Name: rs9275669
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.

rs9275669

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:32718899 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.226355 (59914/264690, TOPMED)
A=0.232004 (32514/140144, GnomAD)
A=0.08323 (2352/28258, 14KJPN) (+ 12 more)
A=0.21685 (4016/18520, ALFA)
A=0.08741 (1465/16760, 8.3KJPN)
A=0.2011 (1288/6404, 1000G_30x)
A=0.1987 (995/5008, 1000G)
A=0.1938 (868/4480, Estonian)
A=0.1249 (366/2930, KOREAN)
A=0.222 (222/998, GoNL)
A=0.233 (140/600, NorthernSweden)
A=0.227 (49/216, Qatari)
A=0.111 (23/208, Vietnamese)
G=0.442 (68/154, SGDP_PRJ)
G=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC102725019 : 500B Downstream 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	18520	G=0.78315	A=0.21685
European	Sub	14152	G=0.79847	A=0.20153
African	Sub	2898	G=0.6867	A=0.3133
African Others	Sub	114	G=0.667	A=0.333
African American	Sub	2784	G=0.6875	A=0.3125
Asian	Sub	112	G=0.857	A=0.143
East Asian	Sub	86	G=0.84	A=0.16
Other Asian	Sub	26	G=0.92	A=0.08
Latin American 1	Sub	146	G=0.767	A=0.233
Latin American 2	Sub	610	G=0.862	A=0.138
South Asian	Sub	98	G=0.91	A=0.09
Other	Sub	504	G=0.776	A=0.224

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=0.773645	A=0.226355
gnomAD - Genomes	Global	Study-wide	140144	G=0.767996	A=0.232004
gnomAD - Genomes	European	Sub	75898	G=0.79685	A=0.20315
gnomAD - Genomes	African	Sub	41980	G=0.69624	A=0.30376
gnomAD - Genomes	American	Sub	13654	G=0.81090	A=0.18910
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.7530	A=0.2470
gnomAD - Genomes	East Asian	Sub	3134	G=0.8596	A=0.1404
gnomAD - Genomes	Other	Sub	2154	G=0.7679	A=0.2321
14KJPN	JAPANESE	Study-wide	28258	G=0.91677	A=0.08323
Allele Frequency Aggregator	Total	Global	18520	G=0.78315	A=0.21685
Allele Frequency Aggregator	European	Sub	14152	G=0.79847	A=0.20153
Allele Frequency Aggregator	African	Sub	2898	G=0.6867	A=0.3133
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.862	A=0.138
Allele Frequency Aggregator	Other	Sub	504	G=0.776	A=0.224
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.767	A=0.233
Allele Frequency Aggregator	Asian	Sub	112	G=0.857	A=0.143
Allele Frequency Aggregator	South Asian	Sub	98	G=0.91	A=0.09
8.3KJPN	JAPANESE	Study-wide	16760	G=0.91259	A=0.08741
1000Genomes_30x	Global	Study-wide	6404	G=0.7989	A=0.2011
1000Genomes_30x	African	Sub	1786	G=0.6557	A=0.3443
1000Genomes_30x	Europe	Sub	1266	G=0.8112	A=0.1888
1000Genomes_30x	South Asian	Sub	1202	G=0.8852	A=0.1148
1000Genomes_30x	East Asian	Sub	1170	G=0.8615	A=0.1385
1000Genomes_30x	American	Sub	980	G=0.863	A=0.137
1000Genomes	Global	Study-wide	5008	G=0.8013	A=0.1987
1000Genomes	African	Sub	1322	G=0.6589	A=0.3411
1000Genomes	East Asian	Sub	1008	G=0.8641	A=0.1359
1000Genomes	Europe	Sub	1006	G=0.8091	A=0.1909
1000Genomes	South Asian	Sub	978	G=0.878	A=0.122
1000Genomes	American	Sub	694	G=0.862	A=0.138
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8063	A=0.1938
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8751	A=0.1249
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.778	A=0.222
Northern Sweden	ACPOP	Study-wide	600	G=0.767	A=0.233
Qatari	Global	Study-wide	216	G=0.773	A=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	208	G=0.889	A=0.111
SGDP_PRJ	Global	Study-wide	154	G=0.442	A=0.558
Siberian	Global	Study-wide	22	G=0.45	A=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 6	NC_000006.12:g.32718899G>A
GRCh37.p13 chr 6	NC_000006.11:g.32686676G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.4132179A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.4132285A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.3913151G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.3918747G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.3963009G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.3968594G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.4119042G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.4118340G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.4138202G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.4143822G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.4017637G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.4023222G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.2:g.4024747A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.1:g.3974663A>G

Gene: LOC102725019, uncharacterized LOC102725019 (plus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102725019 transcript variant X1	XR_001743875.3:n.	N/A	Downstream 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
GRCh38.p14 chr 6	NC_000006.12:g.32718899=	NC_000006.12:g.32718899G>A
GRCh37.p13 chr 6	NC_000006.11:g.32686676=	NC_000006.11:g.32686676G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.4132179A>G	NT_113891.3:g.4132179=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.4132285A>G	NT_113891.2:g.4132285=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.3913151=	NT_167248.2:g.3913151G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.3918747=	NT_167248.1:g.3918747G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.3963009=	NT_167245.2:g.3963009G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.3968594=	NT_167245.1:g.3968594G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.4119042=	NT_167249.2:g.4119042G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.4118340=	NT_167249.1:g.4118340G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.4138202=	NT_167246.2:g.4138202G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.4143822=	NT_167246.1:g.4143822G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.4017637=	NT_167247.2:g.4017637G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.4023222=	NT_167247.1:g.4023222G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.2:g.4024747A>G	NT_167244.2:g.4024747=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.1:g.3974663A>G	NT_167244.1:g.3974663=

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#.

49 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SI_MHC_SNP	ss12700785	Oct 31, 2003 (118)
2	BCMHGSC_JDW	ss93438912	Mar 24, 2008 (129)
3	ENSEMBL	ss161753339	Dec 01, 2009 (131)
4	COMPLETE_GENOMICS	ss166460788	Jul 04, 2010 (135)
5	1000GENOMES	ss211818917	Jul 14, 2010 (137)
6	1000GENOMES	ss222318722	Jul 14, 2010 (137)
7	1000GENOMES	ss233416101	Jul 14, 2010 (137)
8	BL	ss254213558	May 09, 2011 (137)
9	GMI	ss278741757	May 04, 2012 (137)
10	PJP	ss293831352	May 09, 2011 (137)
11	SSMP	ss653052507	Apr 25, 2013 (138)
12	EVA-GONL	ss982786569	Aug 21, 2014 (142)
13	1000GENOMES	ss1319598504	Aug 21, 2014 (142)
14	EVA_DECODE	ss1592320802	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1804367654	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1926044365	Feb 12, 2016 (147)
17	JJLAB	ss2023657108	Sep 14, 2016 (149)
18	USC_VALOUEV	ss2151832870	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2282993678	Dec 20, 2016 (150)
20	SYSTEMSBIOZJU	ss2626316379	Nov 08, 2017 (151)
21	GRF	ss2707427699	Nov 08, 2017 (151)
22	GNOMAD	ss2837519320	Nov 08, 2017 (151)
23	SWEGEN	ss2998841565	Nov 08, 2017 (151)
24	BIOINF_KMB_FNS_UNIBA	ss3025619728	Nov 08, 2017 (151)
25	URBANLAB	ss3648322073	Oct 12, 2018 (152)
26	EGCUT_WGS	ss3666729110	Jul 13, 2019 (153)
27	ACPOP	ss3733382082	Jul 13, 2019 (153)
28	EVA	ss3764846862	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3808003085	Jul 13, 2019 (153)
30	EVA	ss3829850843	Apr 26, 2020 (154)
31	EVA	ss3838402979	Apr 26, 2020 (154)
32	EVA	ss3843846949	Apr 26, 2020 (154)
33	SGDP_PRJ	ss3864302773	Apr 26, 2020 (154)
34	KRGDB	ss3911080795	Apr 26, 2020 (154)
35	VINODS	ss4025173020	Apr 26, 2021 (155)
36	VINODS	ss4025195692	Apr 26, 2021 (155)
37	VINODS	ss4025294600	Apr 26, 2021 (155)
38	TOPMED	ss4698588256	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5176911962	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5267973733	Oct 13, 2022 (156)
41	HUGCELL_USP	ss5465695113	Oct 13, 2022 (156)
42	EVA	ss5508438068	Oct 13, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5553649024	Oct 13, 2022 (156)
44	SANFORD_IMAGENETICS	ss5640131386	Oct 13, 2022 (156)
45	TOMMO_GENOMICS	ss5714782326	Oct 13, 2022 (156)
46	YY_MCH	ss5807344494	Oct 13, 2022 (156)
47	EVA	ss5842050742	Oct 13, 2022 (156)
48	EVA	ss5883278684	Oct 13, 2022 (156)
49	EVA	ss5968620564	Oct 13, 2022 (156)
50	1000Genomes	NC_000006.11 - 32686676	Oct 12, 2018 (152)
51	1000Genomes_30x	NC_000006.12 - 32718899	Oct 13, 2022 (156)
52	Genetic variation in the Estonian population	NC_000006.11 - 32686676	Oct 12, 2018 (152)
53	gnomAD - Genomes	NC_000006.12 - 32718899	Apr 26, 2021 (155)
54	Genome of the Netherlands Release 5	NC_000006.11 - 32686676	Apr 26, 2020 (154)
55	KOREAN population from KRGDB	NC_000006.11 - 32686676	Apr 26, 2020 (154)
56	Northern Sweden	NC_000006.11 - 32686676	Jul 13, 2019 (153)
57	Qatari	NC_000006.11 - 32686676	Apr 26, 2020 (154)
58	SGDP_PRJ	NC_000006.11 - 32686676	Apr 26, 2020 (154)
59	Siberian	NC_000006.11 - 32686676	Apr 26, 2020 (154)
60	8.3KJPN	NC_000006.11 - 32686676	Apr 26, 2021 (155)
61	14KJPN	NC_000006.12 - 32718899	Oct 13, 2022 (156)
62	TopMed	NC_000006.12 - 32718899	Apr 26, 2021 (155)
63	A Vietnamese Genetic Variation Database	NC_000006.11 - 32686676	Jul 13, 2019 (153)
64	ALFA	NC_000006.12 - 32718899	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)
rs113084283	Sep 17, 2011 (135)
rs115352779	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss12700785, ss93438912, ss166460788, ss211818917, ss254213558, ss278741757, ss293831352, ss1592320802	NC_000006.10:32794653:G:A	NC_000006.12:32718898:G:A	(self)
31367289, 12467358, 7781008, 18258189, 6666947, 8086295, 16319753, 4349224, 34881269, 3880413, ss222318722, ss233416101, ss653052507, ss982786569, ss1319598504, ss1804367654, ss1926044365, ss2023657108, ss2151832870, ss2626316379, ss2707427699, ss2837519320, ss2998841565, ss3666729110, ss3733382082, ss3764846862, ss3829850843, ss3838402979, ss3864302773, ss3911080795, ss5176911962, ss5508438068, ss5640131386, ss5842050742, ss5968620564	NC_000006.11:32686675:G:A	NC_000006.12:32718898:G:A	(self)
41174959, 221435662, 48619430, 535965814, 1596242249, ss2282993678, ss3025619728, ss3648322073, ss3808003085, ss3843846949, ss4698588256, ss5267973733, ss5465695113, ss5553649024, ss5714782326, ss5807344494, ss5883278684	NC_000006.12:32718898:G:A	NC_000006.12:32718898:G:A	(self)
ss161753339	NT_007592.15:32626675:G:A	NC_000006.12:32718898:G:A	(self)
ss4025195692	NT_113891.3:4132178:A:A	NC_000006.12:32718898:G:A	(self)
ss4025173020	NT_167244.2:4024746:A:A	NC_000006.12:32718898:G:A	(self)
ss4025294600	NT_167249.2:4119041:G:A	NC_000006.12:32718898:G:A	(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 rs9275669

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

rs9275669