Name: rs1176169
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.

rs1176169

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:247617711 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.304535 (40410/132694, GnomAD)
C=0.26208 (7396/28220, 14KJPN)
C=0.25630 (4295/16758, 8.3KJPN) (+ 9 more)
C=0.33281 (3591/10790, ALFA)
C=0.2458 (1231/5008, 1000G)
C=0.2290 (671/2930, KOREAN)
C=0.363 (362/998, GoNL)
C=0.358 (215/600, NorthernSweden)
C=0.208 (108/518, SGDP_PRJ)
C=0.458 (99/216, Qatari)
C=0.19 (8/42, Siberian)
C=0.47 (19/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: OR14L1P : Intron Variant
LOC102724446 : Intron Variant
Publications: 0 citations
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	10790	C=0.33281	A=0.00000, T=0.66719
European	Sub	7040	C=0.3646	A=0.0000, T=0.6354
African	Sub	2326	C=0.2670	A=0.0000, T=0.7330
African Others	Sub	84	C=0.23	A=0.00, T=0.77
African American	Sub	2242	C=0.2685	A=0.0000, T=0.7315
Asian	Sub	108	C=0.250	A=0.000, T=0.750
East Asian	Sub	84	C=0.25	A=0.00, T=0.75
Other Asian	Sub	24	C=0.25	A=0.00, T=0.75
Latin American 1	Sub	146	C=0.308	A=0.000, T=0.692
Latin American 2	Sub	610	C=0.279	A=0.000, T=0.721
South Asian	Sub	94	C=0.32	A=0.00, T=0.68
Other	Sub	466	C=0.281	A=0.000, T=0.719

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
gnomAD - Genomes	Global	Study-wide	132694	C=0.304535	T=0.695465
gnomAD - Genomes	European	Sub	72874	C=0.34903	T=0.65097
gnomAD - Genomes	African	Sub	38410	C=0.22137	T=0.77863
gnomAD - Genomes	American	Sub	13098	C=0.31150	T=0.68850
gnomAD - Genomes	Ashkenazi Jewish	Sub	3228	C=0.3683	T=0.6317
gnomAD - Genomes	East Asian	Sub	3054	C=0.1902	T=0.8098
gnomAD - Genomes	Other	Sub	2030	C=0.3064	T=0.6936
14KJPN	JAPANESE	Study-wide	28220	C=0.26208	T=0.73792
8.3KJPN	JAPANESE	Study-wide	16758	C=0.25630	T=0.74370
Allele Frequency Aggregator	Total	Global	10790	C=0.33281	A=0.00000, T=0.66719
Allele Frequency Aggregator	European	Sub	7040	C=0.3646	A=0.0000, T=0.6354
Allele Frequency Aggregator	African	Sub	2326	C=0.2670	A=0.0000, T=0.7330
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.279	A=0.000, T=0.721
Allele Frequency Aggregator	Other	Sub	466	C=0.281	A=0.000, T=0.719
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.308	A=0.000, T=0.692
Allele Frequency Aggregator	Asian	Sub	108	C=0.250	A=0.000, T=0.750
Allele Frequency Aggregator	South Asian	Sub	94	C=0.32	A=0.00, T=0.68
1000Genomes	Global	Study-wide	5008	C=0.2458	T=0.7542
1000Genomes	African	Sub	1322	C=0.0809	T=0.9191
1000Genomes	East Asian	Sub	1008	C=0.2262	T=0.7738
1000Genomes	Europe	Sub	1006	C=0.3380	T=0.6620
1000Genomes	South Asian	Sub	978	C=0.367	T=0.633
1000Genomes	American	Sub	694	C=0.284	T=0.716
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2290	T=0.7710
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.363	T=0.637
Northern Sweden	ACPOP	Study-wide	600	C=0.358	T=0.642
SGDP_PRJ	Global	Study-wide	518	C=0.208	T=0.792
Qatari	Global	Study-wide	216	C=0.458	T=0.542
Siberian	Global	Study-wide	42	C=0.19	T=0.81
The Danish reference pan genome	Danish	Study-wide	40	C=0.47	T=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 1	NC_000001.11:g.247617711C>A
GRCh38.p14 chr 1	NC_000001.11:g.247617711C>T
GRCh37.p13 chr 1	NC_000001.10:g.247781013C>A
GRCh37.p13 chr 1	NC_000001.10:g.247781013C>T

Gene: OR14L1P, olfactory receptor family 14 subfamily L member 1 pseudogene (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OR14L1 transcript	NM_001396106.1:c.37+311C>A	N/A	Intron Variant

Gene: LOC102724446, uncharacterized LOC102724446 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102724446 transcript	XR_426948.4:n.	N/A	Intron 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	C=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.247617711=	NC_000001.11:g.247617711C>A	NC_000001.11:g.247617711C>T
GRCh37.p13 chr 1	NC_000001.10:g.247781013=	NC_000001.10:g.247781013C>A	NC_000001.10:g.247781013C>T
OR14L1 transcript	NM_001396106.1:c.37+311=	NM_001396106.1:c.37+311C>A	NM_001396106.1:c.37+311C>T

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#.

49 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1620422	Oct 18, 2000 (87)
2	KWOK	ss1620738	Oct 18, 2000 (123)
3	TSC-CSHL	ss2089188	Oct 23, 2000 (88)
4	WI_SSAHASNP	ss6810032	Feb 20, 2003 (111)
5	ABI	ss41071151	Mar 14, 2006 (126)
6	HGSV	ss84155015	Dec 15, 2007 (130)
7	HGSV	ss86083514	Dec 15, 2007 (130)
8	HGSV	ss86086190	Dec 15, 2007 (130)
9	HUMANGENOME_JCVI	ss98020328	Feb 13, 2009 (131)
10	BGI	ss102843113	Feb 23, 2009 (131)
11	1000GENOMES	ss109138065	Jan 23, 2009 (130)
12	ILLUMINA-UK	ss119288436	Feb 15, 2009 (130)
13	ENSEMBL	ss138997296	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss165640345	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss165962779	Jul 04, 2010 (132)
16	BUSHMAN	ss199906237	Jul 04, 2010 (132)
17	BL	ss253949926	May 09, 2011 (134)
18	GMI	ss276311254	May 04, 2012 (137)
19	PJP	ss290789848	May 09, 2011 (134)
20	1000GENOMES	ss329364739	May 09, 2011 (134)
21	EVA-GONL	ss976385472	Aug 21, 2014 (142)
22	1000GENOMES	ss1295534474	Aug 21, 2014 (142)
23	EVA_GENOME_DK	ss1574834197	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1796089570	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1919609742	Feb 12, 2016 (147)
26	JJLAB	ss2020333234	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2148372943	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2171872713	Dec 20, 2016 (150)
29	GRF	ss2698380452	Nov 08, 2017 (151)
30	CSHL	ss3344023820	Nov 08, 2017 (151)
31	URBANLAB	ss3646940303	Oct 11, 2018 (152)
32	ACPOP	ss3728066524	Jul 12, 2019 (153)
33	EVA	ss3747615508	Jul 12, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3800619811	Jul 12, 2019 (153)
35	EVA	ss3826766984	Apr 25, 2020 (154)
36	EVA	ss3836787488	Apr 25, 2020 (154)
37	EVA	ss3842200902	Apr 25, 2020 (154)
38	SGDP_PRJ	ss3851373959	Apr 25, 2020 (154)
39	KRGDB	ss3896743683	Apr 25, 2020 (154)
40	GNOMAD	ss4015045068	Apr 25, 2021 (155)
41	TOMMO_GENOMICS	ss5149447875	Apr 25, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5246578702	Oct 12, 2022 (156)
43	HUGCELL_USP	ss5446935634	Oct 12, 2022 (156)
44	EVA	ss5506265174	Oct 12, 2022 (156)
45	TOMMO_GENOMICS	ss5677502511	Oct 12, 2022 (156)
46	YY_MCH	ss5801842343	Oct 12, 2022 (156)
47	EVA	ss5849389214	Oct 12, 2022 (156)
48	EVA	ss5912858901	Oct 12, 2022 (156)
49	EVA	ss5939747057	Oct 12, 2022 (156)
50	1000Genomes	NC_000001.10 - 247781013	Oct 11, 2018 (152)
51	The Danish reference pan genome	NC_000001.10 - 247781013	Apr 25, 2020 (154)
52	gnomAD - Genomes	NC_000001.11 - 247617711	Apr 25, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000001.10 - 247781013	Apr 25, 2020 (154)
54	KOREAN population from KRGDB	NC_000001.10 - 247781013	Apr 25, 2020 (154)
55	Northern Sweden	NC_000001.10 - 247781013	Jul 12, 2019 (153)
56	Qatari	NC_000001.10 - 247781013	Apr 25, 2020 (154)
57	SGDP_PRJ	NC_000001.10 - 247781013	Apr 25, 2020 (154)
58	Siberian	NC_000001.10 - 247781013	Apr 25, 2020 (154)
59	8.3KJPN	NC_000001.10 - 247781013	Apr 25, 2021 (155)
60	14KJPN	NC_000001.11 - 247617711	Oct 12, 2022 (156)
61	ALFA	NC_000001.11 - 247617711	Apr 25, 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)
rs1306164	Sep 24, 2004 (123)
rs60176394	May 25, 2008 (130)
rs71535205	Dec 02, 2009 (131)
rs74227712	Dec 02, 2009 (131)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
5654956759	NC_000001.11:247617710:C:A	NC_000001.11:247617710:C:A	(self)
ss84155015, ss86083514, ss86086190	NC_000001.8:244107053:C:T	NC_000001.11:247617710:C:T	(self)
ss109138065, ss119288436, ss165640345, ss165962779, ss199906237, ss253949926, ss276311254, ss290789848	NC_000001.9:245847635:C:T	NC_000001.11:247617710:C:T	(self)
6422439, 1983153, 1561556, 3921077, 1351389, 1651672, 3390939, 889297, 7417182, ss329364739, ss976385472, ss1295534474, ss1574834197, ss1796089570, ss1919609742, ss2020333234, ss2148372943, ss2698380452, ss3344023820, ss3728066524, ss3747615508, ss3826766984, ss3836787488, ss3851373959, ss3896743683, ss5149447875, ss5506265174, ss5939747057	NC_000001.10:247781012:C:T	NC_000001.11:247617710:C:T	(self)
45869676, 11339615, 5654956759, ss2171872713, ss3646940303, ss3800619811, ss3842200902, ss4015045068, ss5246578702, ss5446935634, ss5677502511, ss5801842343, ss5849389214, ss5912858901	NC_000001.11:247617710:C:T	NC_000001.11:247617710:C:T	(self)
ss1620422, ss1620738, ss2089188, ss6810032, ss41071151, ss98020328, ss102843113, ss138997296	NT_167186.1:41298791:C:T	NC_000001.11:247617710:C:T	(self)

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

No publications for rs1176169

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1176169