Name: rs2123741
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.

rs2123741

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:194894153 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.000204 (54/264690, TOPMED)
A=0.000171 (24/140108, GnomAD)
A=0.00000 (0/28256, 14KJPN) (+ 14 more)
A=0.00005 (1/18520, ALFA)
A=0.00000 (0/16760, 8.3KJPN)
A=0.0003 (2/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
A=0.0000 (0/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.0003 (1/2930, KOREAN)
A=0.0000 (0/1832, Korea1K)
A=0.000 (0/600, NorthernSweden)
A=0.000 (0/558, SGDP_PRJ)
A=0.000 (0/216, Qatari)
A=0.000 (0/212, Vietnamese)
A=0.00 (0/56, Siberian)
A=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105376755 : 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	18520	A=0.00005	C=0.99995
European	Sub	14152	A=0.00000	C=1.00000
African	Sub	2898	A=0.0003	C=0.9997
African Others	Sub	114	A=0.000	C=1.000
African American	Sub	2784	A=0.0004	C=0.9996
Asian	Sub	112	A=0.000	C=1.000
East Asian	Sub	86	A=0.00	C=1.00
Other Asian	Sub	26	A=0.00	C=1.00
Latin American 1	Sub	146	A=0.000	C=1.000
Latin American 2	Sub	610	A=0.000	C=1.000
South Asian	Sub	98	A=0.00	C=1.00
Other	Sub	504	A=0.000	C=1.000

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	A=0.000204	C=0.999796
gnomAD - Genomes	Global	Study-wide	140108	A=0.000171	C=0.999829
gnomAD - Genomes	European	Sub	75872	A=0.00000	C=1.00000
gnomAD - Genomes	African	Sub	42010	A=0.00057	C=0.99943
gnomAD - Genomes	American	Sub	13620	A=0.00000	C=1.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.0000	C=1.0000
gnomAD - Genomes	East Asian	Sub	3132	A=0.0000	C=1.0000
gnomAD - Genomes	Other	Sub	2152	A=0.0000	C=1.0000
14KJPN	JAPANESE	Study-wide	28256	A=0.00000	C=1.00000
Allele Frequency Aggregator	Total	Global	18520	A=0.00005	C=0.99995
Allele Frequency Aggregator	European	Sub	14152	A=0.00000	C=1.00000
Allele Frequency Aggregator	African	Sub	2898	A=0.0003	C=0.9997
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.000	C=1.000
Allele Frequency Aggregator	Other	Sub	504	A=0.000	C=1.000
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.000	C=1.000
Allele Frequency Aggregator	Asian	Sub	112	A=0.000	C=1.000
Allele Frequency Aggregator	South Asian	Sub	98	A=0.00	C=1.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.00000	C=1.00000
1000Genomes_30x	Global	Study-wide	6404	A=0.0003	C=0.9997
1000Genomes_30x	African	Sub	1786	A=0.0000	C=1.0000
1000Genomes_30x	Europe	Sub	1266	A=0.0000	C=1.0000
1000Genomes_30x	South Asian	Sub	1202	A=0.0000	C=1.0000
1000Genomes_30x	East Asian	Sub	1170	A=0.0000	C=1.0000
1000Genomes_30x	American	Sub	980	A=0.002	C=0.998
1000Genomes	Global	Study-wide	5008	A=0.0002	C=0.9998
1000Genomes	African	Sub	1322	A=0.0000	C=1.0000
1000Genomes	East Asian	Sub	1008	A=0.0000	C=1.0000
1000Genomes	Europe	Sub	1006	A=0.0000	C=1.0000
1000Genomes	South Asian	Sub	978	A=0.000	C=1.000
1000Genomes	American	Sub	694	A=0.001	C=0.999
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.0000	C=1.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.0000	C=1.0000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.0003	C=0.9997
Korean Genome Project	KOREAN	Study-wide	1832	A=0.0000	C=1.0000
Northern Sweden	ACPOP	Study-wide	600	A=0.000	C=1.000
SGDP_PRJ	Global	Study-wide	558	A=0.000	C=1.000
Qatari	Global	Study-wide	216	A=0.000	C=1.000
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.000	C=1.000
Siberian	Global	Study-wide	56	A=0.00	C=1.00
The Danish reference pan genome	Danish	Study-wide	40	A=0.00	C=1.00

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 2	NC_000002.12:g.194894153A>C
GRCh37.p13 chr 2	NC_000002.11:g.195758877A>C

Gene: LOC105376755, uncharacterized LOC105376755 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105376755 transcript variant X3	XR_007088699.1:n.	N/A	Intron Variant
LOC105376755 transcript variant X1	XR_001739834.1:n.	N/A	Genic Downstream Transcript Variant
LOC105376755 transcript variant X2	XR_001739835.1:n.	N/A	Genic 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	A=	C
GRCh38.p14 chr 2	NC_000002.12:g.194894153=	NC_000002.12:g.194894153A>C
GRCh37.p13 chr 2	NC_000002.11:g.195758877=	NC_000002.11:g.195758877A>C

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#.

77 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3046403	Jun 15, 2001 (96)
2	SC_JCM	ss5667895	Feb 20, 2003 (126)
3	BCM_SSAHASNP	ss9925249	Jul 11, 2003 (116)
4	WI_SSAHASNP	ss11449037	Jul 11, 2003 (116)
5	WUGSC_SSAHASNP	ss14469269	Dec 05, 2003 (126)
6	SC_SNP	ss15438133	Feb 28, 2004 (126)
7	CSHL-HAPMAP	ss19412457	Feb 27, 2004 (120)
8	SSAHASNP	ss21576299	Apr 05, 2004 (121)
9	HGSV	ss80001112	Dec 15, 2007 (130)
10	HGSV	ss83136335	Dec 15, 2007 (130)
11	HGSV	ss83899366	Dec 15, 2007 (130)
12	HGSV	ss85600335	Dec 15, 2007 (130)
13	BCMHGSC_JDW	ss91497123	Mar 24, 2008 (129)
14	HUMANGENOME_JCVI	ss96461078	Feb 05, 2009 (130)
15	BGI	ss106151915	Feb 05, 2009 (130)
16	1000GENOMES	ss110523753	Jan 24, 2009 (130)
17	1000GENOMES	ss111469207	Jan 25, 2009 (130)
18	ILLUMINA-UK	ss118028690	Dec 01, 2009 (131)
19	ENSEMBL	ss136014260	Dec 01, 2009 (131)
20	ENSEMBL	ss138605444	Dec 01, 2009 (131)
21	GMI	ss154522399	Dec 01, 2009 (131)
22	COMPLETE_GENOMICS	ss165193269	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss165789915	Jul 04, 2010 (132)
24	COMPLETE_GENOMICS	ss167514551	Jul 04, 2010 (132)
25	BUSHMAN	ss201560599	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss205592021	Jul 04, 2010 (132)
27	GMI	ss276847647	May 04, 2012 (137)
28	GMI	ss284514774	Apr 25, 2013 (138)
29	PJP	ss292461381	May 09, 2011 (134)
30	1000GENOMES	ss330226443	May 09, 2011 (134)
31	TISHKOFF	ss556129863	Apr 25, 2013 (138)
32	SSMP	ss649794770	Apr 25, 2013 (138)
33	JMKIDD_LAB	ss1069828043	Aug 21, 2014 (142)
34	1000GENOMES	ss1301057160	Aug 21, 2014 (142)
35	DDI	ss1428867403	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1579263661	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1605480713	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1648474746	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1798139164	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1921056908	Feb 12, 2016 (147)
41	GENOMED	ss1968990139	Jul 19, 2016 (147)
42	JJLAB	ss2021069449	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2149134352	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2237908055	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2625038046	Nov 08, 2017 (151)
46	GRF	ss2703779610	Nov 08, 2017 (151)
47	GNOMAD	ss2784633115	Nov 08, 2017 (151)
48	SWEGEN	ss2991119727	Nov 08, 2017 (151)
49	CSHL	ss3344677302	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3645605027	Oct 11, 2018 (152)
51	URBANLAB	ss3647242430	Oct 11, 2018 (152)
52	EVA_DECODE	ss3705733435	Jul 13, 2019 (153)
53	ACPOP	ss3729245290	Jul 13, 2019 (153)
54	EVA	ss3757910067	Jul 13, 2019 (153)
55	PACBIO	ss3784111301	Jul 13, 2019 (153)
56	PACBIO	ss3789656240	Jul 13, 2019 (153)
57	PACBIO	ss3794529389	Jul 13, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3802269430	Jul 13, 2019 (153)
59	EVA	ss3827431895	Apr 25, 2020 (154)
60	EVA	ss3837135749	Apr 25, 2020 (154)
61	EVA	ss3842556678	Apr 25, 2020 (154)
62	SGDP_PRJ	ss3854296405	Apr 25, 2020 (154)
63	KRGDB	ss3899971304	Apr 25, 2020 (154)
64	KOGIC	ss3949797082	Apr 25, 2020 (154)
65	TOPMED	ss4539384528	Apr 26, 2021 (155)
66	TOMMO_GENOMICS	ss5155827862	Apr 26, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5251517661	Oct 12, 2022 (156)
68	EVA	ss5335094465	Oct 12, 2022 (156)
69	HUGCELL_USP	ss5451184648	Oct 12, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5528599595	Oct 12, 2022 (156)
71	SANFORD_IMAGENETICS	ss5630665896	Oct 12, 2022 (156)
72	TOMMO_GENOMICS	ss5686513975	Oct 12, 2022 (156)
73	YY_MCH	ss5803101441	Oct 12, 2022 (156)
74	EVA	ss5821391957	Oct 12, 2022 (156)
75	EVA	ss5852895841	Oct 12, 2022 (156)
76	EVA	ss5934114380	Oct 12, 2022 (156)
77	EVA	ss5956907935	Oct 12, 2022 (156)
78	1000Genomes	NC_000002.11 - 195758877	Oct 11, 2018 (152)
79	1000Genomes_30x	NC_000002.12 - 194894153	Oct 12, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 195758877	Oct 11, 2018 (152)
81	The Danish reference pan genome	NC_000002.11 - 195758877	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000002.12 - 194894153	Apr 26, 2021 (155)
83	KOREAN population from KRGDB	NC_000002.11 - 195758877	Apr 25, 2020 (154)
84	Korean Genome Project	NC_000002.12 - 194894153	Apr 25, 2020 (154)
85	Northern Sweden	NC_000002.11 - 195758877	Jul 13, 2019 (153)
86	Qatari	NC_000002.11 - 195758877	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000002.11 - 195758877	Apr 25, 2020 (154)
88	Siberian	NC_000002.11 - 195758877	Apr 25, 2020 (154)
89	8.3KJPN	NC_000002.11 - 195758877	Apr 26, 2021 (155)
90	14KJPN	NC_000002.12 - 194894153	Oct 12, 2022 (156)
91	TopMed	NC_000002.12 - 194894153	Apr 26, 2021 (155)
92	UK 10K study - Twins	NC_000002.11 - 195758877	Oct 11, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000002.11 - 195758877	Jul 13, 2019 (153)
94	ALFA	NC_000002.12 - 194894153	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)
rs4284847	Mar 11, 2006 (126)
rs10323566	Mar 11, 2006 (126)
rs11489042	Mar 11, 2006 (126)
rs59251084	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80001112, ss83136335, ss83899366, ss85600335	NC_000002.9:195584382:A:C	NC_000002.12:194894152:A:C	(self)
ss91497123, ss110523753, ss111469207, ss118028690, ss165193269, ss165789915, ss167514551, ss201560599, ss205592021, ss276847647, ss284514774, ss292461381	NC_000002.10:195467121:A:C	NC_000002.12:194894152:A:C	(self)
12139718, 6706114, 5428600, 7148698, 2530155, 3098838, 6313385, 1650706, 13797169, 6706114, 1462808, ss330226443, ss556129863, ss649794770, ss1069828043, ss1301057160, ss1428867403, ss1579263661, ss1605480713, ss1648474746, ss1798139164, ss1921056908, ss1968990139, ss2021069449, ss2149134352, ss2625038046, ss2703779610, ss2784633115, ss2991119727, ss3344677302, ss3729245290, ss3757910067, ss3784111301, ss3789656240, ss3794529389, ss3827431895, ss3837135749, ss3854296405, ss3899971304, ss5155827862, ss5335094465, ss5630665896, ss5821391957, ss5956907935	NC_000002.11:195758876:A:C	NC_000002.12:194894152:A:C	(self)
16125530, 86544059, 6175083, 20351079, 343207407, 1184970549, ss2237908055, ss3645605027, ss3647242430, ss3705733435, ss3802269430, ss3842556678, ss3949797082, ss4539384528, ss5251517661, ss5451184648, ss5528599595, ss5686513975, ss5803101441, ss5852895841, ss5934114380	NC_000002.12:194894152:A:C	NC_000002.12:194894152:A:C	(self)
ss9925249, ss11449037	NT_005403.13:45918213:A:C	NC_000002.12:194894152:A:C	(self)
ss14469269, ss15438133, ss19412457, ss21576299	NT_005403.14:45968292:A:C	NC_000002.12:194894152:A:C	(self)
ss3046403, ss5667895, ss96461078, ss106151915, ss136014260, ss138605444, ss154522399	NT_005403.17:45968294:A:C	NC_000002.12:194894152:A:C	(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 rs2123741

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

rs2123741