Name: rs74944517
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.

rs74944517

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:52527060 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.130986 (16465/125700, GnomAD)
T=0.38694 (7560/19538, 14KJPN)
T=0.11415 (1354/11862, ALFA) (+ 12 more)
T=0.38101 (4403/11556, 8.3KJPN)
T=0.2074 (1328/6404, 1000G_30x)
T=0.1803 (903/5008, 1000G)
T=0.3029 (593/1958, KOREAN)
T=0.2951 (360/1220, Korea1K)
T=0.031 (31/998, GoNL)
T=0.063 (32/510, NorthernSweden)
T=0.158 (32/202, Qatari)
T=0.307 (51/166, Vietnamese)
C=0.340 (53/156, SGDP_PRJ)
T=0.06 (2/34, GENOME_DK)
C=0.2 (1/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	11862	C=0.88585	T=0.11415	0.819255	0.047547	0.133198	32
European	Sub	7618	C=0.9491	T=0.0509	0.923602	0.025466	0.050932	32
African	Sub	2816	C=0.7791	T=0.2209	0.62571	0.067472	0.306818	9
African Others	Sub	108	C=0.759	T=0.241	0.592593	0.074074	0.333333	0
African American	Sub	2708	C=0.7799	T=0.2201	0.627031	0.067208	0.305761	9
Asian	Sub	108	C=0.731	T=0.269	0.62963	0.166667	0.203704	7
East Asian	Sub	84	C=0.79	T=0.21	0.690476	0.119048	0.190476	5
Other Asian	Sub	24	C=0.54	T=0.46	0.416667	0.333333	0.25	2
Latin American 1	Sub	146	C=0.788	T=0.212	0.684932	0.109589	0.205479	6
Latin American 2	Sub	610	C=0.695	T=0.305	0.544262	0.154098	0.301639	14
South Asian	Sub	94	C=0.84	T=0.16	0.808511	0.12766	0.06383	15
Other	Sub	470	C=0.823	T=0.177	0.731915	0.085106	0.182979	18

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	125700	C=0.869014	T=0.130986
gnomAD - Genomes	European	Sub	65986	C=0.94349	T=0.05651
gnomAD - Genomes	African	Sub	40554	C=0.78399	T=0.21601
gnomAD - Genomes	American	Sub	12208	C=0.75762	T=0.24238
gnomAD - Genomes	Ashkenazi Jewish	Sub	2932	C=0.9608	T=0.0392
gnomAD - Genomes	East Asian	Sub	2118	C=0.7210	T=0.2790
gnomAD - Genomes	Other	Sub	1902	C=0.8365	T=0.1635
14KJPN	JAPANESE	Study-wide	19538	C=0.61306	T=0.38694
Allele Frequency Aggregator	Total	Global	11862	C=0.88585	T=0.11415
Allele Frequency Aggregator	European	Sub	7618	C=0.9491	T=0.0509
Allele Frequency Aggregator	African	Sub	2816	C=0.7791	T=0.2209
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.695	T=0.305
Allele Frequency Aggregator	Other	Sub	470	C=0.823	T=0.177
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.788	T=0.212
Allele Frequency Aggregator	Asian	Sub	108	C=0.731	T=0.269
Allele Frequency Aggregator	South Asian	Sub	94	C=0.84	T=0.16
8.3KJPN	JAPANESE	Study-wide	11556	C=0.61899	T=0.38101
1000Genomes_30x	Global	Study-wide	6404	C=0.7926	T=0.2074
1000Genomes_30x	African	Sub	1786	C=0.7693	T=0.2307
1000Genomes_30x	Europe	Sub	1266	C=0.9352	T=0.0648
1000Genomes_30x	South Asian	Sub	1202	C=0.8361	T=0.1639
1000Genomes_30x	East Asian	Sub	1170	C=0.6718	T=0.3282
1000Genomes_30x	American	Sub	980	C=0.742	T=0.258
1000Genomes	Global	Study-wide	5008	C=0.8197	T=0.1803
1000Genomes	African	Sub	1322	C=0.7678	T=0.2322
1000Genomes	East Asian	Sub	1008	C=0.7708	T=0.2292
1000Genomes	Europe	Sub	1006	C=0.9423	T=0.0577
1000Genomes	South Asian	Sub	978	C=0.857	T=0.143
1000Genomes	American	Sub	694	C=0.759	T=0.241
KOREAN population from KRGDB	KOREAN	Study-wide	1958	C=0.6971	T=0.3029
Korean Genome Project	KOREAN	Study-wide	1220	C=0.7049	T=0.2951
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.969	T=0.031
Northern Sweden	ACPOP	Study-wide	510	C=0.937	T=0.063
Qatari	Global	Study-wide	202	C=0.842	T=0.158
A Vietnamese Genetic Variation Database	Global	Study-wide	166	C=0.693	T=0.307
SGDP_PRJ	Global	Study-wide	156	C=0.340	T=0.660
The Danish reference pan genome	Danish	Study-wide	34	C=0.94	T=0.06
Siberian	Global	Study-wide	4	C=0.2	T=0.8

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 2	NC_000002.12:g.52527060C>T
GRCh37.p13 chr 2	NC_000002.11:g.52754198C>T

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=	T
GRCh38.p14 chr 2	NC_000002.12:g.52527060=	NC_000002.12:g.52527060C>T
GRCh37.p13 chr 2	NC_000002.11:g.52754198=	NC_000002.11:g.52754198C>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#.

43 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	COMPLETE_GENOMICS	ss163446532	Jul 04, 2010 (132)
2	BUSHMAN	ss200445056	Jul 04, 2010 (132)
3	1000GENOMES	ss210895734	Jul 14, 2010 (132)
4	1000GENOMES	ss219248163	Jul 14, 2010 (132)
5	1000GENOMES	ss231169803	Jul 14, 2010 (132)
6	GMI	ss276470375	May 04, 2012 (137)
7	TISHKOFF	ss555566754	Apr 25, 2013 (138)
8	EVA-GONL	ss976830833	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1069117071	Aug 21, 2014 (142)
10	1000GENOMES	ss1297224688	Aug 21, 2014 (142)
11	DDI	ss1428577458	Apr 01, 2015 (144)
12	EVA_GENOME_DK	ss1578879409	Apr 01, 2015 (144)
13	HAMMER_LAB	ss1796755988	Sep 08, 2015 (146)
14	WEILL_CORNELL_DGM	ss1920065375	Feb 12, 2016 (147)
15	GENOMED	ss1968770907	Jul 19, 2016 (147)
16	JJLAB	ss2020566814	Sep 14, 2016 (149)
17	USC_VALOUEV	ss2148610160	Dec 20, 2016 (150)
18	SYSTEMSBIOZJU	ss2624794481	Nov 08, 2017 (151)
19	GRF	ss2703177157	Nov 08, 2017 (151)
20	GNOMAD	ss2773428510	Nov 08, 2017 (151)
21	SWEGEN	ss2989498678	Nov 08, 2017 (151)
22	EVA_DECODE	ss3703884263	Jul 13, 2019 (153)
23	ACPOP	ss3728431855	Jul 13, 2019 (153)
24	EVA	ss3756756484	Jul 13, 2019 (153)
25	PACBIO	ss3783863101	Jul 13, 2019 (153)
26	PACBIO	ss3789450966	Jul 13, 2019 (153)
27	PACBIO	ss3794323829	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3801129265	Jul 13, 2019 (153)
29	EVA	ss3826981675	Apr 25, 2020 (154)
30	SGDP_PRJ	ss3852262755	Apr 25, 2020 (154)
31	KRGDB	ss3897725814	Apr 25, 2020 (154)
32	KOGIC	ss3947744244	Apr 25, 2020 (154)
33	TOMMO_GENOMICS	ss5151341153	Apr 26, 2021 (155)
34	EVA	ss5328906773	Oct 12, 2022 (156)
35	HUGCELL_USP	ss5448254042	Oct 12, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5523257552	Oct 12, 2022 (156)
37	SANFORD_IMAGENETICS	ss5628733742	Oct 12, 2022 (156)
38	TOMMO_GENOMICS	ss5679958044	Oct 12, 2022 (156)
39	YY_MCH	ss5802200900	Oct 12, 2022 (156)
40	EVA	ss5820092115	Oct 12, 2022 (156)
41	EVA	ss5852521333	Oct 12, 2022 (156)
42	EVA	ss5930348278	Oct 12, 2022 (156)
43	EVA	ss5954962999	Oct 12, 2022 (156)
44	1000Genomes	NC_000002.11 - 52754198	Oct 11, 2018 (152)
45	1000Genomes_30x	NC_000002.12 - 52527060	Oct 12, 2022 (156)
46	The Danish reference pan genome	NC_000002.11 - 52754198	Apr 25, 2020 (154)
47	gnomAD - Genomes	NC_000002.12 - 52527060	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000002.11 - 52754198	Apr 25, 2020 (154)
49	KOREAN population from KRGDB	NC_000002.11 - 52754198	Apr 25, 2020 (154)
50	Korean Genome Project	NC_000002.12 - 52527060	Apr 25, 2020 (154)
51	Northern Sweden	NC_000002.11 - 52754198	Jul 13, 2019 (153)
52	Qatari	NC_000002.11 - 52754198	Apr 25, 2020 (154)
53	SGDP_PRJ	NC_000002.11 - 52754198	Apr 25, 2020 (154)
54	Siberian	NC_000002.11 - 52754198	Apr 25, 2020 (154)
55	8.3KJPN	NC_000002.11 - 52754198	Apr 26, 2021 (155)
56	14KJPN	NC_000002.12 - 52527060	Oct 12, 2022 (156)
57	A Vietnamese Genetic Variation Database	NC_000002.11 - 52754198	Jul 13, 2019 (153)
58	ALFA	NC_000002.12 - 52527060	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss163446532, ss200445056, ss210895734, ss276470375	NC_000002.10:52607701:C:T	NC_000002.12:52527059:C:T	(self)
8168597, 5051859, 1994893, 4903208, 1716720, 2107305, 4279735, 1126514, 9310460, 987038, ss219248163, ss231169803, ss555566754, ss976830833, ss1069117071, ss1297224688, ss1428577458, ss1578879409, ss1796755988, ss1920065375, ss1968770907, ss2020566814, ss2148610160, ss2624794481, ss2703177157, ss2773428510, ss2989498678, ss3728431855, ss3756756484, ss3783863101, ss3789450966, ss3794323829, ss3826981675, ss3852262755, ss3897725814, ss5151341153, ss5328906773, ss5628733742, ss5820092115, ss5954962999	NC_000002.11:52754197:C:T	NC_000002.12:52527059:C:T	(self)
10783487, 57976547, 4122245, 13795148, 5490646867, ss3703884263, ss3801129265, ss3947744244, ss5448254042, ss5523257552, ss5679958044, ss5802200900, ss5852521333, ss5930348278	NC_000002.12:52527059:C:T	NC_000002.12:52527059:C:T	(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 rs74944517

PMID	Title	Author	Year	Journal
27928975	Assessing causality in associations between cannabis use and schizophrenia risk: a two-sample Mendelian randomization study.	Gage SH et al.	2017	Psychological medicine

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

rs74944517