Name: rs12910281
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs12910281

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:60903550 (GRCh38.p14) 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>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.439677 (116378/264690, TOPMED)
C=0.455831 (63841/140054, GnomAD)
C=0.45729 (12922/28258, 14KJPN) (+ 15 more)
C=0.43003 (10018/23296, ALFA)
C=0.45853 (7685/16760, 8.3KJPN)
C=0.4366 (2796/6404, 1000G_30x)
C=0.4395 (2201/5008, 1000G)
T=0.4451 (1994/4480, Estonian)
C=0.4935 (1902/3854, ALSPAC)
C=0.4744 (1759/3708, TWINSUK)
C=0.4768 (1397/2930, KOREAN)
C=0.455 (454/998, GoNL)
C=0.457 (274/600, NorthernSweden)
T=0.318 (110/346, SGDP_PRJ)
C=0.412 (89/216, Qatari)
C=0.481 (101/210, Vietnamese)
T=0.28 (14/50, Siberian)
T=0.47 (19/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RORA : Intron Variant
Publications: 1 citation
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	23296	T=0.56997	A=0.00000, C=0.43003
European	Sub	19606	T=0.54111	A=0.00000, C=0.45889
African	Sub	1628	T=0.7598	A=0.0000, C=0.2402
African Others	Sub	62	T=0.68	A=0.00, C=0.32
African American	Sub	1566	T=0.7631	A=0.0000, C=0.2369
Asian	Sub	46	T=0.83	A=0.00, C=0.17
East Asian	Sub	38	T=0.87	A=0.00, C=0.13
Other Asian	Sub	8	T=0.6	A=0.0, C=0.4
Latin American 1	Sub	78	T=0.91	A=0.00, C=0.09
Latin American 2	Sub	346	T=0.916	A=0.000, C=0.084
South Asian	Sub	58	T=0.78	A=0.00, C=0.22
Other	Sub	1534	T=0.6265	A=0.0000, C=0.3735

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	264690	T=0.560323	C=0.439677
gnomAD - Genomes	Global	Study-wide	140054	T=0.544169	C=0.455831
gnomAD - Genomes	European	Sub	75856	T=0.50161	C=0.49839
gnomAD - Genomes	African	Sub	41944	T=0.58948	C=0.41052
gnomAD - Genomes	American	Sub	13650	T=0.62154	C=0.37846
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.6291	C=0.3709
gnomAD - Genomes	East Asian	Sub	3132	T=0.5329	C=0.4671
gnomAD - Genomes	Other	Sub	2150	T=0.5558	C=0.4442
14KJPN	JAPANESE	Study-wide	28258	T=0.54271	C=0.45729
Allele Frequency Aggregator	Total	Global	23296	T=0.56997	A=0.00000, C=0.43003
Allele Frequency Aggregator	European	Sub	19606	T=0.54111	A=0.00000, C=0.45889
Allele Frequency Aggregator	African	Sub	1628	T=0.7598	A=0.0000, C=0.2402
Allele Frequency Aggregator	Other	Sub	1534	T=0.6265	A=0.0000, C=0.3735
Allele Frequency Aggregator	Latin American 2	Sub	346	T=0.916	A=0.000, C=0.084
Allele Frequency Aggregator	Latin American 1	Sub	78	T=0.91	A=0.00, C=0.09
Allele Frequency Aggregator	South Asian	Sub	58	T=0.78	A=0.00, C=0.22
Allele Frequency Aggregator	Asian	Sub	46	T=0.83	A=0.00, C=0.17
8.3KJPN	JAPANESE	Study-wide	16760	T=0.54147	C=0.45853
1000Genomes_30x	Global	Study-wide	6404	T=0.5634	C=0.4366
1000Genomes_30x	African	Sub	1786	T=0.5941	C=0.4059
1000Genomes_30x	Europe	Sub	1266	T=0.5142	C=0.4858
1000Genomes_30x	South Asian	Sub	1202	T=0.5433	C=0.4567
1000Genomes_30x	East Asian	Sub	1170	T=0.5214	C=0.4786
1000Genomes_30x	American	Sub	980	T=0.646	C=0.354
1000Genomes	Global	Study-wide	5008	T=0.5605	C=0.4395
1000Genomes	African	Sub	1322	T=0.5885	C=0.4115
1000Genomes	East Asian	Sub	1008	T=0.5278	C=0.4722
1000Genomes	Europe	Sub	1006	T=0.5169	C=0.4831
1000Genomes	South Asian	Sub	978	T=0.541	C=0.459
1000Genomes	American	Sub	694	T=0.646	C=0.354
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4451	C=0.5549
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5065	C=0.4935
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5256	C=0.4744
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.5229	A=0.0003, C=0.4768
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.545	C=0.455
Northern Sweden	ACPOP	Study-wide	600	T=0.543	C=0.457
SGDP_PRJ	Global	Study-wide	346	T=0.318	C=0.682
Qatari	Global	Study-wide	216	T=0.588	C=0.412
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.519	C=0.481
Siberian	Global	Study-wide	50	T=0.28	C=0.72
The Danish reference pan genome	Danish	Study-wide	40	T=0.47	C=0.53

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.p14 chr 15	NC_000015.10:g.60903550T>A
GRCh38.p14 chr 15	NC_000015.10:g.60903550T>C
GRCh37.p13 chr 15	NC_000015.9:g.61195749T>A
GRCh37.p13 chr 15	NC_000015.9:g.61195749T>C
RORA RefSeqGene	NG_029246.1:g.330754A>T
RORA RefSeqGene	NG_029246.1:g.330754A>G

Gene: RORA, RAR related orphan receptor A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RORA transcript variant 1	NM_134261.3:c.167-224864A… NM_134261.3:c.167-224864A>T	N/A	Intron Variant
RORA transcript variant 3	NM_002943.4:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant 2	NM_134260.3:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant 4	NM_134262.3:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant X4	XM_047432928.1:c.-1751-22… XM_047432928.1:c.-1751-224864A>T	N/A	Intron Variant
RORA transcript variant X1	XM_011521874.2:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant X2	XM_011521875.3:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant X3	XM_011521877.4:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant X7	XM_011521879.4:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant X5	XM_047432929.1:c.	N/A	Genic Upstream Transcript Variant
RORA transcript variant X6	XM_047432930.1:c.	N/A	Genic Upstream Transcript 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

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=	A	C
GRCh38.p14 chr 15	NC_000015.10:g.60903550=	NC_000015.10:g.60903550T>A	NC_000015.10:g.60903550T>C
GRCh37.p13 chr 15	NC_000015.9:g.61195749=	NC_000015.9:g.61195749T>A	NC_000015.9:g.61195749T>C
RORA RefSeqGene	NG_029246.1:g.330754=	NG_029246.1:g.330754A>T	NG_029246.1:g.330754A>G
RORA transcript variant 1	NM_134261.2:c.167-224864=	NM_134261.2:c.167-224864A>T	NM_134261.2:c.167-224864A>G
RORA transcript variant 1	NM_134261.3:c.167-224864=	NM_134261.3:c.167-224864A>T	NM_134261.3:c.167-224864A>G
RORA transcript variant X4	XM_047432928.1:c.-1751-224864=	XM_047432928.1:c.-1751-224864A>T	XM_047432928.1:c.-1751-224864A>G

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#.

84 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21273618	Apr 05, 2004 (121)
2	PERLEGEN	ss24718842	Sep 20, 2004 (123)
3	ABI	ss43773336	Mar 15, 2006 (126)
4	HGSV	ss77209999	Dec 06, 2007 (129)
5	HGSV	ss78104340	Dec 06, 2007 (129)
6	HGSV	ss78642909	Dec 06, 2007 (129)
7	HUMANGENOME_JCVI	ss96816794	Feb 06, 2009 (130)
8	BGI	ss103244980	Dec 01, 2009 (131)
9	1000GENOMES	ss108872642	Jan 23, 2009 (130)
10	ILLUMINA-UK	ss118253584	Feb 14, 2009 (130)
11	ENSEMBL	ss136884396	Dec 01, 2009 (131)
12	GMI	ss156624022	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss168147753	Jul 04, 2010 (132)
14	BUSHMAN	ss200927344	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss207274197	Jul 04, 2010 (132)
16	1000GENOMES	ss211620586	Jul 14, 2010 (132)
17	1000GENOMES	ss226929052	Jul 14, 2010 (132)
18	1000GENOMES	ss236804263	Jul 15, 2010 (132)
19	1000GENOMES	ss243186993	Jul 15, 2010 (132)
20	BL	ss255037486	May 09, 2011 (134)
21	GMI	ss282284096	May 04, 2012 (137)
22	GMI	ss286966199	Apr 25, 2013 (138)
23	PJP	ss291734430	May 09, 2011 (134)
24	ILLUMINA	ss483416663	May 04, 2012 (137)
25	ILLUMINA	ss483596567	May 04, 2012 (137)
26	ILLUMINA	ss535801862	Sep 08, 2015 (146)
27	TISHKOFF	ss564522673	Apr 25, 2013 (138)
28	SSMP	ss660253611	Apr 25, 2013 (138)
29	ILLUMINA	ss780337038	Aug 21, 2014 (142)
30	ILLUMINA	ss782241719	Aug 21, 2014 (142)
31	ILLUMINA	ss835824494	Aug 21, 2014 (142)
32	EVA-GONL	ss991857143	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1080181652	Aug 21, 2014 (142)
34	1000GENOMES	ss1353742357	Aug 21, 2014 (142)
35	DDI	ss1427647724	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1577658078	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1633146321	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1676140354	Apr 01, 2015 (144)
39	EVA_DECODE	ss1695878328	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1808235528	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1935264538	Feb 12, 2016 (147)
42	GENOMED	ss1968125536	Jul 19, 2016 (147)
43	JJLAB	ss2028411950	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2156816681	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2207357322	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2628701384	Nov 08, 2017 (151)
47	ILLUMINA	ss2633238622	Nov 08, 2017 (151)
48	GRF	ss2701290676	Nov 08, 2017 (151)
49	GNOMAD	ss2935691280	Nov 08, 2017 (151)
50	AFFY	ss2985676639	Nov 08, 2017 (151)
51	SWEGEN	ss3013394189	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3028030239	Nov 08, 2017 (151)
53	CSHL	ss3351147522	Nov 08, 2017 (151)
54	ILLUMINA	ss3627377248	Oct 12, 2018 (152)
55	ILLUMINA	ss3631230745	Oct 12, 2018 (152)
56	ILLUMINA	ss3641917308	Oct 12, 2018 (152)
57	URBANLAB	ss3650369854	Oct 12, 2018 (152)
58	EGCUT_WGS	ss3680539920	Jul 13, 2019 (153)
59	EVA_DECODE	ss3698027616	Jul 13, 2019 (153)
60	ACPOP	ss3740984128	Jul 13, 2019 (153)
61	EVA	ss3753171947	Jul 13, 2019 (153)
62	PACBIO	ss3787866956	Jul 13, 2019 (153)
63	PACBIO	ss3792876012	Jul 13, 2019 (153)
64	PACBIO	ss3797760604	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3818489154	Jul 13, 2019 (153)
66	EVA	ss3834270560	Apr 27, 2020 (154)
67	EVA	ss3840733961	Apr 27, 2020 (154)
68	EVA	ss3846223026	Apr 27, 2020 (154)
69	SGDP_PRJ	ss3883062338	Apr 27, 2020 (154)
70	KRGDB	ss3932245697	Apr 27, 2020 (154)
71	TOPMED	ss4993815609	Apr 26, 2021 (155)
72	TOMMO_GENOMICS	ss5216512224	Apr 26, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5298684286	Oct 16, 2022 (156)
74	EVA	ss5315789627	Oct 16, 2022 (156)
75	EVA	ss5419677160	Oct 16, 2022 (156)
76	HUGCELL_USP	ss5492388762	Oct 16, 2022 (156)
77	1000G_HIGH_COVERAGE	ss5600209010	Oct 16, 2022 (156)
78	SANFORD_IMAGENETICS	ss5657649491	Oct 16, 2022 (156)
79	TOMMO_GENOMICS	ss5770409898	Oct 16, 2022 (156)
80	YY_MCH	ss5815395951	Oct 16, 2022 (156)
81	EVA	ss5828295681	Oct 16, 2022 (156)
82	EVA	ss5851322899	Oct 16, 2022 (156)
83	EVA	ss5876157259	Oct 16, 2022 (156)
84	EVA	ss5949056559	Oct 16, 2022 (156)
85	1000Genomes	NC_000015.9 - 61195749	Oct 12, 2018 (152)
86	1000Genomes_30x	NC_000015.10 - 60903550	Oct 16, 2022 (156)
87	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 61195749	Oct 12, 2018 (152)
88	Genetic variation in the Estonian population	NC_000015.9 - 61195749	Oct 12, 2018 (152)
89	The Danish reference pan genome	NC_000015.9 - 61195749	Apr 27, 2020 (154)
90	gnomAD - Genomes	NC_000015.10 - 60903550	Apr 26, 2021 (155)
91	Genome of the Netherlands Release 5	NC_000015.9 - 61195749	Apr 27, 2020 (154)
92	KOREAN population from KRGDB	NC_000015.9 - 61195749	Apr 27, 2020 (154)
93	Northern Sweden	NC_000015.9 - 61195749	Jul 13, 2019 (153)
94	Qatari	NC_000015.9 - 61195749	Apr 27, 2020 (154)
95	SGDP_PRJ	NC_000015.9 - 61195749	Apr 27, 2020 (154)
96	Siberian	NC_000015.9 - 61195749	Apr 27, 2020 (154)
97	8.3KJPN	NC_000015.9 - 61195749	Apr 26, 2021 (155)
98	14KJPN	NC_000015.10 - 60903550	Oct 16, 2022 (156)
99	TopMed	NC_000015.10 - 60903550	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000015.9 - 61195749	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000015.9 - 61195749	Jul 13, 2019 (153)
102	ALFA	NC_000015.10 - 60903550	Apr 26, 2021 (155)

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)
rs17204614	Oct 08, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
39423091, ss3932245697	NC_000015.9:61195748:T:A	NC_000015.10:60903549:T:A	(self)
5343984911	NC_000015.10:60903549:T:A	NC_000015.10:60903549:T:A	(self)
ss77209999, ss78104340, ss78642909, ss108872642, ss118253584, ss168147753, ss200927344, ss207274197, ss211620586, ss255037486, ss282284096, ss286966199, ss291734430, ss483416663, ss1695878328	NC_000015.8:58983040:T:C	NC_000015.10:60903549:T:C	(self)
66824000, 37099328, 26278168, 3885850, 16563770, 39423091, 14268993, 17306468, 35079318, 9333035, 74481531, 37099328, 8254699, ss226929052, ss236804263, ss243186993, ss483596567, ss535801862, ss564522673, ss660253611, ss780337038, ss782241719, ss835824494, ss991857143, ss1080181652, ss1353742357, ss1427647724, ss1577658078, ss1633146321, ss1676140354, ss1808235528, ss1935264538, ss1968125536, ss2028411950, ss2156816681, ss2628701384, ss2633238622, ss2701290676, ss2935691280, ss2985676639, ss3013394189, ss3351147522, ss3627377248, ss3631230745, ss3641917308, ss3680539920, ss3740984128, ss3753171947, ss3787866956, ss3792876012, ss3797760604, ss3834270560, ss3840733961, ss3883062338, ss3932245697, ss5216512224, ss5315789627, ss5419677160, ss5657649491, ss5828295681, ss5949056559	NC_000015.9:61195748:T:C	NC_000015.10:60903549:T:C	(self)
87734945, 471086393, 104247002, 209361269, 5343984911, ss2207357322, ss3028030239, ss3650369854, ss3698027616, ss3818489154, ss3846223026, ss4993815609, ss5298684286, ss5492388762, ss5600209010, ss5770409898, ss5815395951, ss5851322899, ss5876157259	NC_000015.10:60903549:T:C	NC_000015.10:60903549:T:C	(self)
ss21273618	NT_010194.16:31986305:T:C	NC_000015.10:60903549:T:C	(self)
ss24718842, ss43773336, ss96816794, ss103244980, ss136884396, ss156624022	NT_010194.17:31986305:T:C	NC_000015.10:60903549:T:C	(self)

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

1 citation for rs12910281

PMID	Title	Author	Year	Journal
25789810	Investigation of associations between NR1D1, RORA and RORB genes and bipolar disorder.	Lai YC et al.	2015	PloS one

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12910281