Name: rs13042767
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.

rs13042767

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:2755458 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.066017 (17474/264690, TOPMED)
C=0.058360 (8174/140062, GnomAD)
C=0.18770 (5304/28258, 14KJPN) (+ 13 more)
C=0.05718 (1092/19096, ALFA)
C=0.18383 (3081/16760, 8.3KJPN)
C=0.0795 (509/6404, 1000G_30x)
C=0.0797 (399/5008, 1000G)
C=0.0594 (266/4480, Estonian)
C=0.1877 (550/2930, KOREAN)
C=0.1834 (336/1832, Korea1K)
C=0.043 (26/600, NorthernSweden)
C=0.060 (13/216, Qatari)
G=0.42 (42/100, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
G=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: EBF4 : 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	19096	G=0.94282	C=0.05718
European	Sub	14422	G=0.94793	C=0.05207
African	Sub	2976	G=0.9533	C=0.0467
African Others	Sub	114	G=0.965	C=0.035
African American	Sub	2862	G=0.9528	C=0.0472
Asian	Sub	114	G=0.816	C=0.184
East Asian	Sub	88	G=0.82	C=0.18
Other Asian	Sub	26	G=0.81	C=0.19
Latin American 1	Sub	150	G=0.960	C=0.040
Latin American 2	Sub	626	G=0.810	C=0.190
South Asian	Sub	98	G=0.95	C=0.05
Other	Sub	710	G=0.928	C=0.072

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=0.933983	C=0.066017
gnomAD - Genomes	Global	Study-wide	140062	G=0.941640	C=0.058360
gnomAD - Genomes	European	Sub	75856	G=0.94781	C=0.05219
gnomAD - Genomes	African	Sub	41964	G=0.95877	C=0.04123
gnomAD - Genomes	American	Sub	13640	G=0.87170	C=0.12830
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9543	C=0.0457
gnomAD - Genomes	East Asian	Sub	3126	G=0.8580	C=0.1420
gnomAD - Genomes	Other	Sub	2152	G=0.9354	C=0.0646
14KJPN	JAPANESE	Study-wide	28258	G=0.81230	C=0.18770
Allele Frequency Aggregator	Total	Global	19096	G=0.94282	C=0.05718
Allele Frequency Aggregator	European	Sub	14422	G=0.94793	C=0.05207
Allele Frequency Aggregator	African	Sub	2976	G=0.9533	C=0.0467
Allele Frequency Aggregator	Other	Sub	710	G=0.928	C=0.072
Allele Frequency Aggregator	Latin American 2	Sub	626	G=0.810	C=0.190
Allele Frequency Aggregator	Latin American 1	Sub	150	G=0.960	C=0.040
Allele Frequency Aggregator	Asian	Sub	114	G=0.816	C=0.184
Allele Frequency Aggregator	South Asian	Sub	98	G=0.95	C=0.05
8.3KJPN	JAPANESE	Study-wide	16760	G=0.81617	C=0.18383
1000Genomes_30x	Global	Study-wide	6404	G=0.9205	C=0.0795
1000Genomes_30x	African	Sub	1786	G=0.9642	C=0.0358
1000Genomes_30x	Europe	Sub	1266	G=0.9660	C=0.0340
1000Genomes_30x	South Asian	Sub	1202	G=0.9251	C=0.0749
1000Genomes_30x	East Asian	Sub	1170	G=0.8641	C=0.1359
1000Genomes_30x	American	Sub	980	G=0.844	C=0.156
1000Genomes	Global	Study-wide	5008	G=0.9203	C=0.0797
1000Genomes	African	Sub	1322	G=0.9644	C=0.0356
1000Genomes	East Asian	Sub	1008	G=0.8651	C=0.1349
1000Genomes	Europe	Sub	1006	G=0.9662	C=0.0338
1000Genomes	South Asian	Sub	978	G=0.928	C=0.072
1000Genomes	American	Sub	694	G=0.839	C=0.161
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9406	C=0.0594
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8123	C=0.1877
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8166	C=0.1834
Northern Sweden	ACPOP	Study-wide	600	G=0.957	C=0.043
Qatari	Global	Study-wide	216	G=0.940	C=0.060
SGDP_PRJ	Global	Study-wide	100	G=0.42	C=0.58
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	C=0.03
Siberian	Global	Study-wide	4	G=0.5	C=0.5

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 20	NC_000020.11:g.2755458G>C
GRCh37.p13 chr 20	NC_000020.10:g.2736104G>C

Gene: EBF4, EBF family member 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EBF4 transcript variant 1	NM_001110514.1:c.1529-169… NM_001110514.1:c.1529-169G>C	N/A	Intron Variant
EBF4 transcript variant 3	NM_001395167.1:c.1541-169… NM_001395167.1:c.1541-169G>C	N/A	Intron Variant
EBF4 transcript variant 4	NM_001395168.1:c.1310-169… NM_001395168.1:c.1310-169G>C	N/A	Intron Variant
EBF4 transcript variant 2	NR_138537.2:n.	N/A	Intron Variant
EBF4 transcript variant X2	XM_006723600.2:c.1643-169… XM_006723600.2:c.1643-169G>C	N/A	Intron Variant
EBF4 transcript variant X1	XM_017027984.2:c.1673-169… XM_017027984.2:c.1673-169G>C	N/A	Intron Variant
EBF4 transcript variant X3	XM_017027985.1:c.842-169G… XM_017027985.1:c.842-169G>C	N/A	Intron Variant
EBF4 transcript variant X4	XM_047440335.1:c.1451-182… XM_047440335.1:c.1451-182G>C	N/A	Intron 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=	C
GRCh38.p14 chr 20	NC_000020.11:g.2755458=	NC_000020.11:g.2755458G>C
GRCh37.p13 chr 20	NC_000020.10:g.2736104=	NC_000020.10:g.2736104G>C
EBF4 transcript variant 1	NM_001110514.1:c.1529-169=	NM_001110514.1:c.1529-169G>C
EBF4 transcript variant 3	NM_001395167.1:c.1541-169=	NM_001395167.1:c.1541-169G>C
EBF4 transcript variant 4	NM_001395168.1:c.1310-169=	NM_001395168.1:c.1310-169G>C
EBF4 transcript variant X1	XM_005260770.1:c.1541-169=	XM_005260770.1:c.1541-169G>C
EBF4 transcript variant X2	XM_005260771.1:c.842-169=	XM_005260771.1:c.842-169G>C
EBF4 transcript variant X2	XM_006723600.2:c.1643-169=	XM_006723600.2:c.1643-169G>C
EBF4 transcript variant X1	XM_017027984.2:c.1673-169=	XM_017027984.2:c.1673-169G>C
EBF4 transcript variant X3	XM_017027985.1:c.842-169=	XM_017027985.1:c.842-169G>C
EBF4 transcript variant X4	XM_047440335.1:c.1451-182=	XM_047440335.1:c.1451-182G>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#.

61 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21788201	Apr 05, 2004 (121)
2	ABI	ss41390782	Mar 13, 2006 (126)
3	HUMANGENOME_JCVI	ss96182044	Feb 03, 2009 (130)
4	IGMI-SNU	ss115458669	Feb 03, 2009 (130)
5	ENSEMBL	ss133033941	Dec 01, 2009 (131)
6	GMI	ss156088237	Dec 01, 2009 (131)
7	1000GENOMES	ss228223277	Jul 14, 2010 (132)
8	1000GENOMES	ss237738984	Jul 15, 2010 (132)
9	1000GENOMES	ss243930468	Jul 15, 2010 (132)
10	BL	ss255437566	May 09, 2011 (134)
11	GMI	ss283277279	May 04, 2012 (137)
12	PJP	ss292565093	May 09, 2011 (134)
13	ILLUMINA	ss483619222	May 04, 2012 (137)
14	ILLUMINA	ss484177046	May 04, 2012 (137)
15	ILLUMINA	ss535823375	Sep 08, 2015 (146)
16	SSMP	ss661967186	Apr 25, 2013 (138)
17	ILLUMINA	ss780345522	Sep 08, 2015 (146)
18	ILLUMINA	ss782252962	Sep 08, 2015 (146)
19	ILLUMINA	ss835833145	Sep 08, 2015 (146)
20	EVA-GONL	ss994479094	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1082026276	Aug 21, 2014 (142)
22	1000GENOMES	ss1363845311	Aug 21, 2014 (142)
23	EVA_GENOME_DK	ss1579411897	Apr 01, 2015 (144)
24	EVA_DECODE	ss1698533302	Apr 01, 2015 (144)
25	WEILL_CORNELL_DGM	ss1937988147	Feb 12, 2016 (147)
26	JJLAB	ss2029770703	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2158324471	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2240873403	Dec 20, 2016 (150)
29	SYSTEMSBIOZJU	ss2629382905	Nov 08, 2017 (151)
30	ILLUMINA	ss2633768750	Nov 08, 2017 (151)
31	GRF	ss2703996014	Nov 08, 2017 (151)
32	GNOMAD	ss2964818912	Nov 08, 2017 (151)
33	SWEGEN	ss3017776716	Nov 08, 2017 (151)
34	CSHL	ss3352390924	Nov 08, 2017 (151)
35	ILLUMINA	ss3628336713	Oct 12, 2018 (152)
36	ILLUMINA	ss3631726957	Oct 12, 2018 (152)
37	ILLUMINA	ss3642169309	Oct 12, 2018 (152)
38	URBANLAB	ss3650958022	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3684490567	Jul 13, 2019 (153)
40	EVA_DECODE	ss3706446783	Jul 13, 2019 (153)
41	ACPOP	ss3743198098	Jul 13, 2019 (153)
42	EVA	ss3758352662	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3821524506	Jul 13, 2019 (153)
44	EVA	ss3835556812	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3888614122	Apr 27, 2020 (154)
46	KRGDB	ss3938792893	Apr 27, 2020 (154)
47	KOGIC	ss3981718338	Apr 27, 2020 (154)
48	TOPMED	ss5080391539	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5228592987	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5307890803	Oct 16, 2022 (156)
51	EVA	ss5315989383	Oct 16, 2022 (156)
52	EVA	ss5435907322	Oct 16, 2022 (156)
53	HUGCELL_USP	ss5500310576	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5613878846	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5662752334	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5787510172	Oct 16, 2022 (156)
57	YY_MCH	ss5817766550	Oct 16, 2022 (156)
58	EVA	ss5845365897	Oct 16, 2022 (156)
59	EVA	ss5853043541	Oct 16, 2022 (156)
60	EVA	ss5922452438	Oct 16, 2022 (156)
61	EVA	ss5957650229	Oct 16, 2022 (156)
62	1000Genomes	NC_000020.10 - 2736104	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000020.11 - 2755458	Oct 16, 2022 (156)
64	Genetic variation in the Estonian population	NC_000020.10 - 2736104	Oct 12, 2018 (152)
65	The Danish reference pan genome	NC_000020.10 - 2736104	Apr 27, 2020 (154)
66	gnomAD - Genomes	NC_000020.11 - 2755458	Apr 26, 2021 (155)
67	KOREAN population from KRGDB	NC_000020.10 - 2736104	Apr 27, 2020 (154)
68	Korean Genome Project	NC_000020.11 - 2755458	Apr 27, 2020 (154)
69	Northern Sweden	NC_000020.10 - 2736104	Jul 13, 2019 (153)
70	Qatari	NC_000020.10 - 2736104	Apr 27, 2020 (154)
71	SGDP_PRJ	NC_000020.10 - 2736104	Apr 27, 2020 (154)
72	Siberian	NC_000020.10 - 2736104	Apr 27, 2020 (154)
73	8.3KJPN	NC_000020.10 - 2736104	Apr 26, 2021 (155)
74	14KJPN	NC_000020.11 - 2755458	Oct 16, 2022 (156)
75	TopMed	NC_000020.11 - 2755458	Apr 26, 2021 (155)
76	ALFA	NC_000020.11 - 2755458	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss255437566, ss283277279, ss292565093, ss484177046, ss1698533302	NC_000020.9:2684103:G:C	NC_000020.11:2755457:G:C	(self)
77276961, 30228815, 5576836, 45970287, 16482963, 20030069, 40631102, 10840825, 86562294, ss228223277, ss237738984, ss243930468, ss483619222, ss535823375, ss661967186, ss780345522, ss782252962, ss835833145, ss994479094, ss1082026276, ss1363845311, ss1579411897, ss1937988147, ss2029770703, ss2158324471, ss2629382905, ss2633768750, ss2703996014, ss2964818912, ss3017776716, ss3352390924, ss3628336713, ss3631726957, ss3642169309, ss3684490567, ss3743198098, ss3758352662, ss3835556812, ss3888614122, ss3938792893, ss5228592987, ss5315989383, ss5435907322, ss5662752334, ss5845365897, ss5957650229	NC_000020.10:2736103:G:C	NC_000020.11:2755457:G:C	(self)
101404781, 544925553, 38096339, 121347276, 355500484, 807345458, ss2240873403, ss3650958022, ss3706446783, ss3821524506, ss3981718338, ss5080391539, ss5307890803, ss5500310576, ss5613878846, ss5787510172, ss5817766550, ss5853043541, ss5922452438	NC_000020.11:2755457:G:C	NC_000020.11:2755457:G:C	(self)
ss21788201, ss41390782, ss96182044, ss115458669, ss133033941, ss156088237	NT_011387.8:2676103:G:C	NC_000020.11:2755457:G: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 rs13042767

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

rs13042767