Name: rs2523520
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.

rs2523520

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:31372714 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.436122 (115437/264690, TOPMED)
A=0.438393 (60913/138946, GnomAD)
A=0.27693 (7646/27610, 14KJPN) (+ 16 more)
A=0.40452 (10371/25638, ALFA)
A=0.27212 (4453/16364, 8.3KJPN)
A=0.4024 (2577/6404, 1000G_30x)
A=0.3956 (1981/5008, 1000G)
A=0.4268 (1908/4470, Estonian)
A=0.3454 (1331/3854, ALSPAC)
A=0.3576 (1326/3708, TWINSUK)
A=0.3458 (1007/2912, KOREAN)
A=0.4218 (475/1126, Daghestan)
A=0.368 (367/998, GoNL)
A=0.380 (227/598, NorthernSweden)
A=0.242 (101/418, SGDP_PRJ)
A=0.290 (62/214, Qatari)
A=0.29 (20/70, Ancient Sardinia)
A=0.36 (16/44, Siberian)
A=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	25732	A=0.40529	G=0.59471
European	Sub	20540	A=0.38807	G=0.61193
African	Sub	2974	A=0.4892	G=0.5108
African Others	Sub	114	A=0.561	G=0.439
African American	Sub	2860	A=0.4864	G=0.5136
Asian	Sub	118	A=0.398	G=0.602
East Asian	Sub	90	A=0.40	G=0.60
Other Asian	Sub	28	A=0.39	G=0.61
Latin American 1	Sub	154	A=0.416	G=0.584
Latin American 2	Sub	616	A=0.558	G=0.442
South Asian	Sub	100	A=0.32	G=0.68
Other	Sub	1230	A=0.4195	G=0.5805

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=0.436122	G=0.563878
gnomAD - Genomes	Global	Study-wide	138946	A=0.438393	G=0.561607
gnomAD - Genomes	European	Sub	75390	A=0.39593	G=0.60407
gnomAD - Genomes	African	Sub	41762	A=0.50151	G=0.49849
gnomAD - Genomes	American	Sub	13268	A=0.48658	G=0.51342
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	A=0.5868	G=0.4132
gnomAD - Genomes	East Asian	Sub	3078	A=0.2749	G=0.7251
gnomAD - Genomes	Other	Sub	2140	A=0.4098	G=0.5902
14KJPN	JAPANESE	Study-wide	27610	A=0.27693	G=0.72307
Allele Frequency Aggregator	Total	Global	25638	A=0.40452	G=0.59548
Allele Frequency Aggregator	European	Sub	20464	A=0.38707	G=0.61293
Allele Frequency Aggregator	African	Sub	2974	A=0.4892	G=0.5108
Allele Frequency Aggregator	Other	Sub	1212	A=0.4191	G=0.5809
Allele Frequency Aggregator	Latin American 2	Sub	616	A=0.558	G=0.442
Allele Frequency Aggregator	Latin American 1	Sub	154	A=0.416	G=0.584
Allele Frequency Aggregator	Asian	Sub	118	A=0.398	G=0.602
Allele Frequency Aggregator	South Asian	Sub	100	A=0.32	G=0.68
8.3KJPN	JAPANESE	Study-wide	16364	A=0.27212	G=0.72788
1000Genomes_30x	Global	Study-wide	6404	A=0.4024	G=0.5976
1000Genomes_30x	African	Sub	1786	A=0.4899	G=0.5101
1000Genomes_30x	Europe	Sub	1266	A=0.3831	G=0.6169
1000Genomes_30x	South Asian	Sub	1202	A=0.3111	G=0.6889
1000Genomes_30x	East Asian	Sub	1170	A=0.2812	G=0.7188
1000Genomes_30x	American	Sub	980	A=0.524	G=0.476
1000Genomes	Global	Study-wide	5008	A=0.3956	G=0.6044
1000Genomes	African	Sub	1322	A=0.4871	G=0.5129
1000Genomes	East Asian	Sub	1008	A=0.2887	G=0.7113
1000Genomes	Europe	Sub	1006	A=0.3917	G=0.6083
1000Genomes	South Asian	Sub	978	A=0.302	G=0.698
1000Genomes	American	Sub	694	A=0.514	G=0.486
Genetic variation in the Estonian population	Estonian	Study-wide	4470	A=0.4268	G=0.5732
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.3454	G=0.6546
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.3576	G=0.6424
KOREAN population from KRGDB	KOREAN	Study-wide	2912	A=0.3458	G=0.6542
Genome-wide autozygosity in Daghestan	Global	Study-wide	1126	A=0.4218	G=0.5782
Genome-wide autozygosity in Daghestan	Daghestan	Sub	624	A=0.466	G=0.534
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	A=0.375	G=0.625
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	A=0.418	G=0.582
Genome-wide autozygosity in Daghestan	Europe	Sub	108	A=0.398	G=0.602
Genome-wide autozygosity in Daghestan	South Asian	Sub	92	A=0.26	G=0.74
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	A=0.33	G=0.67
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.368	G=0.632
Northern Sweden	ACPOP	Study-wide	598	A=0.380	G=0.620
SGDP_PRJ	Global	Study-wide	418	A=0.242	G=0.758
Qatari	Global	Study-wide	214	A=0.290	G=0.710
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	70	A=0.29	G=0.71
Siberian	Global	Study-wide	44	A=0.36	G=0.64
The Danish reference pan genome	Danish	Study-wide	40	A=0.38	G=0.62

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 6	NC_000006.12:g.31372714A>G
GRCh37.p13 chr 6	NC_000006.11:g.31340491A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2853053G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2853159G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2628415G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2634011G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2674934G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2674232G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2681330G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2686950G>A

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=	G
GRCh38.p14 chr 6	NC_000006.12:g.31372714=	NC_000006.12:g.31372714A>G
GRCh37.p13 chr 6	NC_000006.11:g.31340491=	NC_000006.11:g.31340491A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2853053G>A	NT_113891.3:g.2853053=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2853159G>A	NT_113891.2:g.2853159=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2628415G>A	NT_167248.2:g.2628415=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2634011G>A	NT_167248.1:g.2634011=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2674934G>A	NT_167249.2:g.2674934=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2674232G>A	NT_167249.1:g.2674232=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2681330G>A	NT_167246.2:g.2681330=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2686950G>A	NT_167246.1:g.2686950=

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#.

76 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3537158	Sep 28, 2001 (100)
2	BCM_SSAHASNP	ss10328373	Jul 11, 2003 (126)
3	SI_MHC_SNP	ss12690067	Oct 31, 2003 (126)
4	SSAHASNP	ss22477168	Apr 05, 2004 (126)
5	BGI	ss104296319	Dec 01, 2009 (131)
6	1000GENOMES	ss109897585	Feb 13, 2009 (137)
7	ILLUMINA-UK	ss116393001	Feb 14, 2009 (130)
8	GMI	ss156739749	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss162194999	Jul 04, 2010 (135)
10	COMPLETE_GENOMICS	ss163342574	Jul 04, 2010 (135)
11	COMPLETE_GENOMICS	ss166423418	Jul 04, 2010 (135)
12	BUSHMAN	ss201620740	Jul 04, 2010 (137)
13	BCM-HGSC-SUB	ss207634583	Jul 04, 2010 (135)
14	1000GENOMES	ss211811732	Jul 14, 2010 (137)
15	1000GENOMES	ss222302120	Jul 14, 2010 (137)
16	1000GENOMES	ss233397044	Jul 14, 2010 (137)
17	1000GENOMES	ss240468043	Jul 15, 2010 (137)
18	BL	ss254183465	May 09, 2011 (137)
19	GMI	ss278724733	May 04, 2012 (137)
20	GMI	ss285373411	Apr 25, 2013 (138)
21	ILLUMINA	ss533642932	Sep 08, 2015 (146)
22	TISHKOFF	ss559112293	Apr 25, 2013 (138)
23	SSMP	ss653032687	Apr 25, 2013 (138)
24	EVA-GONL	ss982762757	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1073503728	Aug 21, 2014 (142)
26	1000GENOMES	ss1319552007	Aug 21, 2014 (142)
27	HAMMER_LAB	ss1397449508	Sep 08, 2015 (146)
28	EVA_GENOME_DK	ss1581604815	Apr 01, 2015 (144)
29	EVA_DECODE	ss1592307241	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1615273868	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1658267901	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1804356549	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1926014747	Feb 12, 2016 (147)
34	ILLUMINA	ss1958887258	Feb 12, 2016 (147)
35	GENOMED	ss1970356192	Jul 19, 2016 (147)
36	JJLAB	ss2023639867	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2151805998	Dec 20, 2016 (150)
38	HUMAN_LONGEVITY	ss2282938351	Dec 20, 2016 (150)
39	SYSTEMSBIOZJU	ss2626306849	Nov 08, 2017 (151)
40	GRF	ss2707399375	Nov 08, 2017 (151)
41	AFFY	ss2985361096	Nov 08, 2017 (151)
42	AFFY	ss2985993545	Nov 08, 2017 (151)
43	SWEGEN	ss2998791387	Nov 08, 2017 (151)
44	ILLUMINA	ss3022598542	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3025606687	Nov 08, 2017 (151)
46	ILLUMINA	ss3629501738	Oct 12, 2018 (152)
47	ILLUMINA	ss3653110955	Oct 12, 2018 (152)
48	ILLUMINA	ss3654127893	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3666707670	Jul 13, 2019 (153)
50	EVA_DECODE	ss3716903591	Jul 13, 2019 (153)
51	ACPOP	ss3733358468	Jul 13, 2019 (153)
52	EVA	ss3764818970	Jul 13, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3807974328	Jul 13, 2019 (153)
54	EVA	ss3829830557	Apr 26, 2020 (154)
55	EVA	ss3838393262	Apr 26, 2020 (154)
56	EVA	ss3843835326	Apr 26, 2020 (154)
57	SGDP_PRJ	ss3864248509	Apr 26, 2020 (154)
58	KRGDB	ss3911023685	Apr 26, 2020 (154)
59	EVA	ss3985212794	Apr 26, 2021 (155)
60	VINODS	ss4025186855	Apr 26, 2021 (155)
61	VINODS	ss4025228207	Apr 26, 2021 (155)
62	VINODS	ss4025265620	Apr 26, 2021 (155)
63	VINODS	ss4025285838	Apr 26, 2021 (155)
64	TOPMED	ss4698354709	Apr 26, 2021 (155)
65	TOMMO_GENOMICS	ss5176828660	Apr 26, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5267930605	Oct 13, 2022 (156)
67	EVA	ss5364715105	Oct 13, 2022 (156)
68	EVA	ss5508425984	Oct 13, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5553585447	Oct 13, 2022 (156)
70	SANFORD_IMAGENETICS	ss5640084897	Oct 13, 2022 (156)
71	TOMMO_GENOMICS	ss5714681353	Oct 13, 2022 (156)
72	YY_MCH	ss5807303926	Oct 13, 2022 (156)
73	EVA	ss5842022780	Oct 13, 2022 (156)
74	EVA	ss5855282010	Oct 13, 2022 (156)
75	EVA	ss5883238293	Oct 13, 2022 (156)
76	EVA	ss5968587069	Oct 13, 2022 (156)
77	1000Genomes	NC_000006.11 - 31340491	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000006.12 - 31372714	Oct 13, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 31340491	Oct 12, 2018 (152)
80	Genome-wide autozygosity in Daghestan	NC_000006.10 - 31448470	Apr 26, 2020 (154)
81	Genetic variation in the Estonian population	NC_000006.11 - 31340491	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000006.11 - 31340491	Apr 26, 2020 (154)
83	gnomAD - Genomes	NC_000006.12 - 31372714	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000006.11 - 31340491	Apr 26, 2020 (154)
85	KOREAN population from KRGDB	NC_000006.11 - 31340491	Apr 26, 2020 (154)
86	Northern Sweden	NC_000006.11 - 31340491	Jul 13, 2019 (153)
87	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000006.11 - 31340491	Apr 26, 2021 (155)
88	Qatari	NC_000006.11 - 31340491	Apr 26, 2020 (154)
89	SGDP_PRJ	NC_000006.11 - 31340491	Apr 26, 2020 (154)
90	Siberian	NC_000006.11 - 31340491	Apr 26, 2020 (154)
91	8.3KJPN	NC_000006.11 - 31340491	Apr 26, 2021 (155)
92	14KJPN	NC_000006.12 - 31372714	Oct 13, 2022 (156)
93	TopMed	NC_000006.12 - 31372714	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000006.11 - 31340491	Oct 12, 2018 (152)
95	ALFA	NC_000006.12 - 31372714	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)
rs6930912	Mar 11, 2006 (126)
rs9266498	Mar 11, 2006 (126)
rs111291574	Sep 17, 2011 (135)
rs113513758	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
424160, ss109897585, ss116393001, ss162194999, ss163342574, ss166423418, ss201620740, ss207634583, ss211811732, ss254183465, ss278724733, ss285373411, ss1397449508, ss1592307241	NC_000006.10:31448469:A:G	NC_000006.12:31372713:A:G	(self)
31319119, 17462936, 12445918, 7769754, 7761779, 18201079, 6643333, 438721, 8056677, 16265489, 4322352, 34797967, 17462936, ss222302120, ss233397044, ss240468043, ss533642932, ss559112293, ss653032687, ss982762757, ss1073503728, ss1319552007, ss1581604815, ss1615273868, ss1658267901, ss1804356549, ss1926014747, ss1958887258, ss1970356192, ss2023639867, ss2151805998, ss2626306849, ss2707399375, ss2985361096, ss2985993545, ss2998791387, ss3022598542, ss3629501738, ss3653110955, ss3654127893, ss3666707670, ss3733358468, ss3764818970, ss3829830557, ss3838393262, ss3864248509, ss3911023685, ss3985212794, ss5176828660, ss5364715105, ss5508425984, ss5640084897, ss5842022780, ss5968587069	NC_000006.11:31340490:A:G	NC_000006.12:31372713:A:G	(self)
41111382, 221182067, 48518457, 535732267, 6164132798, ss2282938351, ss3025606687, ss3716903591, ss3807974328, ss3843835326, ss4698354709, ss5267930605, ss5553585447, ss5714681353, ss5807303926, ss5855282010, ss5883238293	NC_000006.12:31372713:A:G	NC_000006.12:31372713:A:G	(self)
ss10328373, ss22477168	NT_007592.13:22194933:G:G	NC_000006.12:31372713:A:G	(self)
ss3537158, ss12690067, ss104296319, ss156739749	NT_007592.15:31280490:A:G	NC_000006.12:31372713:A:G	(self)
ss4025186855	NT_113891.3:2853052:G:G	NC_000006.12:31372713:A:G	(self)
ss4025228207	NT_167246.2:2681329:G:G	NC_000006.12:31372713:A:G	(self)
ss4025265620	NT_167248.2:2628414:G:G	NC_000006.12:31372713:A:G	(self)
ss4025285838	NT_167249.2:2674933:G:G	NC_000006.12:31372713: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 rs2523520

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

rs2523520