Name: rs12021511
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.

rs12021511

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:107509235 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.272360 (72091/264690, TOPMED)
G=0.42455 (11996/28256, 14KJPN)
G=0.42601 (7140/16760, 8.3KJPN) (+ 16 more)
A=0.16287 (2162/13274, ALFA)
A=0.3156 (2021/6404, 1000G_30x)
A=0.3219 (1612/5008, 1000G)
A=0.2944 (1319/4480, Estonian)
A=0.3358 (1294/3854, ALSPAC)
A=0.3528 (1308/3708, TWINSUK)
G=0.4113 (1205/2930, KOREAN)
G=0.4023 (737/1832, Korea1K)
A=0.316 (315/998, GoNL)
A=0.268 (161/600, NorthernSweden)
G=0.375 (120/320, SGDP_PRJ)
A=0.321 (97/302, HapMap)
A=0.301 (65/216, Qatari)
G=0.486 (104/214, Vietnamese)
A=0.38 (15/40, GENOME_DK)
G=0.26 (9/34, Siberian)

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	13274	G=0.83713	A=0.16287, C=0.00000, T=0.00000
European	Sub	10042	G=0.79337	A=0.20663, C=0.00000, T=0.00000
African	Sub	2314	G=0.9914	A=0.0086, C=0.0000, T=0.0000
African Others	Sub	94	G=0.99	A=0.01, C=0.00, T=0.00
African American	Sub	2220	G=0.9914	A=0.0086, C=0.0000, T=0.0000
Asian	Sub	22	G=0.95	A=0.05, C=0.00, T=0.00
East Asian	Sub	16	G=0.94	A=0.06, C=0.00, T=0.00
Other Asian	Sub	6	G=1.0	A=0.0, C=0.0, T=0.0
Latin American 1	Sub	70	G=1.00	A=0.00, C=0.00, T=0.00
Latin American 2	Sub	306	G=1.000	A=0.000, C=0.000, T=0.000
South Asian	Sub	40	G=1.00	A=0.00, C=0.00, T=0.00
Other	Sub	480	G=0.863	A=0.138, C=0.000, T=0.000

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=0.727640	A=0.272360
14KJPN	JAPANESE	Study-wide	28256	G=0.42455	A=0.57545
8.3KJPN	JAPANESE	Study-wide	16760	G=0.42601	A=0.57399
Allele Frequency Aggregator	Total	Global	13274	G=0.83713	A=0.16287, C=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	10042	G=0.79337	A=0.20663, C=0.00000, T=0.00000
Allele Frequency Aggregator	African	Sub	2314	G=0.9914	A=0.0086, C=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	480	G=0.863	A=0.138, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	306	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	70	G=1.00	A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	40	G=1.00	A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	22	G=0.95	A=0.05, C=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.6844	A=0.3156
1000Genomes_30x	African	Sub	1786	G=0.9132	A=0.0868
1000Genomes_30x	Europe	Sub	1266	G=0.6098	A=0.3902
1000Genomes_30x	South Asian	Sub	1202	G=0.6514	A=0.3486
1000Genomes_30x	East Asian	Sub	1170	G=0.4248	A=0.5752
1000Genomes_30x	American	Sub	980	G=0.714	A=0.286
1000Genomes	Global	Study-wide	5008	G=0.6781	A=0.3219
1000Genomes	African	Sub	1322	G=0.9070	A=0.0930
1000Genomes	East Asian	Sub	1008	G=0.4306	A=0.5694
1000Genomes	Europe	Sub	1006	G=0.6233	A=0.3767
1000Genomes	South Asian	Sub	978	G=0.653	A=0.347
1000Genomes	American	Sub	694	G=0.716	A=0.284
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7056	A=0.2944
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6642	A=0.3358
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6472	A=0.3528
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4113	A=0.5887
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4023	A=0.5977
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.684	A=0.316
Northern Sweden	ACPOP	Study-wide	600	G=0.732	A=0.268
SGDP_PRJ	Global	Study-wide	320	G=0.375	A=0.625
HapMap	Global	Study-wide	302	G=0.679	A=0.321
HapMap	African	Sub	114	G=0.947	A=0.053
HapMap	American	Sub	108	G=0.556	A=0.444
HapMap	Asian	Sub	80	G=0.46	A=0.54
Qatari	Global	Study-wide	216	G=0.699	A=0.301
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.486	A=0.514
The Danish reference pan genome	Danish	Study-wide	40	G=0.62	A=0.38
Siberian	Global	Study-wide	34	G=0.26	A=0.74

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 1	NC_000001.11:g.107509235G>A
GRCh38.p14 chr 1	NC_000001.11:g.107509235G>C
GRCh38.p14 chr 1	NC_000001.11:g.107509235G>T
GRCh37.p13 chr 1	NC_000001.10:g.108051857G>A
GRCh37.p13 chr 1	NC_000001.10:g.108051857G>C
GRCh37.p13 chr 1	NC_000001.10:g.108051857G>T

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	T
GRCh38.p14 chr 1	NC_000001.11:g.107509235=	NC_000001.11:g.107509235G>A	NC_000001.11:g.107509235G>C	NC_000001.11:g.107509235G>T
GRCh37.p13 chr 1	NC_000001.10:g.108051857=	NC_000001.10:g.108051857G>A	NC_000001.10:g.108051857G>C	NC_000001.10:g.108051857G>T

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#.

63 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18069728	Feb 28, 2004 (120)
2	HGSV	ss78330063	Dec 06, 2007 (129)
3	BGI	ss106593757	Feb 06, 2009 (130)
4	1000GENOMES	ss108504620	Jan 23, 2009 (130)
5	GMI	ss155498826	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss164972252	Jul 04, 2010 (132)
7	BCM-HGSC-SUB	ss205360678	Jul 04, 2010 (132)
8	1000GENOMES	ss210612744	Jul 14, 2010 (132)
9	1000GENOMES	ss218583820	Jul 14, 2010 (132)
10	1000GENOMES	ss230681843	Jul 14, 2010 (132)
11	1000GENOMES	ss238342403	Jul 15, 2010 (132)
12	BL	ss253361454	May 09, 2011 (134)
13	GMI	ss275969028	May 04, 2012 (137)
14	GMI	ss284116822	Apr 25, 2013 (138)
15	PJP	ss290593372	May 09, 2011 (134)
16	TISHKOFF	ss554543229	Apr 25, 2013 (138)
17	SSMP	ss648296064	Apr 25, 2013 (138)
18	EVA-GONL	ss975544941	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1068174308	Aug 21, 2014 (142)
20	1000GENOMES	ss1292335436	Aug 21, 2014 (142)
21	DDI	ss1425929558	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1574306579	Apr 01, 2015 (144)
23	EVA_DECODE	ss1584923763	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1600937395	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1643931428	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1794894762	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1918745230	Feb 12, 2016 (147)
28	JJLAB	ss2019896517	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2147913733	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2165513016	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2624457994	Nov 08, 2017 (151)
32	GRF	ss2697843162	Nov 08, 2017 (151)
33	GNOMAD	ss2759278429	Nov 08, 2017 (151)
34	SWEGEN	ss2987397433	Nov 08, 2017 (151)
35	BIOINF_KMB_FNS_UNIBA	ss3023712014	Nov 08, 2017 (151)
36	CSHL	ss3343623533	Nov 08, 2017 (151)
37	EGCUT_WGS	ss3655486484	Jul 12, 2019 (153)
38	EVA_DECODE	ss3687481295	Jul 12, 2019 (153)
39	ACPOP	ss3727367053	Jul 12, 2019 (153)
40	EVA	ss3746642336	Jul 12, 2019 (153)
41	PACBIO	ss3783512446	Jul 12, 2019 (153)
42	PACBIO	ss3789155302	Jul 12, 2019 (153)
43	PACBIO	ss3794028174	Jul 12, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3799646718	Jul 12, 2019 (153)
45	EVA	ss3826356292	Apr 25, 2020 (154)
46	EVA	ss3836569512	Apr 25, 2020 (154)
47	EVA	ss3841977888	Apr 25, 2020 (154)
48	SGDP_PRJ	ss3849598775	Apr 25, 2020 (154)
49	KRGDB	ss3894685304	Apr 25, 2020 (154)
50	KOGIC	ss3945196663	Apr 25, 2020 (154)
51	TOPMED	ss4462744000	Apr 25, 2021 (155)
52	TOMMO_GENOMICS	ss5145568256	Apr 25, 2021 (155)
53	1000G_HIGH_COVERAGE	ss5243525365	Oct 12, 2022 (156)
54	EVA	ss5321030575	Oct 12, 2022 (156)
55	HUGCELL_USP	ss5444458377	Oct 12, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5516476458	Oct 12, 2022 (156)
57	SANFORD_IMAGENETICS	ss5626250468	Oct 12, 2022 (156)
58	TOMMO_GENOMICS	ss5670802991	Oct 12, 2022 (156)
59	YY_MCH	ss5800910771	Oct 12, 2022 (156)
60	EVA	ss5832449972	Oct 12, 2022 (156)
61	EVA	ss5849057802	Oct 12, 2022 (156)
62	EVA	ss5909704041	Oct 12, 2022 (156)
63	EVA	ss5938114757	Oct 12, 2022 (156)
64	1000Genomes	NC_000001.10 - 108051857	Oct 11, 2018 (152)
65	1000Genomes_30x	NC_000001.11 - 107509235	Oct 12, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 108051857	Oct 11, 2018 (152)
67	Genetic variation in the Estonian population	NC_000001.10 - 108051857	Oct 11, 2018 (152)
68	The Danish reference pan genome	NC_000001.10 - 108051857	Apr 25, 2020 (154)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 21979846 (NC_000001.11:107509234:G:A 37351/139918) Row 21979847 (NC_000001.11:107509234:G:C 1/139958)	-	Apr 25, 2021 (155)
70	gnomAD - Genomes Submission ignored due to conflicting rows: Row 21979846 (NC_000001.11:107509234:G:A 37351/139918) Row 21979847 (NC_000001.11:107509234:G:C 1/139958)	-	Apr 25, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000001.10 - 108051857	Apr 25, 2020 (154)
72	HapMap	NC_000001.11 - 107509235	Apr 25, 2020 (154)
73	KOREAN population from KRGDB	NC_000001.10 - 108051857	Apr 25, 2020 (154)
74	Korean Genome Project	NC_000001.11 - 107509235	Apr 25, 2020 (154)
75	Northern Sweden	NC_000001.10 - 108051857	Jul 12, 2019 (153)
76	Qatari	NC_000001.10 - 108051857	Apr 25, 2020 (154)
77	SGDP_PRJ	NC_000001.10 - 108051857	Apr 25, 2020 (154)
78	Siberian	NC_000001.10 - 108051857	Apr 25, 2020 (154)
79	8.3KJPN	NC_000001.10 - 108051857	Apr 25, 2021 (155)
80	14KJPN	NC_000001.11 - 107509235	Oct 12, 2022 (156)
81	TopMed	NC_000001.11 - 107509235	Apr 25, 2021 (155)
82	UK 10K study - Twins	NC_000001.10 - 108051857	Oct 11, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000001.10 - 108051857	Jul 12, 2019 (153)
84	ALFA	NC_000001.11 - 107509235	Apr 25, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78330063	NC_000001.8:107763898:G:A	NC_000001.11:107509234:G:A	(self)
ss108504620, ss164972252, ss205360678, ss210612744, ss253361454, ss275969028, ss284116822, ss290593372, ss1584923763	NC_000001.9:107853379:G:A	NC_000001.11:107509234:G:A	(self)
3107814, 1716079, 1224732, 1654253, 747340, 1862698, 651918, 787160, 1615755, 430087, 3537563, 1716079, 372388, ss218583820, ss230681843, ss238342403, ss554543229, ss648296064, ss975544941, ss1068174308, ss1292335436, ss1425929558, ss1574306579, ss1600937395, ss1643931428, ss1794894762, ss1918745230, ss2019896517, ss2147913733, ss2624457994, ss2697843162, ss2759278429, ss2987397433, ss3343623533, ss3655486484, ss3727367053, ss3746642336, ss3783512446, ss3789155302, ss3794028174, ss3826356292, ss3836569512, ss3849598775, ss3894685304, ss5145568256, ss5321030575, ss5626250468, ss5832449972, ss5938114757	NC_000001.10:108051856:G:A	NC_000001.11:107509234:G:A	(self)
4002393, 149267, 1574664, 4640095, 26350335, 11555585591, ss2165513016, ss3023712014, ss3687481295, ss3799646718, ss3841977888, ss3945196663, ss4462744000, ss5243525365, ss5444458377, ss5516476458, ss5670802991, ss5800910771, ss5849057802, ss5909704041	NC_000001.11:107509234:G:A	NC_000001.11:107509234:G:A	(self)
ss18069728	NT_029860.11:4127967:G:A	NC_000001.11:107509234:G:A	(self)
ss106593757, ss155498826	NT_032977.9:78023774:G:A	NC_000001.11:107509234:G:A	(self)
11555585591	NC_000001.11:107509234:G:C	NC_000001.11:107509234:G:C	(self)
11555585591	NC_000001.11:107509234:G:T	NC_000001.11:107509234:G:T	(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 rs12021511

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

rs12021511