Name: rs6725877
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.

rs6725877

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:168154981 (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: A>C / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.425940 (112742/264690, TOPMED)
A=0.32503 (9184/28256, 14KJPN)
A=0.32631 (5469/16760, 8.3KJPN) (+ 12 more)
G=0.17178 (2106/12260, ALFA)
A=0.4799 (3073/6404, 1000G_30x)
A=0.4740 (2374/5008, 1000G)
G=0.2719 (1218/4480, Estonian)
A=0.3375 (989/2930, KOREAN)
A=0.3510 (643/1832, Korea1K)
G=0.154 (154/998, GoNL)
G=0.257 (154/600, NorthernSweden)
A=0.296 (120/406, SGDP_PRJ)
G=0.468 (101/216, Qatari)
G=0.28 (11/40, GENOME_DK)
A=0.41 (14/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: STK39 : 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	12260	A=0.82822	C=0.00000, G=0.17178
European	Sub	10750	A=0.82828	C=0.00000, G=0.17172
African	Sub	532	A=0.825	C=0.000, G=0.175
African Others	Sub	10	A=0.5	C=0.0, G=0.5
African American	Sub	522	A=0.831	C=0.000, G=0.169
Asian	Sub	20	A=0.75	C=0.00, G=0.25
East Asian	Sub	12	A=0.92	C=0.00, G=0.08
Other Asian	Sub	8	A=0.5	C=0.0, G=0.5
Latin American 1	Sub	52	A=0.90	C=0.00, G=0.10
Latin American 2	Sub	228	A=1.000	C=0.000, G=0.000
South Asian	Sub	46	A=0.96	C=0.00, G=0.04
Other	Sub	632	A=0.755	C=0.000, G=0.245

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	A=0.574060	G=0.425940
14KJPN	JAPANESE	Study-wide	28256	A=0.32503	G=0.67497
8.3KJPN	JAPANESE	Study-wide	16760	A=0.32631	G=0.67369
Allele Frequency Aggregator	Total	Global	12260	A=0.82822	C=0.00000, G=0.17178
Allele Frequency Aggregator	European	Sub	10750	A=0.82828	C=0.00000, G=0.17172
Allele Frequency Aggregator	Other	Sub	632	A=0.755	C=0.000, G=0.245
Allele Frequency Aggregator	African	Sub	532	A=0.825	C=0.000, G=0.175
Allele Frequency Aggregator	Latin American 2	Sub	228	A=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	52	A=0.90	C=0.00, G=0.10
Allele Frequency Aggregator	South Asian	Sub	46	A=0.96	C=0.00, G=0.04
Allele Frequency Aggregator	Asian	Sub	20	A=0.75	C=0.00, G=0.25
1000Genomes_30x	Global	Study-wide	6404	A=0.4799	G=0.5201
1000Genomes_30x	African	Sub	1786	A=0.3197	G=0.6803
1000Genomes_30x	Europe	Sub	1266	A=0.7164	G=0.2836
1000Genomes_30x	South Asian	Sub	1202	A=0.5616	G=0.4384
1000Genomes_30x	East Asian	Sub	1170	A=0.3214	G=0.6786
1000Genomes_30x	American	Sub	980	A=0.555	G=0.445
1000Genomes	Global	Study-wide	5008	A=0.4740	G=0.5260
1000Genomes	African	Sub	1322	A=0.3132	G=0.6868
1000Genomes	East Asian	Sub	1008	A=0.3155	G=0.6845
1000Genomes	Europe	Sub	1006	A=0.7107	G=0.2893
1000Genomes	South Asian	Sub	978	A=0.556	G=0.444
1000Genomes	American	Sub	694	A=0.552	G=0.448
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7281	G=0.2719
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.3375	C=0.0000, G=0.6625
Korean Genome Project	KOREAN	Study-wide	1832	A=0.3510	G=0.6490
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.846	G=0.154
Northern Sweden	ACPOP	Study-wide	600	A=0.743	G=0.257
SGDP_PRJ	Global	Study-wide	406	A=0.296	G=0.704
Qatari	Global	Study-wide	216	A=0.532	G=0.468
The Danish reference pan genome	Danish	Study-wide	40	A=0.72	G=0.28
Siberian	Global	Study-wide	34	A=0.41	G=0.59

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.168154981A>C
GRCh38.p14 chr 2	NC_000002.12:g.168154981A>G
GRCh37.p13 chr 2	NC_000002.11:g.169011491A>C
GRCh37.p13 chr 2	NC_000002.11:g.169011491A>G
STK39 RefSeqGene	NG_052783.1:g.97615T>G
STK39 RefSeqGene	NG_052783.1:g.97615T>C

Gene: STK39, serine/threonine kinase 39 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
STK39 transcript variant 1	NM_013233.3:c.628+6806T>G	N/A	Intron Variant
STK39 transcript variant X2	XM_005246465.3:c.628+6806… XM_005246465.3:c.628+6806T>G	N/A	Intron Variant
STK39 transcript variant X1	XM_017003813.3:c.628+6806… XM_017003813.3:c.628+6806T>G	N/A	Intron Variant
STK39 transcript variant X3	XM_017003814.3:c.628+6806… XM_017003814.3:c.628+6806T>G	N/A	Intron Variant
STK39 transcript variant X5	XM_017003816.3:c.628+6806… XM_017003816.3:c.628+6806T>G	N/A	Intron Variant
STK39 transcript variant X6	XM_017003817.3:c.136+6806… XM_017003817.3:c.136+6806T>G	N/A	Intron Variant
STK39 transcript variant X2	XM_047443941.1:c.628+6806… XM_047443941.1:c.628+6806T>G	N/A	Intron Variant
STK39 transcript variant X4	XM_047443944.1:c.322+6806… XM_047443944.1:c.322+6806T>G	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	A=	C	G
GRCh38.p14 chr 2	NC_000002.12:g.168154981=	NC_000002.12:g.168154981A>C	NC_000002.12:g.168154981A>G
GRCh37.p13 chr 2	NC_000002.11:g.169011491=	NC_000002.11:g.169011491A>C	NC_000002.11:g.169011491A>G
STK39 RefSeqGene	NG_052783.1:g.97615=	NG_052783.1:g.97615T>G	NG_052783.1:g.97615T>C
STK39 transcript	NM_013233.2:c.628+6806=	NM_013233.2:c.628+6806T>G	NM_013233.2:c.628+6806T>C
STK39 transcript variant 1	NM_013233.3:c.628+6806=	NM_013233.3:c.628+6806T>G	NM_013233.3:c.628+6806T>C
STK39 transcript variant X1	XM_005246465.1:c.628+6806=	XM_005246465.1:c.628+6806T>G	XM_005246465.1:c.628+6806T>C
STK39 transcript variant X2	XM_005246465.3:c.628+6806=	XM_005246465.3:c.628+6806T>G	XM_005246465.3:c.628+6806T>C
STK39 transcript variant X2	XM_005246466.1:c.136+6806=	XM_005246466.1:c.136+6806T>G	XM_005246466.1:c.136+6806T>C
STK39 transcript variant X1	XM_017003813.3:c.628+6806=	XM_017003813.3:c.628+6806T>G	XM_017003813.3:c.628+6806T>C
STK39 transcript variant X3	XM_017003814.3:c.628+6806=	XM_017003814.3:c.628+6806T>G	XM_017003814.3:c.628+6806T>C
STK39 transcript variant X5	XM_017003816.3:c.628+6806=	XM_017003816.3:c.628+6806T>G	XM_017003816.3:c.628+6806T>C
STK39 transcript variant X6	XM_017003817.3:c.136+6806=	XM_017003817.3:c.136+6806T>G	XM_017003817.3:c.136+6806T>C
STK39 transcript variant X2	XM_047443941.1:c.628+6806=	XM_047443941.1:c.628+6806T>G	XM_047443941.1:c.628+6806T>C
STK39 transcript variant X4	XM_047443944.1:c.322+6806=	XM_047443944.1:c.322+6806T>G	XM_047443944.1:c.322+6806T>C

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#.

61 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9945455	Jul 11, 2003 (116)
2	ABI	ss41794637	Mar 15, 2006 (126)
3	HGSV	ss85830028	Dec 15, 2007 (130)
4	BCMHGSC_JDW	ss91431354	Mar 24, 2008 (129)
5	BGI	ss106137187	Feb 05, 2009 (130)
6	ILLUMINA-UK	ss117961596	Feb 14, 2009 (130)
7	ENSEMBL	ss138573185	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss164782344	Jul 04, 2010 (132)
9	COMPLETE_GENOMICS	ss165577760	Jul 04, 2010 (132)
10	BUSHMAN	ss201342769	Jul 04, 2010 (132)
11	1000GENOMES	ss211038958	Jul 14, 2010 (132)
12	1000GENOMES	ss219641786	Jul 14, 2010 (132)
13	1000GENOMES	ss231459263	Jul 14, 2010 (132)
14	1000GENOMES	ss238949725	Jul 15, 2010 (132)
15	BL	ss253660075	May 09, 2011 (134)
16	GMI	ss276777653	May 04, 2012 (137)
17	ILLUMINA	ss533176500	Sep 08, 2015 (146)
18	TISHKOFF	ss556021605	Apr 25, 2013 (138)
19	SSMP	ss649672833	Apr 25, 2013 (138)
20	EVA-GONL	ss977619585	Aug 21, 2014 (142)
21	1000GENOMES	ss1300336835	Aug 21, 2014 (142)
22	DDI	ss1428813549	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1579188245	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1797879616	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1920871796	Feb 12, 2016 (147)
26	GENOMED	ss1968947232	Jul 19, 2016 (147)
27	JJLAB	ss2020969646	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2149034437	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2236390269	Dec 20, 2016 (150)
30	GRF	ss2703671484	Nov 08, 2017 (151)
31	GNOMAD	ss2782559430	Nov 08, 2017 (151)
32	SWEGEN	ss2990826868	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3024245216	Nov 08, 2017 (151)
34	CSHL	ss3344594409	Nov 08, 2017 (151)
35	ILLUMINA	ss3628216260	Oct 11, 2018 (152)
36	URBANLAB	ss3647200730	Oct 11, 2018 (152)
37	EGCUT_WGS	ss3658696738	Jul 13, 2019 (153)
38	EVA_DECODE	ss3705377507	Jul 13, 2019 (153)
39	ACPOP	ss3729085467	Jul 13, 2019 (153)
40	EVA	ss3757692164	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3802050779	Jul 13, 2019 (153)
42	EVA	ss3827341571	Apr 25, 2020 (154)
43	EVA	ss3837088500	Apr 25, 2020 (154)
44	EVA	ss3842508278	Apr 25, 2020 (154)
45	SGDP_PRJ	ss3853926415	Apr 25, 2020 (154)
46	KRGDB	ss3899554642	Apr 25, 2020 (154)
47	KOGIC	ss3949454548	Apr 25, 2020 (154)
48	TOPMED	ss4532958214	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5155013425	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5250888993	Oct 12, 2022 (156)
51	EVA	ss5333954570	Oct 12, 2022 (156)
52	HUGCELL_USP	ss5450614897	Oct 12, 2022 (156)
53	EVA	ss5506680774	Oct 12, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5527636789	Oct 12, 2022 (156)
55	SANFORD_IMAGENETICS	ss5630310372	Oct 12, 2022 (156)
56	TOMMO_GENOMICS	ss5685466578	Oct 12, 2022 (156)
57	YY_MCH	ss5802944291	Oct 12, 2022 (156)
58	EVA	ss5821145650	Oct 12, 2022 (156)
59	EVA	ss5852820819	Oct 12, 2022 (156)
60	EVA	ss5933387646	Oct 12, 2022 (156)
61	EVA	ss5956532673	Oct 12, 2022 (156)
62	1000Genomes	NC_000002.11 - 169011491	Oct 11, 2018 (152)
63	1000Genomes_30x	NC_000002.12 - 168154981	Oct 12, 2022 (156)
64	Genetic variation in the Estonian population	NC_000002.11 - 169011491	Oct 11, 2018 (152)
65	The Danish reference pan genome	NC_000002.11 - 169011491	Apr 25, 2020 (154)
66	gnomAD - Genomes Submission ignored due to conflicting rows: Row 81209269 (NC_000002.12:168154980:A:C 1/139858) Row 81209270 (NC_000002.12:168154980:A:G 56543/139784)	-	Apr 26, 2021 (155)
67	gnomAD - Genomes Submission ignored due to conflicting rows: Row 81209269 (NC_000002.12:168154980:A:C 1/139858) Row 81209270 (NC_000002.12:168154980:A:G 56543/139784)	-	Apr 26, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000002.11 - 169011491	Apr 25, 2020 (154)
69	KOREAN population from KRGDB	NC_000002.11 - 169011491	Apr 25, 2020 (154)
70	Korean Genome Project	NC_000002.12 - 168154981	Apr 25, 2020 (154)
71	Northern Sweden	NC_000002.11 - 169011491	Jul 13, 2019 (153)
72	Qatari	NC_000002.11 - 169011491	Apr 25, 2020 (154)
73	SGDP_PRJ	NC_000002.11 - 169011491	Apr 25, 2020 (154)
74	Siberian	NC_000002.11 - 169011491	Apr 25, 2020 (154)
75	8.3KJPN	NC_000002.11 - 169011491	Apr 26, 2021 (155)
76	14KJPN	NC_000002.12 - 168154981	Oct 12, 2022 (156)
77	TopMed	NC_000002.12 - 168154981	Apr 26, 2021 (155)
78	ALFA	NC_000002.12 - 168154981	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)
rs59228072	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
6732036, ss3899554642	NC_000002.11:169011490:A:C	NC_000002.12:168154980:A:C	(self)
15069665651	NC_000002.12:168154980:A:C	NC_000002.12:168154980:A:C	(self)
ss85830028	NC_000002.9:168836997:A:G	NC_000002.12:168154980:A:G	(self)
ss91431354, ss117961596, ss164782344, ss165577760, ss201342769, ss211038958, ss253660075, ss276777653	NC_000002.10:168719736:A:G	NC_000002.12:168154980:A:G	(self)
11390716, 4434986, 5353184, 2760605, 6732036, 2370332, 2913726, 5943395, 1550791, 12982732, ss219641786, ss231459263, ss238949725, ss533176500, ss556021605, ss649672833, ss977619585, ss1300336835, ss1428813549, ss1579188245, ss1797879616, ss1920871796, ss1968947232, ss2020969646, ss2149034437, ss2703671484, ss2782559430, ss2990826868, ss3344594409, ss3628216260, ss3658696738, ss3729085467, ss3757692164, ss3827341571, ss3837088500, ss3853926415, ss3899554642, ss5155013425, ss5333954570, ss5506680774, ss5630310372, ss5821145650, ss5956532673	NC_000002.11:169011490:A:G	NC_000002.12:168154980:A:G	(self)
15162724, 5832549, 19303682, 336781093, 15069665651, ss2236390269, ss3024245216, ss3647200730, ss3705377507, ss3802050779, ss3842508278, ss3949454548, ss4532958214, ss5250888993, ss5450614897, ss5527636789, ss5685466578, ss5802944291, ss5852820819, ss5933387646	NC_000002.12:168154980:A:G	NC_000002.12:168154980:A:G	(self)
ss9945455	NT_005403.13:19170828:A:G	NC_000002.12:168154980:A:G	(self)
ss41794637, ss106137187, ss138573185	NT_005403.17:19220908:A:G	NC_000002.12:168154980:A: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 rs6725877

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

rs6725877