Name: rs2866038
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.

rs2866038

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99189601 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.320507 (84835/264690, TOPMED)
C=0.18887 (5337/28258, 14KJPN)
C=0.18652 (3126/16760, 8.3KJPN) (+ 13 more)
G=0.12846 (1662/12938, ALFA)
G=0.4332 (2774/6404, 1000G_30x)
G=0.4407 (2207/5008, 1000G)
G=0.2315 (1037/4480, Estonian)
C=0.2338 (685/2930, KOREAN)
C=0.2129 (390/1832, Korea1K)
G=0.222 (222/998, GoNL)
G=0.197 (118/600, NorthernSweden)
C=0.345 (102/296, SGDP_PRJ)
G=0.315 (68/216, Qatari)
C=0.199 (43/216, Vietnamese)
G=0.28 (11/40, GENOME_DK)
C=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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	12938	C=0.87154	A=0.00000, G=0.12846
European	Sub	11040	C=0.85942	A=0.00000, G=0.14058
African	Sub	962	C=0.947	A=0.000, G=0.053
African Others	Sub	34	C=0.94	A=0.00, G=0.06
African American	Sub	928	C=0.947	A=0.000, G=0.053
Asian	Sub	6	C=0.5	A=0.0, G=0.5
East Asian	Sub	2	C=0.0	A=0.0, G=1.0
Other Asian	Sub	4	C=0.8	A=0.0, G=0.2
Latin American 1	Sub	68	C=1.00	A=0.00, G=0.00
Latin American 2	Sub	398	C=1.000	A=0.000, G=0.000
South Asian	Sub	30	C=0.93	A=0.00, G=0.07
Other	Sub	434	C=0.876	A=0.000, G=0.124

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	C=0.679493	G=0.320507
14KJPN	JAPANESE	Study-wide	28258	C=0.18887	G=0.81113
8.3KJPN	JAPANESE	Study-wide	16760	C=0.18652	G=0.81348
Allele Frequency Aggregator	Total	Global	12938	C=0.87154	A=0.00000, G=0.12846
Allele Frequency Aggregator	European	Sub	11040	C=0.85942	A=0.00000, G=0.14058
Allele Frequency Aggregator	African	Sub	962	C=0.947	A=0.000, G=0.053
Allele Frequency Aggregator	Other	Sub	434	C=0.876	A=0.000, G=0.124
Allele Frequency Aggregator	Latin American 2	Sub	398	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	68	C=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	South Asian	Sub	30	C=0.93	A=0.00, G=0.07
Allele Frequency Aggregator	Asian	Sub	6	C=0.5	A=0.0, G=0.5
1000Genomes_30x	Global	Study-wide	6404	C=0.5668	G=0.4332
1000Genomes_30x	African	Sub	1786	C=0.5269	G=0.4731
1000Genomes_30x	Europe	Sub	1266	C=0.7559	G=0.2441
1000Genomes_30x	South Asian	Sub	1202	C=0.5424	G=0.4576
1000Genomes_30x	East Asian	Sub	1170	C=0.2239	G=0.7761
1000Genomes_30x	American	Sub	980	C=0.835	G=0.165
1000Genomes	Global	Study-wide	5008	C=0.5593	G=0.4407
1000Genomes	African	Sub	1322	C=0.5340	G=0.4660
1000Genomes	East Asian	Sub	1008	C=0.2192	G=0.7808
1000Genomes	Europe	Sub	1006	C=0.7674	G=0.2326
1000Genomes	South Asian	Sub	978	C=0.542	G=0.458
1000Genomes	American	Sub	694	C=0.824	G=0.176
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7685	G=0.2315
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2338	G=0.7662
Korean Genome Project	KOREAN	Study-wide	1832	C=0.2129	G=0.7871
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.778	G=0.222
Northern Sweden	ACPOP	Study-wide	600	C=0.803	G=0.197
SGDP_PRJ	Global	Study-wide	296	C=0.345	G=0.655
Qatari	Global	Study-wide	216	C=0.685	G=0.315
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.199	G=0.801
The Danish reference pan genome	Danish	Study-wide	40	C=0.72	G=0.28
Siberian	Global	Study-wide	22	C=0.45	G=0.55

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 4	NC_000004.12:g.99189601C>A
GRCh38.p14 chr 4	NC_000004.12:g.99189601C>G
GRCh37.p13 chr 4	NC_000004.11:g.100110758C>A
GRCh37.p13 chr 4	NC_000004.11:g.100110758C>G

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1: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	G
GRCh38.p14 chr 4	NC_000004.12:g.99189601=	NC_000004.12:g.99189601C>A	NC_000004.12:g.99189601C>G
GRCh37.p13 chr 4	NC_000004.11:g.100110758=	NC_000004.11:g.100110758C>A	NC_000004.11:g.100110758C>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#.

67 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss4055284	Nov 05, 2001 (101)
2	SC_JCM	ss6134243	Feb 20, 2003 (117)
3	CSHL-HAPMAP	ss17787181	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss20197514	Feb 27, 2004 (120)
5	SSAHASNP	ss22133502	Apr 05, 2004 (121)
6	ABI	ss42303841	Mar 14, 2006 (126)
7	HGSV	ss78507558	Dec 07, 2007 (129)
8	BCMHGSC_JDW	ss92703145	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss98986757	Feb 05, 2009 (130)
10	ILLUMINA-UK	ss117113542	Dec 01, 2009 (131)
11	ENSEMBL	ss135208049	Dec 01, 2009 (131)
12	ENSEMBL	ss139781973	Dec 01, 2009 (131)
13	GMI	ss157650283	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss163916738	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166943573	Jul 04, 2010 (132)
16	BUSHMAN	ss198920827	Jul 04, 2010 (132)
17	BCM-HGSC-SUB	ss206511490	Jul 04, 2010 (132)
18	GMI	ss277844241	May 04, 2012 (137)
19	GMI	ss284967822	Apr 25, 2013 (138)
20	PJP	ss293147424	May 09, 2011 (134)
21	1000GENOMES	ss331831970	May 09, 2011 (134)
22	TISHKOFF	ss557720920	Apr 25, 2013 (138)
23	SSMP	ss651525502	Apr 25, 2013 (138)
24	EVA-GONL	ss980449711	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1071786875	Aug 21, 2014 (142)
26	1000GENOMES	ss1310978572	Aug 21, 2014 (142)
27	EVA_GENOME_DK	ss1580687274	Apr 01, 2015 (144)
28	EVA_DECODE	ss1589953724	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1610735503	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1610735504	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1653729536	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1653729537	Apr 01, 2015 (144)
33	WEILL_CORNELL_DGM	ss1923689843	Feb 12, 2016 (147)
34	JJLAB	ss2022430864	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2150560028	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2265422272	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2625714407	Nov 08, 2017 (151)
38	GRF	ss2706036945	Nov 08, 2017 (151)
39	GNOMAD	ss2812850426	Nov 08, 2017 (151)
40	SWEGEN	ss2995209946	Nov 08, 2017 (151)
41	CSHL	ss3345861643	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3645814277	Oct 12, 2018 (152)
43	URBANLAB	ss3647802534	Oct 12, 2018 (152)
44	EGCUT_WGS	ss3663105666	Jul 13, 2019 (153)
45	EVA_DECODE	ss3712656182	Jul 13, 2019 (153)
46	EVA_DECODE	ss3712656183	Jul 13, 2019 (153)
47	ACPOP	ss3731421514	Jul 13, 2019 (153)
48	EVA	ss3762166743	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3805315145	Jul 13, 2019 (153)
50	EVA	ss3828703364	Apr 26, 2020 (154)
51	SGDP_PRJ	ss3859609984	Apr 26, 2020 (154)
52	KRGDB	ss3905887352	Apr 26, 2020 (154)
53	KOGIC	ss3954741791	Apr 26, 2020 (154)
54	TOPMED	ss4624627423	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5167077086	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5260287514	Oct 13, 2022 (156)
57	EVA	ss5350974384	Oct 13, 2022 (156)
58	HUGCELL_USP	ss5458930046	Oct 13, 2022 (156)
59	EVA	ss5507641316	Oct 13, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5541954711	Oct 13, 2022 (156)
61	SANFORD_IMAGENETICS	ss5635665005	Oct 13, 2022 (156)
62	TOMMO_GENOMICS	ss5701807922	Oct 13, 2022 (156)
63	YY_MCH	ss5805353785	Oct 13, 2022 (156)
64	EVA	ss5844423740	Oct 13, 2022 (156)
65	EVA	ss5854355849	Oct 13, 2022 (156)
66	EVA	ss5864675828	Oct 13, 2022 (156)
67	EVA	ss5964055634	Oct 13, 2022 (156)
68	1000Genomes	NC_000004.11 - 100110758	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000004.12 - 99189601	Oct 13, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 12471641 (NC_000004.11:100110757:C:C 2944/3854, NC_000004.11:100110757:C:G 910/3854) Row 12471642 (NC_000004.11:100110757:C:C 3853/3854, NC_000004.11:100110757:C:A 1/3854)	-	Oct 12, 2018 (152)
71	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 12471641 (NC_000004.11:100110757:C:C 2944/3854, NC_000004.11:100110757:C:G 910/3854) Row 12471642 (NC_000004.11:100110757:C:C 3853/3854, NC_000004.11:100110757:C:A 1/3854)	-	Oct 12, 2018 (152)
72	Genetic variation in the Estonian population	NC_000004.11 - 100110758	Oct 12, 2018 (152)
73	The Danish reference pan genome	NC_000004.11 - 100110758	Apr 26, 2020 (154)
74	gnomAD - Genomes Submission ignored due to conflicting rows: Row 158823484 (NC_000004.12:99189600:C:A 4/139636) Row 158823485 (NC_000004.12:99189600:C:G 42263/139550)	-	Apr 26, 2021 (155)
75	gnomAD - Genomes Submission ignored due to conflicting rows: Row 158823484 (NC_000004.12:99189600:C:A 4/139636) Row 158823485 (NC_000004.12:99189600:C:G 42263/139550)	-	Apr 26, 2021 (155)
76	Genome of the Netherlands Release 5	NC_000004.11 - 100110758	Apr 26, 2020 (154)
77	KOREAN population from KRGDB	NC_000004.11 - 100110758	Apr 26, 2020 (154)
78	Korean Genome Project	NC_000004.12 - 99189601	Apr 26, 2020 (154)
79	Northern Sweden	NC_000004.11 - 100110758	Jul 13, 2019 (153)
80	Qatari	NC_000004.11 - 100110758	Apr 26, 2020 (154)
81	SGDP_PRJ	NC_000004.11 - 100110758	Apr 26, 2020 (154)
82	Siberian	NC_000004.11 - 100110758	Apr 26, 2020 (154)
83	8.3KJPN	NC_000004.11 - 100110758	Apr 26, 2021 (155)
84	14KJPN	NC_000004.12 - 99189601	Oct 13, 2022 (156)
85	TopMed	NC_000004.12 - 99189601	Apr 26, 2021 (155)
86	UK 10K study - Twins Submission ignored due to conflicting rows: Row 12471641 (NC_000004.11:100110757:C:C 2877/3708, NC_000004.11:100110757:C:G 831/3708) Row 12471642 (NC_000004.11:100110757:C:C 3707/3708, NC_000004.11:100110757:C:A 1/3708)	-	Oct 12, 2018 (152)
87	UK 10K study - Twins Submission ignored due to conflicting rows: Row 12471641 (NC_000004.11:100110757:C:C 2877/3708, NC_000004.11:100110757:C:G 831/3708) Row 12471642 (NC_000004.11:100110757:C:C 3707/3708, NC_000004.11:100110757:C:A 1/3708)	-	Oct 12, 2018 (152)
88	A Vietnamese Genetic Variation Database	NC_000004.11 - 100110758	Jul 13, 2019 (153)
89	ALFA	NC_000004.12 - 99189601	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)
rs4543118	Aug 27, 2003 (117)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1610735504, ss1653729537	NC_000004.11:100110757:C:A	NC_000004.12:99189600:C:A	(self)
6917939266, ss2265422272, ss3712656182	NC_000004.12:99189600:C:A	NC_000004.12:99189600:C:A	(self)
ss78507558	NC_000004.9:100467935:C:G	NC_000004.12:99189600:C:G	(self)
ss92703145, ss117113542, ss163916738, ss166943573, ss198920827, ss206511490, ss277844241, ss284967822, ss293147424, ss1589953724	NC_000004.10:100329780:C:G	NC_000004.12:99189600:C:G	(self)
22420720, 8843914, 6852213, 5513195, 13064746, 4706379, 5731773, 11626964, 3076382, 25046393, 2744211, ss331831970, ss557720920, ss651525502, ss980449711, ss1071786875, ss1310978572, ss1580687274, ss1610735503, ss1653729536, ss1923689843, ss2022430864, ss2150560028, ss2625714407, ss2706036945, ss2812850426, ss2995209946, ss3345861643, ss3663105666, ss3731421514, ss3762166743, ss3828703364, ss3859609984, ss3905887352, ss5167077086, ss5350974384, ss5507641316, ss5635665005, ss5844423740, ss5964055634	NC_000004.11:100110757:C:G	NC_000004.12:99189600:C:G	(self)
29480646, 11119792, 35645026, 462004979, 6917939266, ss2265422272, ss3645814277, ss3647802534, ss3712656183, ss3805315145, ss3954741791, ss4624627423, ss5260287514, ss5458930046, ss5541954711, ss5701807922, ss5805353785, ss5854355849, ss5864675828	NC_000004.12:99189600:C:G	NC_000004.12:99189600:C:G	(self)
ss17787181, ss20197514, ss22133502	NT_016354.16:24605461:C:G	NC_000004.12:99189600:C:G	(self)
ss4055284, ss6134243, ss42303841, ss98986757, ss135208049, ss139781973, ss157650283	NT_016354.19:24658478:C:G	NC_000004.12:99189600:C:G	(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 rs2866038

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

rs2866038