Name: rs7676539
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.

rs7676539

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:121698791 (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>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.443179 (117305/264690, TOPMED)
A=0.496450 (101810/205076, GENOGRAPHIC)
G=0.446417 (62501/140006, GnomAD) (+ 18 more)
A=0.18282 (5166/28258, 14KJPN)
G=0.45533 (12129/26638, ALFA)
A=0.18669 (3129/16760, 8.3KJPN)
G=0.4834 (3096/6404, 1000G_30x)
G=0.4954 (2481/5008, 1000G)
A=0.4781 (2142/4480, Estonian)
A=0.4878 (1880/3854, ALSPAC)
G=0.4895 (1815/3708, TWINSUK)
A=0.2440 (713/2922, KOREAN)
G=0.4376 (827/1890, HapMap)
G=0.468 (467/998, GoNL)
A=0.375 (235/626, Chileans)
A=0.493 (296/600, NorthernSweden)
G=0.325 (110/338, SGDP_PRJ)
A=0.444 (96/216, Qatari)
A=0.288 (61/212, Vietnamese)
G=0.42 (17/40, GENOME_DK)
G=0.39 (15/38, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ANXA5 : 2KB Upstream Variant
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	26638	G=0.45533	A=0.54467
European	Sub	15666	G=0.50274	A=0.49726
African	Sub	6250	G=0.2818	A=0.7182
African Others	Sub	210	G=0.267	A=0.733
African American	Sub	6040	G=0.2823	A=0.7177
Asian	Sub	160	G=0.713	A=0.287
East Asian	Sub	102	G=0.696	A=0.304
Other Asian	Sub	58	G=0.74	A=0.26
Latin American 1	Sub	292	G=0.442	A=0.558
Latin American 2	Sub	2768	G=0.5513	A=0.4487
South Asian	Sub	108	G=0.602	A=0.398
Other	Sub	1394	G=0.4720	A=0.5280

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=0.443179	A=0.556821
Genographic Project	Global	Study-wide	205076	G=0.503550	A=0.496450
gnomAD - Genomes	Global	Study-wide	140006	G=0.446417	A=0.553583
gnomAD - Genomes	European	Sub	75828	G=0.50964	A=0.49036
gnomAD - Genomes	African	Sub	41950	G=0.27626	A=0.72374
gnomAD - Genomes	American	Sub	13640	G=0.52280	A=0.47720
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.5542	A=0.4458
gnomAD - Genomes	East Asian	Sub	3118	G=0.7261	A=0.2739
gnomAD - Genomes	Other	Sub	2148	G=0.4800	A=0.5200
14KJPN	JAPANESE	Study-wide	28258	G=0.81718	A=0.18282
Allele Frequency Aggregator	Total	Global	26638	G=0.45533	A=0.54467
Allele Frequency Aggregator	European	Sub	15666	G=0.50274	A=0.49726
Allele Frequency Aggregator	African	Sub	6250	G=0.2818	A=0.7182
Allele Frequency Aggregator	Latin American 2	Sub	2768	G=0.5513	A=0.4487
Allele Frequency Aggregator	Other	Sub	1394	G=0.4720	A=0.5280
Allele Frequency Aggregator	Latin American 1	Sub	292	G=0.442	A=0.558
Allele Frequency Aggregator	Asian	Sub	160	G=0.713	A=0.287
Allele Frequency Aggregator	South Asian	Sub	108	G=0.602	A=0.398
8.3KJPN	JAPANESE	Study-wide	16760	G=0.81331	A=0.18669
1000Genomes_30x	Global	Study-wide	6404	G=0.4834	A=0.5166
1000Genomes_30x	African	Sub	1786	G=0.2206	A=0.7794
1000Genomes_30x	Europe	Sub	1266	G=0.4795	A=0.5205
1000Genomes_30x	South Asian	Sub	1202	G=0.6015	A=0.3985
1000Genomes_30x	East Asian	Sub	1170	G=0.7291	A=0.2709
1000Genomes_30x	American	Sub	980	G=0.530	A=0.470
1000Genomes	Global	Study-wide	5008	G=0.4954	A=0.5046
1000Genomes	African	Sub	1322	G=0.2231	A=0.7769
1000Genomes	East Asian	Sub	1008	G=0.7292	A=0.2708
1000Genomes	Europe	Sub	1006	G=0.4901	A=0.5099
1000Genomes	South Asian	Sub	978	G=0.600	A=0.400
1000Genomes	American	Sub	694	G=0.535	A=0.465
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.5219	A=0.4781
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.5122	A=0.4878
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.4895	A=0.5105
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.7560	A=0.2440, C=0.0000
HapMap	Global	Study-wide	1890	G=0.4376	A=0.5624
HapMap	American	Sub	770	G=0.521	A=0.479
HapMap	African	Sub	690	G=0.222	A=0.778
HapMap	Asian	Sub	254	G=0.764	A=0.236
HapMap	Europe	Sub	176	G=0.449	A=0.551
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.468	A=0.532
Chileans	Chilean	Study-wide	626	G=0.625	A=0.375
Northern Sweden	ACPOP	Study-wide	600	G=0.507	A=0.493
SGDP_PRJ	Global	Study-wide	338	G=0.325	A=0.675
Qatari	Global	Study-wide	216	G=0.556	A=0.444
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.712	A=0.288
The Danish reference pan genome	Danish	Study-wide	40	G=0.42	A=0.57
Siberian	Global	Study-wide	38	G=0.39	A=0.61

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.121698791G>A
GRCh38.p14 chr 4	NC_000004.12:g.121698791G>C
GRCh37.p13 chr 4	NC_000004.11:g.122619946G>A
GRCh37.p13 chr 4	NC_000004.11:g.122619946G>C
ANXA5 RefSeqGene (LRG_606)	NG_032042.1:g.3202C>T
ANXA5 RefSeqGene (LRG_606)	NG_032042.1:g.3202C>G

Gene: ANXA5, annexin A5 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ANXA5 transcript	NM_001154.4:c.	N/A	Upstream Transcript Variant
ANXA5 transcript variant X1	XM_017008141.3:c.	N/A	Upstream Transcript 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=	A	C
GRCh38.p14 chr 4	NC_000004.12:g.121698791=	NC_000004.12:g.121698791G>A	NC_000004.12:g.121698791G>C
GRCh37.p13 chr 4	NC_000004.11:g.122619946=	NC_000004.11:g.122619946G>A	NC_000004.11:g.122619946G>C
ANXA5 RefSeqGene (LRG_606)	NG_032042.1:g.3202=	NG_032042.1:g.3202C>T	NG_032042.1:g.3202C>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#.

70 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11652576	Jul 11, 2003 (116)
2	AFFY	ss76521129	Dec 08, 2007 (130)
3	HGSV	ss77125565	Dec 07, 2007 (129)
4	HUMANGENOME_JCVI	ss98999404	Feb 06, 2009 (130)
5	BGI	ss104112333	Dec 01, 2009 (131)
6	1000GENOMES	ss108292951	Jan 23, 2009 (130)
7	1000GENOMES	ss110512706	Jan 24, 2009 (130)
8	ILLUMINA-UK	ss117169487	Feb 14, 2009 (130)
9	ENSEMBL	ss142492262	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss162502093	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss164226668	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss167104426	Jul 04, 2010 (132)
13	BUSHMAN	ss199109978	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss206324490	Jul 04, 2010 (132)
15	1000GENOMES	ss221182911	Jul 14, 2010 (132)
16	1000GENOMES	ss232576558	Jul 14, 2010 (132)
17	1000GENOMES	ss239827471	Jul 15, 2010 (132)
18	BL	ss253482416	May 09, 2011 (134)
19	GMI	ss284996132	Apr 25, 2013 (138)
20	PJP	ss293177546	May 09, 2011 (134)
21	TISHKOFF	ss557818428	Apr 25, 2013 (138)
22	SSMP	ss651627471	Apr 25, 2013 (138)
23	EVA-GONL	ss980616958	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1071911732	Aug 21, 2014 (142)
25	1000GENOMES	ss1311591411	Aug 21, 2014 (142)
26	DDI	ss1430032595	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1580752711	Apr 01, 2015 (144)
28	EVA_DECODE	ss1590124499	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1611059910	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1654053943	Apr 01, 2015 (144)
31	EVA_SVP	ss1712703434	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1802123380	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1923860059	Feb 12, 2016 (147)
34	GENOMED	ss1969854599	Jul 19, 2016 (147)
35	JJLAB	ss2022513480	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2150644311	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2266685338	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2625753557	Nov 08, 2017 (151)
39	GRF	ss2706128195	Nov 08, 2017 (151)
40	GNOMAD	ss2814616479	Nov 08, 2017 (151)
41	SWEGEN	ss2995464113	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3025033798	Nov 08, 2017 (151)
43	CSHL	ss3345935278	Nov 08, 2017 (151)
44	URBANLAB	ss3647836995	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3663365956	Jul 13, 2019 (153)
46	EVA_DECODE	ss3712956336	Jul 13, 2019 (153)
47	ACPOP	ss3731559965	Jul 13, 2019 (153)
48	EVA	ss3762345480	Jul 13, 2019 (153)
49	PACBIO	ss3784844600	Jul 13, 2019 (153)
50	PACBIO	ss3790282871	Jul 13, 2019 (153)
51	PACBIO	ss3795158328	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3805500324	Jul 13, 2019 (153)
53	EVA	ss3828781048	Apr 26, 2020 (154)
54	SGDP_PRJ	ss3859936947	Apr 26, 2020 (154)
55	KRGDB	ss3906237009	Apr 26, 2020 (154)
56	TOPMED	ss4630042720	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5167754919	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5260826809	Oct 13, 2022 (156)
59	GENOGRAPHIC	ss5314500870	Oct 13, 2022 (156)
60	EVA	ss5351940317	Oct 13, 2022 (156)
61	HUGCELL_USP	ss5459405579	Oct 13, 2022 (156)
62	EVA	ss5507707530	Oct 13, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5542780976	Oct 13, 2022 (156)
64	SANFORD_IMAGENETICS	ss5635977591	Oct 13, 2022 (156)
65	TOMMO_GENOMICS	ss5702676193	Oct 13, 2022 (156)
66	YY_MCH	ss5805486144	Oct 13, 2022 (156)
67	EVA	ss5844634952	Oct 13, 2022 (156)
68	EVA	ss5854419624	Oct 13, 2022 (156)
69	EVA	ss5865283582	Oct 13, 2022 (156)
70	EVA	ss5964379336	Oct 13, 2022 (156)
71	1000Genomes	NC_000004.11 - 122619946	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000004.12 - 121698791	Oct 13, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 122619946	Oct 12, 2018 (152)
74	Chileans	NC_000004.11 - 122619946	Apr 26, 2020 (154)
75	Genetic variation in the Estonian population	NC_000004.11 - 122619946	Oct 12, 2018 (152)
76	Genographic Project	NC_000004.12 - 121698791	Oct 13, 2022 (156)
77	The Danish reference pan genome	NC_000004.11 - 122619946	Apr 26, 2020 (154)
78	gnomAD - Genomes	NC_000004.12 - 121698791	Apr 26, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000004.11 - 122619946	Apr 26, 2020 (154)
80	HapMap	NC_000004.12 - 121698791	Apr 26, 2020 (154)
81	KOREAN population from KRGDB	NC_000004.11 - 122619946	Apr 26, 2020 (154)
82	Northern Sweden	NC_000004.11 - 122619946	Jul 13, 2019 (153)
83	Qatari	NC_000004.11 - 122619946	Apr 26, 2020 (154)
84	SGDP_PRJ	NC_000004.11 - 122619946	Apr 26, 2020 (154)
85	Siberian	NC_000004.11 - 122619946	Apr 26, 2020 (154)
86	8.3KJPN	NC_000004.11 - 122619946	Apr 26, 2021 (155)
87	14KJPN	NC_000004.12 - 121698791	Oct 13, 2022 (156)
88	TopMed	NC_000004.12 - 121698791	Apr 26, 2021 (155)
89	UK 10K study - Twins	NC_000004.11 - 122619946	Oct 12, 2018 (152)
90	A Vietnamese Genetic Variation Database	NC_000004.11 - 122619946	Jul 13, 2019 (153)
91	ALFA	NC_000004.12 - 121698791	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)
rs56472310	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77125565	NC_000004.9:122977550:G:A	NC_000004.12:121698790:G:A	(self)
ss108292951, ss110512706, ss117169487, ss162502093, ss164226668, ss167104426, ss199109978, ss206324490, ss253482416, ss284996132, ss293177546, ss1590124499, ss1712703434	NC_000004.10:122839395:G:A	NC_000004.12:121698790:G:A	(self)
23057697, 12828178, 326076, 9104204, 6917650, 5676436, 13414403, 4844830, 5901989, 11953927, 3160665, 25724226, 12828178, 2822620, ss221182911, ss232576558, ss239827471, ss557818428, ss651627471, ss980616958, ss1071911732, ss1311591411, ss1430032595, ss1580752711, ss1611059910, ss1654053943, ss1802123380, ss1923860059, ss1969854599, ss2022513480, ss2150644311, ss2625753557, ss2706128195, ss2814616479, ss2995464113, ss3345935278, ss3663365956, ss3731559965, ss3762345480, ss3784844600, ss3790282871, ss3795158328, ss3828781048, ss3859936947, ss3906237009, ss5167754919, ss5351940317, ss5507707530, ss5635977591, ss5844634952, ss5964379336	NC_000004.11:122619945:G:A	NC_000004.12:121698790:G:A	(self)
30306911, 44625, 163337100, 2700102, 36513297, 467420276, 12713587123, ss2266685338, ss3025033798, ss3647836995, ss3712956336, ss3805500324, ss4630042720, ss5260826809, ss5314500870, ss5459405579, ss5542780976, ss5702676193, ss5805486144, ss5854419624, ss5865283582	NC_000004.12:121698790:G:A	NC_000004.12:121698790:G:A	(self)
ss11652576	NT_016354.15:47115076:G:A	NC_000004.12:121698790:G:A	(self)
ss76521129, ss98999404, ss104112333, ss142492262	NT_016354.19:47167666:G:A	NC_000004.12:121698790:G:A	(self)
13414403, ss3906237009	NC_000004.11:122619945:G:C	NC_000004.12:121698790:G:C	(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 rs7676539

PMID	Title	Author	Year	Journal
30774014	Genetic polymorphisms near IL-21 gene associated with Th17 cytokines confer risk for systemic lupus erythematosus in Chinese Han population.	Meng Y et al.	2019	Lupus

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

rs7676539