Name: rs1320759
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.

rs1320759

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:121850314 (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=0.215263 (56978/264690, TOPMED)
G=0.208368 (29169/139988, GnomAD)
G=0.44069 (12453/28258, 14KJPN) (+ 18 more)
G=0.15294 (2889/18890, ALFA)
G=0.43926 (7362/16760, 8.3KJPN)
G=0.2748 (1760/6404, 1000G_30x)
G=0.2762 (1383/5008, 1000G)
G=0.0967 (433/4480, Estonian)
G=0.0872 (336/3854, ALSPAC)
G=0.0971 (360/3708, TWINSUK)
G=0.4645 (1361/2930, KOREAN)
G=0.4733 (867/1832, Korea1K)
G=0.126 (126/998, GoNL)
G=0.117 (70/600, NorthernSweden)
G=0.299 (98/328, HapMap)
A=0.403 (95/236, SGDP_PRJ)
G=0.199 (43/216, Qatari)
G=0.420 (89/212, Vietnamese)
G=0.04 (2/48, Ancient Sardinia)
G=0.12 (5/40, GENOME_DK)
A=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105377979 : 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	18890	A=0.84706	G=0.15294
European	Sub	14286	A=0.90571	G=0.09429
African	Sub	2946	A=0.5669	G=0.4331
African Others	Sub	114	A=0.465	G=0.535
African American	Sub	2832	A=0.5710	G=0.4290
Asian	Sub	112	A=0.580	G=0.420
East Asian	Sub	86	A=0.62	G=0.38
Other Asian	Sub	26	A=0.46	G=0.54
Latin American 1	Sub	146	A=0.829	G=0.171
Latin American 2	Sub	610	A=0.907	G=0.093
South Asian	Sub	98	A=0.89	G=0.11
Other	Sub	692	A=0.818	G=0.182

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	A=0.784737	G=0.215263
gnomAD - Genomes	Global	Study-wide	139988	A=0.791632	G=0.208368
gnomAD - Genomes	European	Sub	75894	A=0.89736	G=0.10264
gnomAD - Genomes	African	Sub	41886	A=0.57783	G=0.42217
gnomAD - Genomes	American	Sub	13622	A=0.89062	G=0.10938
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.9048	G=0.0952
gnomAD - Genomes	East Asian	Sub	3114	A=0.5311	G=0.4689
gnomAD - Genomes	Other	Sub	2152	A=0.8002	G=0.1998
14KJPN	JAPANESE	Study-wide	28258	A=0.55931	G=0.44069
Allele Frequency Aggregator	Total	Global	18890	A=0.84706	G=0.15294
Allele Frequency Aggregator	European	Sub	14286	A=0.90571	G=0.09429
Allele Frequency Aggregator	African	Sub	2946	A=0.5669	G=0.4331
Allele Frequency Aggregator	Other	Sub	692	A=0.818	G=0.182
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.907	G=0.093
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.829	G=0.171
Allele Frequency Aggregator	Asian	Sub	112	A=0.580	G=0.420
Allele Frequency Aggregator	South Asian	Sub	98	A=0.89	G=0.11
8.3KJPN	JAPANESE	Study-wide	16760	A=0.56074	G=0.43926
1000Genomes_30x	Global	Study-wide	6404	A=0.7252	G=0.2748
1000Genomes_30x	African	Sub	1786	A=0.4961	G=0.5039
1000Genomes_30x	Europe	Sub	1266	A=0.8997	G=0.1003
1000Genomes_30x	South Asian	Sub	1202	A=0.9126	G=0.0874
1000Genomes_30x	East Asian	Sub	1170	A=0.5453	G=0.4547
1000Genomes_30x	American	Sub	980	A=0.902	G=0.098
1000Genomes	Global	Study-wide	5008	A=0.7238	G=0.2762
1000Genomes	African	Sub	1322	A=0.4962	G=0.5038
1000Genomes	East Asian	Sub	1008	A=0.5476	G=0.4524
1000Genomes	Europe	Sub	1006	A=0.8926	G=0.1074
1000Genomes	South Asian	Sub	978	A=0.913	G=0.087
1000Genomes	American	Sub	694	A=0.902	G=0.098
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9033	G=0.0967
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9128	G=0.0872
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9029	G=0.0971
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5355	C=0.0000, G=0.4645
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5267	G=0.4733
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.874	G=0.126
Northern Sweden	ACPOP	Study-wide	600	A=0.883	G=0.117
HapMap	Global	Study-wide	328	A=0.701	G=0.299
HapMap	African	Sub	120	A=0.550	G=0.450
HapMap	American	Sub	120	A=0.917	G=0.083
HapMap	Asian	Sub	88	A=0.61	G=0.39
SGDP_PRJ	Global	Study-wide	236	A=0.403	G=0.597
Qatari	Global	Study-wide	216	A=0.801	G=0.199
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.580	G=0.420
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	48	A=0.96	G=0.04
The Danish reference pan genome	Danish	Study-wide	40	A=0.88	G=0.12
Siberian	Global	Study-wide	22	A=0.45	G=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.121850314A>C
GRCh38.p14 chr 6	NC_000006.12:g.121850314A>G
GRCh37.p13 chr 6	NC_000006.11:g.122171460A>C
GRCh37.p13 chr 6	NC_000006.11:g.122171460A>G

Gene: LOC105377979, uncharacterized LOC105377979 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105377979 transcript variant X4	XR_942936.3:n.	N/A	Intron Variant
LOC105377979 transcript variant X1	XR_942937.4:n.	N/A	Intron Variant
LOC105377979 transcript variant X2	XR_001744321.2:n.	N/A	Genic Upstream Transcript Variant
LOC105377979 transcript variant X5	XR_001744323.2:n.	N/A	Genic Upstream Transcript Variant
LOC105377979 transcript variant X6	XR_001744324.2:n.	N/A	Genic Upstream Transcript Variant
LOC105377979 transcript variant X3	XR_001744325.2:n.	N/A	Genic Upstream Transcript Variant
LOC105377979 transcript variant X7	XR_007059731.1:n.	N/A	Genic 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	A=	C	G
GRCh38.p14 chr 6	NC_000006.12:g.121850314=	NC_000006.12:g.121850314A>C	NC_000006.12:g.121850314A>G
GRCh37.p13 chr 6	NC_000006.11:g.122171460=	NC_000006.11:g.122171460A>C	NC_000006.11:g.122171460A>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#.

63 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2089193	Oct 23, 2000 (88)
2	BCM_SSAHASNP	ss10288707	Jul 11, 2003 (116)
3	PERLEGEN	ss24194694	Sep 20, 2004 (123)
4	ABI	ss44765945	Mar 13, 2006 (126)
5	HGSV	ss85965693	Dec 14, 2007 (130)
6	BGI	ss104355747	Dec 01, 2009 (131)
7	1000GENOMES	ss115030653	Jan 25, 2009 (130)
8	ILLUMINA-UK	ss116697967	Feb 14, 2009 (130)
9	GMI	ss157530878	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss164415267	Jul 04, 2010 (132)
11	BUSHMAN	ss202359620	Jul 04, 2010 (132)
12	1000GENOMES	ss222646943	Jul 14, 2010 (132)
13	1000GENOMES	ss233664659	Jul 15, 2010 (132)
14	1000GENOMES	ss240683338	Jul 15, 2010 (132)
15	BL	ss254684851	May 09, 2011 (134)
16	GMI	ss279003642	May 04, 2012 (137)
17	PJP	ss293714066	May 09, 2011 (134)
18	TISHKOFF	ss559491661	Apr 25, 2013 (138)
19	SSMP	ss653686255	Apr 25, 2013 (138)
20	EVA-GONL	ss983448302	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1073994668	Aug 21, 2014 (142)
22	1000GENOMES	ss1322070078	Aug 21, 2014 (142)
23	DDI	ss1430880998	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1581878514	Apr 01, 2015 (144)
25	EVA_DECODE	ss1593013887	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1616589396	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1659583429	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1804648007	Sep 08, 2015 (146)
29	WEILL_CORNELL_DGM	ss1926692656	Feb 12, 2016 (147)
30	JJLAB	ss2024001504	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2152196540	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2287957004	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2626496178	Nov 08, 2017 (151)
34	GRF	ss2707825483	Nov 08, 2017 (151)
35	GNOMAD	ss2844542497	Nov 08, 2017 (151)
36	SWEGEN	ss2999873953	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3025795374	Nov 08, 2017 (151)
38	CSHL	ss3347208267	Nov 08, 2017 (151)
39	EGCUT_WGS	ss3667780973	Jul 13, 2019 (153)
40	EVA_DECODE	ss3718181665	Jul 13, 2019 (153)
41	ACPOP	ss3733941180	Jul 13, 2019 (153)
42	EVA	ss3765611020	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3808766542	Jul 13, 2019 (153)
44	EVA	ss3830169745	Apr 26, 2020 (154)
45	SGDP_PRJ	ss3865603471	Apr 26, 2020 (154)
46	KRGDB	ss3912550383	Apr 26, 2020 (154)
47	KOGIC	ss3959989119	Apr 26, 2020 (154)
48	EVA	ss3985248735	Apr 26, 2021 (155)
49	TOPMED	ss4720079918	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5179709255	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5270174837	Oct 13, 2022 (156)
52	EVA	ss5368682635	Oct 13, 2022 (156)
53	HUGCELL_USP	ss5467632432	Oct 13, 2022 (156)
54	EVA	ss5508695390	Oct 13, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5557023550	Oct 13, 2022 (156)
56	SANFORD_IMAGENETICS	ss5641390941	Oct 13, 2022 (156)
57	TOMMO_GENOMICS	ss5718533059	Oct 13, 2022 (156)
58	YY_MCH	ss5807917445	Oct 13, 2022 (156)
59	EVA	ss5842921950	Oct 13, 2022 (156)
60	EVA	ss5855563846	Oct 13, 2022 (156)
61	EVA	ss5885751880	Oct 13, 2022 (156)
62	EVA	ss5969982368	Oct 13, 2022 (156)
63	EVA	ss5969982369	Oct 13, 2022 (156)
64	1000Genomes	NC_000006.11 - 122171460	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000006.12 - 121850314	Oct 13, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 122171460	Oct 12, 2018 (152)
67	Genetic variation in the Estonian population	NC_000006.11 - 122171460	Oct 12, 2018 (152)
68	The Danish reference pan genome	NC_000006.11 - 122171460	Apr 26, 2020 (154)
69	gnomAD - Genomes	NC_000006.12 - 121850314	Apr 26, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000006.11 - 122171460	Apr 26, 2020 (154)
71	HapMap	NC_000006.12 - 121850314	Apr 26, 2020 (154)
72	KOREAN population from KRGDB	NC_000006.11 - 122171460	Apr 26, 2020 (154)
73	Korean Genome Project	NC_000006.12 - 121850314	Apr 26, 2020 (154)
74	Northern Sweden	NC_000006.11 - 122171460	Jul 13, 2019 (153)
75	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000006.11 - 122171460	Apr 26, 2021 (155)
76	Qatari	NC_000006.11 - 122171460	Apr 26, 2020 (154)
77	SGDP_PRJ	NC_000006.11 - 122171460	Apr 26, 2020 (154)
78	Siberian	NC_000006.11 - 122171460	Apr 26, 2020 (154)
79	8.3KJPN	NC_000006.11 - 122171460	Apr 26, 2021 (155)
80	14KJPN	NC_000006.12 - 121850314	Oct 13, 2022 (156)
81	TopMed	NC_000006.12 - 121850314	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000006.11 - 122171460	Oct 12, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000006.11 - 122171460	Jul 13, 2019 (153)
84	ALFA	NC_000006.12 - 121850314	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)
rs17775265	Oct 08, 2004 (123)
rs56800676	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
19727777, ss3912550383	NC_000006.11:122171459:A:C	NC_000006.12:121850313:A:C	(self)
ss85965693	NC_000006.9:122213158:A:G	NC_000006.12:121850313:A:G	(self)
ss115030653, ss116697967, ss164415267, ss202359620, ss254684851, ss279003642, ss293714066, ss1593013887	NC_000006.10:122213158:A:G	NC_000006.12:121850313:A:G	(self)
33931529, 18910679, 13519221, 8043453, 8424033, 19727777, 7226045, 474662, 8734586, 17620451, 4712894, 37678562, 18910679, 4209893, ss222646943, ss233664659, ss240683338, ss559491661, ss653686255, ss983448302, ss1073994668, ss1322070078, ss1430880998, ss1581878514, ss1616589396, ss1659583429, ss1804648007, ss1926692656, ss2024001504, ss2152196540, ss2626496178, ss2707825483, ss2844542497, ss2999873953, ss3347208267, ss3667780973, ss3733941180, ss3765611020, ss3830169745, ss3865603471, ss3912550383, ss3985248735, ss5179709255, ss5368682635, ss5508695390, ss5641390941, ss5842921950, ss5969982368, ss5969982369	NC_000006.11:122171459:A:G	NC_000006.12:121850313:A:G	(self)
44549485, 239629520, 3236802, 16367120, 52370163, 557457476, 1399869461, ss2287957004, ss3025795374, ss3718181665, ss3808766542, ss3959989119, ss4720079918, ss5270174837, ss5467632432, ss5557023550, ss5718533059, ss5807917445, ss5855563846, ss5885751880	NC_000006.12:121850313:A:G	NC_000006.12:121850313:A:G	(self)
ss10288707	NT_025741.12:26275894:A:G	NC_000006.12:121850313:A:G	(self)
ss2089193, ss24194694, ss44765945, ss104355747, ss157530878	NT_025741.15:26340916:A:G	NC_000006.12:121850313: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 rs1320759

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

rs1320759