Name: rs2780103
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.

rs2780103

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:83959653 (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: C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.291148 (77064/264690, TOPMED)
T=0.25281 (7144/28258, 14KJPN)
T=0.18626 (3422/18372, ALFA) (+ 16 more)
T=0.25173 (4219/16760, 8.3KJPN)
T=0.3170 (2030/6404, 1000G_30x)
T=0.3185 (1595/5008, 1000G)
T=0.2598 (1164/4480, Estonian)
T=0.2488 (959/3854, ALSPAC)
T=0.2589 (960/3708, TWINSUK)
T=0.2688 (787/2928, KOREAN)
T=0.3066 (580/1892, HapMap)
T=0.2467 (452/1832, Korea1K)
T=0.293 (292/998, GoNL)
T=0.275 (165/600, NorthernSweden)
C=0.388 (100/258, SGDP_PRJ)
T=0.347 (75/216, Qatari)
T=0.281 (59/210, Vietnamese)
T=0.28 (11/40, GENOME_DK)
C=0.42 (10/24, 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18372	C=0.81374	G=0.00000, T=0.18626	0.679295	0.051818	0.268887	32
European	Sub	14614	C=0.81381	G=0.00000, T=0.18619	0.675517	0.047899	0.276584	30
African	Sub	2250	C=0.7818	G=0.0000, T=0.2182	0.642667	0.079111	0.278222	21
African Others	Sub	76	C=0.82	G=0.00, T=0.18	0.657895	0.026316	0.315789	0
African American	Sub	2174	C=0.7806	G=0.0000, T=0.2194	0.642134	0.080957	0.276909	22
Asian	Sub	76	C=0.93	G=0.00, T=0.07	0.868421	0.0	0.131579	0
East Asian	Sub	62	C=0.94	G=0.00, T=0.06	0.870968	0.0	0.129032	0
Other Asian	Sub	14	C=0.93	G=0.00, T=0.07	0.857143	0.0	0.142857	0
Latin American 1	Sub	92	C=0.90	G=0.00, T=0.10	0.847826	0.043478	0.108696	4
Latin American 2	Sub	498	C=0.970	G=0.000, T=0.030	0.951807	0.012048	0.036145	20
South Asian	Sub	38	C=0.95	G=0.00, T=0.05	0.947368	0.052632	0.0	11
Other	Sub	804	C=0.777	G=0.000, T=0.223	0.631841	0.077114	0.291045	6

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	C=0.708852	T=0.291148
14KJPN	JAPANESE	Study-wide	28258	C=0.74719	T=0.25281
Allele Frequency Aggregator	Total	Global	18372	C=0.81374	G=0.00000, T=0.18626
Allele Frequency Aggregator	European	Sub	14614	C=0.81381	G=0.00000, T=0.18619
Allele Frequency Aggregator	African	Sub	2250	C=0.7818	G=0.0000, T=0.2182
Allele Frequency Aggregator	Other	Sub	804	C=0.777	G=0.000, T=0.223
Allele Frequency Aggregator	Latin American 2	Sub	498	C=0.970	G=0.000, T=0.030
Allele Frequency Aggregator	Latin American 1	Sub	92	C=0.90	G=0.00, T=0.10
Allele Frequency Aggregator	Asian	Sub	76	C=0.93	G=0.00, T=0.07
Allele Frequency Aggregator	South Asian	Sub	38	C=0.95	G=0.00, T=0.05
8.3KJPN	JAPANESE	Study-wide	16760	C=0.74827	T=0.25173
1000Genomes_30x	Global	Study-wide	6404	C=0.6799	G=0.0031, T=0.3170
1000Genomes_30x	African	Sub	1786	C=0.5873	G=0.0112, T=0.4015
1000Genomes_30x	Europe	Sub	1266	C=0.7291	G=0.0000, T=0.2709
1000Genomes_30x	South Asian	Sub	1202	C=0.6256	G=0.0000, T=0.3744
1000Genomes_30x	East Asian	Sub	1170	C=0.7188	G=0.0000, T=0.2812
1000Genomes_30x	American	Sub	980	C=0.805	G=0.000, T=0.195
1000Genomes	Global	Study-wide	5008	C=0.6779	G=0.0036, T=0.3185
1000Genomes	African	Sub	1322	C=0.5930	G=0.0136, T=0.3933
1000Genomes	East Asian	Sub	1008	C=0.7123	G=0.0000, T=0.2877
1000Genomes	Europe	Sub	1006	C=0.7217	G=0.0000, T=0.2783
1000Genomes	South Asian	Sub	978	C=0.628	G=0.000, T=0.372
1000Genomes	American	Sub	694	C=0.797	G=0.000, T=0.203
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7402	T=0.2598
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7512	T=0.2488
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7411	T=0.2589
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.7312	T=0.2688
HapMap	Global	Study-wide	1892	C=0.6934	T=0.3066
HapMap	American	Sub	770	C=0.697	T=0.303
HapMap	African	Sub	692	C=0.688	T=0.312
HapMap	Asian	Sub	254	C=0.728	T=0.272
HapMap	Europe	Sub	176	C=0.648	T=0.352
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7533	T=0.2467
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.707	T=0.293
Northern Sweden	ACPOP	Study-wide	600	C=0.725	T=0.275
SGDP_PRJ	Global	Study-wide	258	C=0.388	G=0.004, T=0.609
Qatari	Global	Study-wide	216	C=0.653	T=0.347
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.719	T=0.281
The Danish reference pan genome	Danish	Study-wide	40	C=0.72	T=0.28
Siberian	Global	Study-wide	24	C=0.42	T=0.58

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 9	NC_000009.12:g.83959653C>G
GRCh38.p14 chr 9	NC_000009.12:g.83959653C>T
GRCh37.p13 chr 9	NC_000009.11:g.86574568C>G
GRCh37.p13 chr 9	NC_000009.11:g.86574568C>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	C=	G	T
GRCh38.p14 chr 9	NC_000009.12:g.83959653=	NC_000009.12:g.83959653C>G	NC_000009.12:g.83959653C>T
GRCh37.p13 chr 9	NC_000009.11:g.86574568=	NC_000009.11:g.86574568C>G	NC_000009.11:g.86574568C>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#.

80 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3932346	Sep 28, 2001 (100)
2	SC_SNP	ss15967644	Feb 27, 2004 (120)
3	SSAHASNP	ss22832421	Apr 05, 2004 (121)
4	ABI	ss43857611	Mar 14, 2006 (126)
5	ILLUMINA	ss65796268	Oct 13, 2006 (127)
6	ILLUMINA	ss74998438	Dec 07, 2007 (129)
7	HGSV	ss84122447	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss94095931	Mar 25, 2008 (129)
9	HUMANGENOME_JCVI	ss97733396	Feb 05, 2009 (130)
10	BGI	ss105685557	Feb 05, 2009 (130)
11	ILLUMINA-UK	ss115749229	Feb 14, 2009 (130)
12	KRIBB_YJKIM	ss119445293	Dec 01, 2009 (131)
13	ENSEMBL	ss134066219	Dec 01, 2009 (131)
14	GMI	ss157656041	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss164320260	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss166617720	Jul 04, 2010 (132)
17	ILLUMINA	ss173460087	Jul 04, 2010 (132)
18	BUSHMAN	ss200529194	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss206693221	Jul 04, 2010 (132)
20	1000GENOMES	ss224303859	Jul 14, 2010 (132)
21	1000GENOMES	ss234859572	Jul 15, 2010 (132)
22	1000GENOMES	ss241625432	Jul 15, 2010 (132)
23	GMI	ss280287513	May 04, 2012 (137)
24	PJP	ss294304026	May 09, 2011 (134)
25	ILLUMINA	ss537125628	Sep 08, 2015 (146)
26	TISHKOFF	ss561450384	Apr 25, 2013 (138)
27	SSMP	ss655941619	Apr 25, 2013 (138)
28	EVA-GONL	ss986680829	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1076386518	Aug 21, 2014 (142)
30	1000GENOMES	ss1334334603	Aug 21, 2014 (142)
31	1000GENOMES	ss1334334604	Aug 21, 2014 (142)
32	DDI	ss1431875019	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1583143530	Apr 01, 2015 (144)
34	EVA_DECODE	ss1596313298	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1622961426	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1665955459	Apr 01, 2015 (144)
37	EVA_SVP	ss1713117535	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1806031505	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1929994440	Feb 12, 2016 (147)
40	JJLAB	ss2025713752	Sep 14, 2016 (149)
41	ILLUMINA	ss2094835663	Dec 20, 2016 (150)
42	ILLUMINA	ss2095222405	Dec 20, 2016 (150)
43	USC_VALOUEV	ss2153939253	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2312148549	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2627323498	Nov 08, 2017 (151)
46	GRF	ss2709805945	Nov 08, 2017 (151)
47	GNOMAD	ss2880037534	Nov 08, 2017 (151)
48	SWEGEN	ss3005132348	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3026638452	Nov 08, 2017 (151)
50	CSHL	ss3348725595	Nov 08, 2017 (151)
51	ILLUMINA	ss3630289525	Oct 12, 2018 (152)
52	ILLUMINA	ss3638819409	Oct 12, 2018 (152)
53	ILLUMINA	ss3643745779	Oct 12, 2018 (152)
54	URBANLAB	ss3649180174	Oct 12, 2018 (152)
55	ILLUMINA	ss3653491040	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3672674839	Jul 13, 2019 (153)
57	EVA_DECODE	ss3724197268	Jul 13, 2019 (153)
58	ACPOP	ss3736628982	Jul 13, 2019 (153)
59	EVA	ss3769337355	Jul 13, 2019 (153)
60	PACBIO	ss3786449098	Jul 13, 2019 (153)
61	PACBIO	ss3791660811	Jul 13, 2019 (153)
62	PACBIO	ss3796542169	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3812507301	Jul 13, 2019 (153)
64	EVA	ss3831715869	Apr 26, 2020 (154)
65	SGDP_PRJ	ss3872484441	Apr 26, 2020 (154)
66	KRGDB	ss3920290768	Apr 26, 2020 (154)
67	KOGIC	ss3966178695	Apr 26, 2020 (154)
68	TOPMED	ss4825774374	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5194024904	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5281193568	Oct 16, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5281193569	Oct 16, 2022 (156)
72	HUGCELL_USP	ss5477162976	Oct 16, 2022 (156)
73	1000G_HIGH_COVERAGE	ss5573761035	Oct 16, 2022 (156)
74	SANFORD_IMAGENETICS	ss5647707581	Oct 16, 2022 (156)
75	TOMMO_GENOMICS	ss5738174241	Oct 16, 2022 (156)
76	YY_MCH	ss5810753932	Oct 16, 2022 (156)
77	EVA	ss5829359263	Oct 16, 2022 (156)
78	EVA	ss5856814329	Oct 16, 2022 (156)
79	EVA	ss5976891600	Oct 16, 2022 (156)
80	EVA	ss5980561403	Oct 16, 2022 (156)
81	1000Genomes	NC_000009.11 - 86574568	Oct 12, 2018 (152)
82	1000Genomes_30x	NC_000009.12 - 83959653	Oct 16, 2022 (156)
83	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 86574568	Oct 12, 2018 (152)
84	Genetic variation in the Estonian population	NC_000009.11 - 86574568	Oct 12, 2018 (152)
85	The Danish reference pan genome	NC_000009.11 - 86574568	Apr 26, 2020 (154)
86	gnomAD - Genomes Submission ignored due to conflicting rows: Row 329564770 (NC_000009.12:83959652:C:G 228/139866) Row 329564771 (NC_000009.12:83959652:C:T 40947/139786)	-	Apr 26, 2021 (155)
87	gnomAD - Genomes Submission ignored due to conflicting rows: Row 329564770 (NC_000009.12:83959652:C:G 228/139866) Row 329564771 (NC_000009.12:83959652:C:T 40947/139786)	-	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000009.11 - 86574568	Apr 26, 2020 (154)
89	HapMap	NC_000009.12 - 83959653	Apr 26, 2020 (154)
90	KOREAN population from KRGDB	NC_000009.11 - 86574568	Apr 26, 2020 (154)
91	Korean Genome Project	NC_000009.12 - 83959653	Apr 26, 2020 (154)
92	Northern Sweden	NC_000009.11 - 86574568	Jul 13, 2019 (153)
93	Qatari	NC_000009.11 - 86574568	Apr 26, 2020 (154)
94	SGDP_PRJ	NC_000009.11 - 86574568	Apr 26, 2020 (154)
95	Siberian	NC_000009.11 - 86574568	Apr 26, 2020 (154)
96	8.3KJPN	NC_000009.11 - 86574568	Apr 26, 2021 (155)
97	14KJPN	NC_000009.12 - 83959653	Oct 16, 2022 (156)
98	TopMed	NC_000009.12 - 83959653	Apr 26, 2021 (155)
99	UK 10K study - Twins	NC_000009.11 - 86574568	Oct 12, 2018 (152)
100	A Vietnamese Genetic Variation Database	NC_000009.11 - 86574568	Jul 13, 2019 (153)
101	ALFA	NC_000009.12 - 83959653	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)
rs59341493	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
46611413, 24501421, ss1334334603, ss2880037534, ss3872484441, ss5647707581	NC_000009.11:86574567:C:G	NC_000009.12:83959652:C:G	(self)
61286970, 10463571355, ss2312148549, ss5281193569, ss5573761035	NC_000009.12:83959652:C:G	NC_000009.12:83959652:C:G	(self)
ss84122447	NC_000009.9:83804121:C:T	NC_000009.12:83959652:C:T	(self)
ss94095931, ss115749229, ss164320260, ss166617720, ss200529194, ss206693221, ss280287513, ss294304026, ss1596313298, ss1713117535, ss3643745779	NC_000009.10:85764387:C:T	NC_000009.12:83959652:C:T	(self)
46611413, 25887430, 18413087, 9308467, 11554365, 27468162, 9913847, 12036370, 24501421, 6455607, 51994211, 25887430, 5751162, ss224303859, ss234859572, ss241625432, ss537125628, ss561450384, ss655941619, ss986680829, ss1076386518, ss1334334604, ss1431875019, ss1583143530, ss1622961426, ss1665955459, ss1806031505, ss1929994440, ss2025713752, ss2094835663, ss2095222405, ss2153939253, ss2627323498, ss2709805945, ss2880037534, ss3005132348, ss3348725595, ss3630289525, ss3638819409, ss3653491040, ss3672674839, ss3736628982, ss3769337355, ss3786449098, ss3791660811, ss3796542169, ss3831715869, ss3872484441, ss3920290768, ss5194024904, ss5647707581, ss5829359263, ss5976891600, ss5980561403	NC_000009.11:86574567:C:T	NC_000009.12:83959652:C:T	(self)
61286970, 3855692, 22556696, 72011345, 663151935, 10463571355, ss2312148549, ss3026638452, ss3649180174, ss3724197268, ss3812507301, ss3966178695, ss4825774374, ss5281193568, ss5477162976, ss5573761035, ss5738174241, ss5810753932, ss5856814329	NC_000009.12:83959652:C:T	NC_000009.12:83959652:C:T	(self)
ss3932346, ss43857611, ss65796268, ss74998438, ss97733396, ss105685557, ss119445293, ss134066219, ss157656041, ss173460087	NT_008470.19:15739099:C:T	NC_000009.12:83959652:C:T	(self)
ss15967644, ss22832421	NT_023935.16:15739099:C:T	NC_000009.12:83959652:C: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 rs2780103

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

rs2780103