622763 Sep 08, 2015 (146)
26 TISHKOFF ss564523282 Apr 25, 2013 (138)
27 SSMP ss660254208 Apr 25, 2013 (138)
28 ILLUMINA ss825345569 Jul 19, 2016 (147)
29 EVA-GONL ss991858023 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1080182318 Aug 21, 2014 (142)
31 1000GENOMES ss1353745328 Aug 21, 2014 (142)
32 HAMMER_LAB ss1397699258 Sep 08, 2015 (146)
33 DDI ss1427648128 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1577658679 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1633148023 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1676142056 Apr 01, 2015 (144)
37 EVA_DECODE ss1695879195 Apr 01, 2015 (144)
38 EVA_SVP ss1713495411 Apr 01, 2015 (144)
39 HAMMER_LAB ss1808235972 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1935265355 Feb 12, 2016 (147)
41 JJLAB ss2028412432 Sep 14, 2016 (149)
42 USC_VALOUEV ss2156817169 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2207363454 Dec 20, 2016 (150)
44 TOPMED ss2371787755 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2628701685 Nov 08, 2017 (151)
46 GRF ss2701291245 Nov 08, 2017 (151)
47 ILLUMINA ss2710818274 Nov 08, 2017 (151)
48 GNOMAD ss2935699707 Nov 08, 2017 (151)
49 AFFY ss2985676923 Nov 08, 2017 (151)
50 SWEGEN ss3013395414 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3028030586 Nov 08, 2017 (151)
52 TOPMED ss3229467909 Nov 08, 2017 (151)
53 CSHL ss3351147988 Nov 08, 2017 (151)
54 ILLUMINA ss3627377477 Oct 12, 2018 (152)
55 ILLUMINA ss3638089696 Oct 12, 2018 (152)
56 ILLUMINA ss3639057936 Oct 12, 2018 (152)
57 ILLUMINA ss3639534317 Oct 12, 2018 (152)
58 ILLUMINA ss3643073659 Oct 12, 2018 (152)
59 1000Genomes NC_000015.9 - 61290188 Oct 12, 2018 (152)
60 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 61290188 Oct 12, 2018 (152)
61 Genetic variation in the Estonian population NC_000015.9 - 61290188 Oct 12, 2018 (152)
62 gnomAD - Genomes NC_000015.9 - 61290188 Oct 12, 2018 (152)
63 TopMed NC_000015.10 - 60997989 Oct 12, 2018 (152)
64 UK 10K study - Twins NC_000015.9 - 61290188 Oct 12, 2018 (152)
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)
rs57661312 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss200928354, ss207171214, ss255038387, ss282284479, ss825345569, ss1397699258, ss1695879195, ss1713495411, ss3639057936, ss3639534317, ss3643073659 NC_000015.8:59077479:C= NC_000015.10:60997988:C= (self)
66827048, 37101175, 26279391, 69401233, 37101175, ss226929590, ss236804646, ss243187326, ss536622763, ss564523282, ss660254208, ss991858023, ss1080182318, ss1353745328, ss1427648128, ss1577658679, ss1633148023, ss1676142056, ss1808235972, ss1935265355, ss2028412432, ss2156817169, ss2371787755, ss2628701685, ss2701291245, ss2710818274, ss2935699707, ss2985676923, ss3013395414, ss3351147988, ss3627377477, ss3638089696 NC_000015.9:61290187:C= NC_000015.10:60997988:C= (self)
130980226, ss2207363454, ss3028030586, ss3229467909 NC_000015.10:60997988:C= NC_000015.10:60997988:C= (self)
ss14921271, ss23812237, ss65938654, ss66825280, ss66895203, ss67003734, ss69178566, ss70375958, ss70491236, ss71015816, ss75871696, ss84979977, ss121366444, ss152789301, ss159136032, ss169553291, ss170354979 NT_010194.17:32080744:C= NC_000015.10:60997988:C= (self)
ss200928354, ss207171214, ss255038387, ss282284479, ss825345569, ss1397699258, ss1695879195, ss1713495411, ss3639057936, ss3639534317, ss3643073659 NC_000015.8:59077479:C>T NC_000015.10:60997988:C>T (self)
66827048, 37101175, 26279391, 69401233, 37101175, ss226929590, ss236804646, ss243187326, ss536622763, ss564523282, ss660254208, ss991858023, ss1080182318, ss1353745328, ss1427648128, ss1577658679, ss1633148023, ss1676142056, ss1808235972, ss1935265355, ss2028412432, ss2156817169, ss2371787755, ss2628701685, ss2701291245, ss2710818274, ss2935699707, ss2985676923, ss3013395414, ss3351147988, ss3627377477, ss3638089696 NC_000015.9:61290187:C>T NC_000015.10:60997988:C>T (self)
130980226, ss2207363454, ss3028030586, ss3229467909 NC_000015.10:60997988:C>T NC_000015.10:60997988:C>T (self)
ss14921271, ss23812237, ss65938654, ss66825280, ss66895203, ss67003734, ss69178566, ss70375958, ss70491236, ss71015816, ss75871696, ss84979977, ss121366444, ss152789301, ss159136032, ss169553291, ss170354979 NT_010194.17:32080744:C>T NC_000015.10:60997988: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.

1 citation for rs10519097
PMID Title Author Year Journal
28177907 Genetic variation of clock genes and cancer risk: a field synopsis and meta-analysis. Benna C et al. 2017 Oncotarget

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.post863+3a64c51