Name: rs604381
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.

rs604381

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:37749874 (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: G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.400450 (105995/264690, TOPMED)
T=0.03549 (1003/28258, 14KJPN)
T=0.03735 (626/16760, 8.3KJPN) (+ 11 more)
T=0.28208 (3464/12280, ALFA)
T=0.3943 (2525/6404, 1000G_30x)
T=0.3854 (1930/5008, 1000G)
T=0.3212 (941/2930, KOREAN)
T=0.328 (247/752, PRJEB37584)
G=0.358 (116/324, SGDP_PRJ)
T=0.409 (130/318, HapMap)
T=0.491 (106/216, Qatari)
T=0.315 (68/216, Vietnamese)
G=0.35 (24/68, Ancient Sardinia)
G=0.48 (23/48, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC107985869 : 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	12280	G=0.71792	C=0.00000, T=0.28208
European	Sub	10606	G=0.70743	C=0.00000, T=0.29257
African	Sub	942	G=0.632	C=0.000, T=0.368
African Others	Sub	40	G=0.50	C=0.00, T=0.50
African American	Sub	902	G=0.637	C=0.000, T=0.363
Asian	Sub	94	G=1.00	C=0.00, T=0.00
East Asian	Sub	68	G=1.00	C=0.00, T=0.00
Other Asian	Sub	26	G=1.00	C=0.00, T=0.00
Latin American 1	Sub	32	G=1.00	C=0.00, T=0.00
Latin American 2	Sub	336	G=1.000	C=0.000, T=0.000
South Asian	Sub	42	G=0.98	C=0.00, T=0.02
Other	Sub	228	G=0.943	C=0.000, T=0.057

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
TopMed	Global	Study-wide	264690	G=0.599550	T=0.400450
14KJPN	JAPANESE	Study-wide	28258	G=0.96451	T=0.03549
8.3KJPN	JAPANESE	Study-wide	16760	G=0.96265	T=0.03735
Allele Frequency Aggregator	Total	Global	12280	G=0.71792	C=0.00000, T=0.28208
Allele Frequency Aggregator	European	Sub	10606	G=0.70743	C=0.00000, T=0.29257
Allele Frequency Aggregator	African	Sub	942	G=0.632	C=0.000, T=0.368
Allele Frequency Aggregator	Latin American 2	Sub	336	G=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	228	G=0.943	C=0.000, T=0.057
Allele Frequency Aggregator	Asian	Sub	94	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	42	G=0.98	C=0.00, T=0.02
Allele Frequency Aggregator	Latin American 1	Sub	32	G=1.00	C=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.6057	T=0.3943
1000Genomes_30x	African	Sub	1786	G=0.3253	T=0.6747
1000Genomes_30x	Europe	Sub	1266	G=0.7046	T=0.2954
1000Genomes_30x	South Asian	Sub	1202	G=0.5624	T=0.4376
1000Genomes_30x	East Asian	Sub	1170	G=0.9436	T=0.0564
1000Genomes_30x	American	Sub	980	G=0.639	T=0.361
1000Genomes	Global	Study-wide	5008	G=0.6146	T=0.3854
1000Genomes	African	Sub	1322	G=0.3306	T=0.6694
1000Genomes	East Asian	Sub	1008	G=0.9405	T=0.0595
1000Genomes	Europe	Sub	1006	G=0.7078	T=0.2922
1000Genomes	South Asian	Sub	978	G=0.555	T=0.445
1000Genomes	American	Sub	694	G=0.631	T=0.369
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.6788	T=0.3212
CNV burdens in cranial meningiomas	Global	Study-wide	752	G=0.672	T=0.328
CNV burdens in cranial meningiomas	CRM	Sub	752	G=0.672	T=0.328
SGDP_PRJ	Global	Study-wide	324	G=0.358	T=0.642
HapMap	Global	Study-wide	318	G=0.591	T=0.409
HapMap	African	Sub	120	G=0.267	T=0.733
HapMap	American	Sub	108	G=0.657	T=0.343
HapMap	Asian	Sub	90	G=0.94	T=0.06
Qatari	Global	Study-wide	216	G=0.509	T=0.491
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.685	T=0.315
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	68	G=0.35	T=0.65
Siberian	Global	Study-wide	48	G=0.48	T=0.52

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.37749874G>C
GRCh38.p14 chr 2	NC_000002.12:g.37749874G>T
GRCh37.p13 chr 2	NC_000002.11:g.37977017G>C
GRCh37.p13 chr 2	NC_000002.11:g.37977017G>T

Gene: LOC107985869, uncharacterized LOC107985869 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985869 transcript	XR_001739409.2: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	G=	C	T
GRCh38.p14 chr 2	NC_000002.12:g.37749874=	NC_000002.12:g.37749874G>C	NC_000002.12:g.37749874G>T
GRCh37.p13 chr 2	NC_000002.11:g.37977017=	NC_000002.11:g.37977017G>C	NC_000002.11:g.37977017G>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#.

71 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss776421	Aug 11, 2000 (83)
2	KWOK	ss1008387	Oct 05, 2000 (89)
3	KWOK	ss1845791	Oct 18, 2000 (89)
4	ABI	ss41694996	Mar 14, 2006 (126)
5	PERLEGEN	ss68810211	May 16, 2007 (127)
6	HGSV	ss85137431	Dec 15, 2007 (130)
7	BCMHGSC_JDW	ss91124938	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss97029117	Feb 05, 2009 (130)
9	BGI	ss103475960	Dec 01, 2009 (131)
10	1000GENOMES	ss110103437	Jan 24, 2009 (130)
11	ENSEMBL	ss138424347	Dec 01, 2009 (131)
12	ENSEMBL	ss143640769	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss163319100	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss164186128	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166440396	Jul 04, 2010 (132)
16	BUSHMAN	ss200295770	Jul 04, 2010 (132)
17	BCM-HGSC-SUB	ss205605152	Jul 04, 2010 (132)
18	BL	ss253041434	May 09, 2011 (134)
19	GMI	ss276424977	May 04, 2012 (137)
20	GMI	ss284326212	Apr 25, 2013 (138)
21	PJP	ss292547781	May 09, 2011 (134)
22	EXOME_CHIP	ss491317820	May 04, 2012 (137)
23	TISHKOFF	ss555484468	Apr 25, 2013 (138)
24	SSMP	ss649069791	Apr 25, 2013 (138)
25	1000GENOMES	ss1296722785	Aug 21, 2014 (142)
26	DDI	ss1428541750	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1796579658	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1919935220	Feb 12, 2016 (147)
29	ILLUMINA	ss1958408012	Feb 12, 2016 (147)
30	GENOMED	ss1968741952	Jul 19, 2016 (147)
31	JJLAB	ss2020499180	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2148543221	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2624762639	Nov 08, 2017 (151)
34	ILLUMINA	ss2633598333	Nov 08, 2017 (151)
35	ILLUMINA	ss2633598334	Nov 08, 2017 (151)
36	GRF	ss2703105392	Nov 08, 2017 (151)
37	GNOMAD	ss2772015140	Nov 08, 2017 (151)
38	AFFY	ss2985164925	Nov 08, 2017 (151)
39	SWEGEN	ss2989305248	Nov 08, 2017 (151)
40	ILLUMINA	ss3021960586	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3024015528	Nov 08, 2017 (151)
42	CSHL	ss3344171372	Nov 08, 2017 (151)
43	URBANLAB	ss3647008876	Oct 11, 2018 (152)
44	ILLUMINA	ss3652390536	Oct 11, 2018 (152)
45	ILLUMINA	ss3653935819	Oct 11, 2018 (152)
46	EVA_DECODE	ss3703647633	Jul 13, 2019 (153)
47	ILLUMINA	ss3744474208	Jul 13, 2019 (153)
48	EVA	ss3756604659	Jul 13, 2019 (153)
49	PACBIO	ss3783832899	Jul 13, 2019 (153)
50	PACBIO	ss3789425674	Jul 13, 2019 (153)
51	PACBIO	ss3794298485	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3800982931	Jul 13, 2019 (153)
53	EVA	ss3826922276	Apr 25, 2020 (154)
54	EVA	ss3842284726	Apr 25, 2020 (154)
55	SGDP_PRJ	ss3852010900	Apr 25, 2020 (154)
56	KRGDB	ss3897442059	Apr 25, 2020 (154)
57	EVA	ss3984480683	Apr 26, 2021 (155)
58	EVA	ss3984885786	Apr 26, 2021 (155)
59	TOPMED	ss4501158367	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5150780616	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5247619890	Oct 13, 2022 (156)
62	EVA	ss5328111267	Oct 13, 2022 (156)
63	HUGCELL_USP	ss5447863680	Oct 13, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5522601570	Oct 13, 2022 (156)
65	SANFORD_IMAGENETICS	ss5624441988	Oct 13, 2022 (156)
66	SANFORD_IMAGENETICS	ss5628494803	Oct 13, 2022 (156)
67	TOMMO_GENOMICS	ss5679236431	Oct 13, 2022 (156)
68	YY_MCH	ss5802097857	Oct 13, 2022 (156)
69	EVA	ss5819930239	Oct 13, 2022 (156)
70	EVA	ss5852473141	Oct 13, 2022 (156)
71	EVA	ss5929847126	Oct 13, 2022 (156)
72	1000Genomes	NC_000002.11 - 37977017	Oct 11, 2018 (152)
73	1000Genomes_30x	NC_000002.12 - 37749874	Oct 13, 2022 (156)
74	gnomAD - Genomes Submission ignored due to conflicting rows: Row 54307667 (NC_000002.12:37749873:G:C 1/140034) Row 54307668 (NC_000002.12:37749873:G:T 55531/139970)	-	Apr 26, 2021 (155)
75	gnomAD - Genomes Submission ignored due to conflicting rows: Row 54307667 (NC_000002.12:37749873:G:C 1/140034) Row 54307668 (NC_000002.12:37749873:G:T 55531/139970)	-	Apr 26, 2021 (155)
76	HapMap	NC_000002.12 - 37749874	Apr 25, 2020 (154)
77	KOREAN population from KRGDB	NC_000002.11 - 37977017	Apr 25, 2020 (154)
78	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000002.11 - 37977017	Apr 26, 2021 (155)
79	CNV burdens in cranial meningiomas	NC_000002.11 - 37977017	Apr 26, 2021 (155)
80	Qatari	NC_000002.11 - 37977017	Apr 25, 2020 (154)
81	SGDP_PRJ	NC_000002.11 - 37977017	Apr 25, 2020 (154)
82	Siberian	NC_000002.11 - 37977017	Apr 25, 2020 (154)
83	8.3KJPN	NC_000002.11 - 37977017	Apr 26, 2021 (155)
84	14KJPN	NC_000002.12 - 37749874	Oct 13, 2022 (156)
85	TopMed	NC_000002.12 - 37749874	Apr 26, 2021 (155)
86	A Vietnamese Genetic Variation Database	NC_000002.11 - 37977017	Jul 13, 2019 (153)
87	ALFA	NC_000002.12 - 37749874	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)
rs800631	Nov 09, 2000 (89)
rs1234172	Nov 09, 2000 (89)
rs58972510	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
9957783720	NC_000002.12:37749873:G:C	NC_000002.12:37749873:G:C	(self)
ss85137431	NC_000002.9:37888667:G:T	NC_000002.12:37749873:G:T	(self)
ss91124938, ss110103437, ss163319100, ss164186128, ss166440396, ss200295770, ss205605152, ss253041434, ss276424977, ss284326212, ss292547781	NC_000002.10:37830520:G:T	NC_000002.12:37749873:G:T	(self)
7652053, 4619453, 111713, 30009, 1977150, 4027880, 1059575, 8749923, 925338, ss491317820, ss555484468, ss649069791, ss1296722785, ss1428541750, ss1796579658, ss1919935220, ss1958408012, ss1968741952, ss2020499180, ss2148543221, ss2624762639, ss2633598333, ss2633598334, ss2703105392, ss2772015140, ss2985164925, ss2989305248, ss3021960586, ss3344171372, ss3652390536, ss3653935819, ss3744474208, ss3756604659, ss3783832899, ss3789425674, ss3794298485, ss3826922276, ss3852010900, ss3897442059, ss3984480683, ss3984885786, ss5150780616, ss5328111267, ss5624441988, ss5628494803, ss5819930239	NC_000002.11:37977016:G:T	NC_000002.12:37749873:G:T	(self)
10127505, 1774508, 13073535, 304981246, 9957783720, ss3024015528, ss3647008876, ss3703647633, ss3800982931, ss3842284726, ss4501158367, ss5247619890, ss5447863680, ss5522601570, ss5679236431, ss5802097857, ss5852473141, ss5929847126	NC_000002.12:37749873:G:T	NC_000002.12:37749873:G:T	(self)
ss776421, ss1008387, ss1845791, ss41694996, ss68810211, ss97029117, ss103475960, ss138424347, ss143640769	NT_022184.15:16798903:G:T	NC_000002.12:37749873:G: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 rs604381

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

rs604381