Name: rs60129138
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.

rs60129138

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:40952214 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.064985 (17201/264690, TOPMED)
T=0.059860 (8371/139844, GnomAD)
T=0.13889 (10931/78702, PAGE_STUDY) (+ 15 more)
T=0.38354 (10838/28258, 14KJPN)
T=0.04523 (1010/22328, ALFA)
T=0.37983 (6366/16760, 8.3KJPN)
T=0.1512 (968/6404, 1000G_30x)
T=0.1538 (770/5008, 1000G)
T=0.0275 (123/4480, Estonian)
T=0.0029 (11/3854, ALSPAC)
T=0.0008 (3/3708, TWINSUK)
T=0.3587 (1051/2930, KOREAN)
T=0.003 (3/998, GoNL)
T=0.043 (26/600, NorthernSweden)
T=0.083 (18/216, Qatari)
T=0.316 (67/212, Vietnamese)
C=0.384 (73/190, SGDP_PRJ)
C=0.40 (8/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ELF1 : 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	22328	C=0.95477	T=0.04523
European	Sub	14364	C=0.98851	T=0.01149
African	Sub	6006	C=0.8913	T=0.1087
African Others	Sub	198	C=0.884	T=0.116
African American	Sub	5808	C=0.8915	T=0.1085
Asian	Sub	146	C=0.671	T=0.329
East Asian	Sub	120	C=0.667	T=0.333
Other Asian	Sub	26	C=0.69	T=0.31
Latin American 1	Sub	146	C=0.945	T=0.055
Latin American 2	Sub	610	C=0.908	T=0.092
South Asian	Sub	104	C=0.923	T=0.077
Other	Sub	952	C=0.924	T=0.076

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=0.935015	T=0.064985
gnomAD - Genomes	Global	Study-wide	139844	C=0.940140	T=0.059860
gnomAD - Genomes	European	Sub	75764	C=0.98344	T=0.01656
gnomAD - Genomes	African	Sub	41868	C=0.88662	T=0.11338
gnomAD - Genomes	American	Sub	13624	C=0.91816	T=0.08184
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9931	T=0.0069
gnomAD - Genomes	East Asian	Sub	3120	C=0.6593	T=0.3407
gnomAD - Genomes	Other	Sub	2148	C=0.9218	T=0.0782
The PAGE Study	Global	Study-wide	78702	C=0.86111	T=0.13889
The PAGE Study	AfricanAmerican	Sub	32516	C=0.89079	T=0.10921
The PAGE Study	Mexican	Sub	10810	C=0.89334	T=0.10666
The PAGE Study	Asian	Sub	8318	C=0.6405	T=0.3595
The PAGE Study	PuertoRican	Sub	7918	C=0.9442	T=0.0558
The PAGE Study	NativeHawaiian	Sub	4534	C=0.6169	T=0.3831
The PAGE Study	Cuban	Sub	4230	C=0.9669	T=0.0331
The PAGE Study	Dominican	Sub	3828	C=0.9169	T=0.0831
The PAGE Study	CentralAmerican	Sub	2450	C=0.8963	T=0.1037
The PAGE Study	SouthAmerican	Sub	1982	C=0.9162	T=0.0838
The PAGE Study	NativeAmerican	Sub	1260	C=0.9254	T=0.0746
The PAGE Study	SouthAsian	Sub	856	C=0.900	T=0.100
14KJPN	JAPANESE	Study-wide	28258	C=0.61646	T=0.38354
Allele Frequency Aggregator	Total	Global	22328	C=0.95477	T=0.04523
Allele Frequency Aggregator	European	Sub	14364	C=0.98851	T=0.01149
Allele Frequency Aggregator	African	Sub	6006	C=0.8913	T=0.1087
Allele Frequency Aggregator	Other	Sub	952	C=0.924	T=0.076
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.908	T=0.092
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.945	T=0.055
Allele Frequency Aggregator	Asian	Sub	146	C=0.671	T=0.329
Allele Frequency Aggregator	South Asian	Sub	104	C=0.923	T=0.077
8.3KJPN	JAPANESE	Study-wide	16760	C=0.62017	T=0.37983
1000Genomes_30x	Global	Study-wide	6404	C=0.8488	T=0.1512
1000Genomes_30x	African	Sub	1786	C=0.8611	T=0.1389
1000Genomes_30x	Europe	Sub	1266	C=0.9818	T=0.0182
1000Genomes_30x	South Asian	Sub	1202	C=0.8794	T=0.1206
1000Genomes_30x	East Asian	Sub	1170	C=0.6009	T=0.3991
1000Genomes_30x	American	Sub	980	C=0.913	T=0.087
1000Genomes	Global	Study-wide	5008	C=0.8462	T=0.1538
1000Genomes	African	Sub	1322	C=0.8661	T=0.1339
1000Genomes	East Asian	Sub	1008	C=0.6111	T=0.3889
1000Genomes	Europe	Sub	1006	C=0.9781	T=0.0219
1000Genomes	South Asian	Sub	978	C=0.878	T=0.122
1000Genomes	American	Sub	694	C=0.914	T=0.086
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9725	T=0.0275
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9971	T=0.0029
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9992	T=0.0008
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6413	T=0.3587
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.997	T=0.003
Northern Sweden	ACPOP	Study-wide	600	C=0.957	T=0.043
Qatari	Global	Study-wide	216	C=0.917	T=0.083
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.684	T=0.316
SGDP_PRJ	Global	Study-wide	190	C=0.384	T=0.616
Siberian	Global	Study-wide	20	C=0.40	T=0.60

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 13	NC_000013.11:g.40952214C>T
GRCh37.p13 chr 13	NC_000013.10:g.41526350C>T

Gene: ELF1, E74 like ETS transcription factor 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ELF1 transcript variant 2	NM_001145353.1:c.254-778G… NM_001145353.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant 3	NM_001370329.1:c.77-778G>A	N/A	Intron Variant
ELF1 transcript variant 4	NM_001370330.1:c.254-778G… NM_001370330.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant 5	NM_001370331.1:c.254-778G… NM_001370331.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant 6	NM_001370332.1:c.254-778G… NM_001370332.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant 1	NM_172373.4:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant X1	XM_047430118.1:c.254-778G… XM_047430118.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant X2	XM_047430119.1:c.254-778G… XM_047430119.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant X3	XM_047430120.1:c.254-778G… XM_047430120.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant X4	XM_047430121.1:c.254-778G… XM_047430121.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant X5	XM_047430122.1:c.254-778G… XM_047430122.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant X6	XM_047430123.1:c.254-778G… XM_047430123.1:c.254-778G>A	N/A	Intron Variant
ELF1 transcript variant X7	XM_047430124.1:c.254-778G… XM_047430124.1:c.254-778G>A	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	C=	T
GRCh38.p14 chr 13	NC_000013.11:g.40952214=	NC_000013.11:g.40952214C>T
GRCh37.p13 chr 13	NC_000013.10:g.41526350=	NC_000013.10:g.41526350C>T
ELF1 transcript variant 2	NM_001145353.1:c.254-778=	NM_001145353.1:c.254-778G>A
ELF1 transcript variant 3	NM_001370329.1:c.77-778=	NM_001370329.1:c.77-778G>A
ELF1 transcript variant 4	NM_001370330.1:c.254-778=	NM_001370330.1:c.254-778G>A
ELF1 transcript variant 5	NM_001370331.1:c.254-778=	NM_001370331.1:c.254-778G>A
ELF1 transcript variant 6	NM_001370332.1:c.254-778=	NM_001370332.1:c.254-778G>A
ELF1 transcript variant 1	NM_172373.3:c.254-778=	NM_172373.3:c.254-778G>A
ELF1 transcript variant 1	NM_172373.4:c.254-778=	NM_172373.4:c.254-778G>A
ELF1 transcript variant X2	XM_005266276.1:c.254-778=	XM_005266276.1:c.254-778G>A
ELF1 transcript variant X2	XM_005266277.1:c.254-778=	XM_005266277.1:c.254-778G>A
ELF1 transcript variant X1	XM_047430118.1:c.254-778=	XM_047430118.1:c.254-778G>A
ELF1 transcript variant X2	XM_047430119.1:c.254-778=	XM_047430119.1:c.254-778G>A
ELF1 transcript variant X3	XM_047430120.1:c.254-778=	XM_047430120.1:c.254-778G>A
ELF1 transcript variant X4	XM_047430121.1:c.254-778=	XM_047430121.1:c.254-778G>A
ELF1 transcript variant X5	XM_047430122.1:c.254-778=	XM_047430122.1:c.254-778G>A
ELF1 transcript variant X6	XM_047430123.1:c.254-778=	XM_047430123.1:c.254-778G>A
ELF1 transcript variant X7	XM_047430124.1:c.254-778=	XM_047430124.1:c.254-778G>A

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#.

55 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss84394447	Dec 15, 2007 (129)
2	GMI	ss154713696	Dec 01, 2009 (131)
3	ENSEMBL	ss161593110	Dec 01, 2009 (131)
4	BUSHMAN	ss199128516	Jul 04, 2010 (132)
5	1000GENOMES	ss226151424	Jul 14, 2010 (132)
6	1000GENOMES	ss242728260	Jul 15, 2010 (132)
7	GMI	ss281689511	May 04, 2012 (137)
8	TISHKOFF	ss563629520	Apr 25, 2013 (138)
9	SSMP	ss659229352	Apr 25, 2013 (138)
10	EVA-GONL	ss990324393	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1079036163	Aug 21, 2014 (142)
12	1000GENOMES	ss1347970340	Aug 21, 2014 (142)
13	DDI	ss1427169571	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1630146752	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1673140785	Apr 01, 2015 (144)
16	EVA_DECODE	ss1684845252	Apr 01, 2015 (144)
17	HAMMER_LAB	ss1807582817	Sep 08, 2015 (146)
18	WEILL_CORNELL_DGM	ss1933692496	Feb 12, 2016 (147)
19	ILLUMINA	ss1959496791	Feb 12, 2016 (147)
20	GENOMED	ss1967767740	Jul 19, 2016 (147)
21	JJLAB	ss2027605095	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2155970340	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2195812678	Dec 20, 2016 (150)
24	SYSTEMSBIOZJU	ss2628292171	Nov 08, 2017 (151)
25	GRF	ss2700345739	Nov 08, 2017 (151)
26	GNOMAD	ss2918925181	Nov 08, 2017 (151)
27	SWEGEN	ss3010916719	Nov 08, 2017 (151)
28	ILLUMINA	ss3021502936	Nov 08, 2017 (151)
29	ILLUMINA	ss3651888776	Oct 12, 2018 (152)
30	EGCUT_WGS	ss3678179953	Jul 13, 2019 (153)
31	ILLUMINA	ss3725389274	Jul 13, 2019 (153)
32	ACPOP	ss3739691815	Jul 13, 2019 (153)
33	EVA	ss3751385768	Jul 13, 2019 (153)
34	PAGE_CC	ss3771742711	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3816717492	Jul 13, 2019 (153)
36	SGDP_PRJ	ss3879843482	Apr 27, 2020 (154)
37	KRGDB	ss3928680747	Apr 27, 2020 (154)
38	TOPMED	ss4944050346	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5209705804	Apr 26, 2021 (155)
40	EVA	ss5237525481	Apr 26, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5293512924	Oct 16, 2022 (156)
42	EVA	ss5410366484	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5487898696	Oct 16, 2022 (156)
44	EVA	ss5510950227	Oct 16, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5592351966	Oct 16, 2022 (156)
46	SANFORD_IMAGENETICS	ss5624322852	Oct 16, 2022 (156)
47	SANFORD_IMAGENETICS	ss5654642945	Oct 16, 2022 (156)
48	TOMMO_GENOMICS	ss5761497716	Oct 16, 2022 (156)
49	YY_MCH	ss5814055212	Oct 16, 2022 (156)
50	EVA	ss5839388651	Oct 16, 2022 (156)
51	EVA	ss5847423316	Oct 16, 2022 (156)
52	EVA	ss5850701424	Oct 16, 2022 (156)
53	EVA	ss5924853202	Oct 16, 2022 (156)
54	EVA	ss5946058294	Oct 16, 2022 (156)
55	EVA	ss5979416624	Oct 16, 2022 (156)
56	1000Genomes	NC_000013.10 - 41526350	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000013.11 - 40952214	Oct 16, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 41526350	Oct 12, 2018 (152)
59	Genetic variation in the Estonian population	NC_000013.10 - 41526350	Oct 12, 2018 (152)
60	gnomAD - Genomes	NC_000013.11 - 40952214	Apr 26, 2021 (155)
61	Genome of the Netherlands Release 5	NC_000013.10 - 41526350	Apr 27, 2020 (154)
62	KOREAN population from KRGDB	NC_000013.10 - 41526350	Apr 27, 2020 (154)
63	Northern Sweden	NC_000013.10 - 41526350	Jul 13, 2019 (153)
64	The PAGE Study	NC_000013.11 - 40952214	Jul 13, 2019 (153)
65	Qatari	NC_000013.10 - 41526350	Apr 27, 2020 (154)
66	SGDP_PRJ	NC_000013.10 - 41526350	Apr 27, 2020 (154)
67	Siberian	NC_000013.10 - 41526350	Apr 27, 2020 (154)
68	8.3KJPN	NC_000013.10 - 41526350	Apr 26, 2021 (155)
69	14KJPN	NC_000013.11 - 40952214	Oct 16, 2022 (156)
70	TopMed	NC_000013.11 - 40952214	Apr 26, 2021 (155)
71	UK 10K study - Twins	NC_000013.10 - 41526350	Oct 12, 2018 (152)
72	A Vietnamese Genetic Variation Database	NC_000013.10 - 41526350	Jul 13, 2019 (153)
73	ALFA	NC_000013.11 - 40952214	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
ss84394447, ss199128516, ss281689511, ss1684845252	NC_000013.9:40424349:C:T	NC_000013.11:40952213:C:T	(self)
60831833, 33792216, 23918201, 15078760, 35858141, 12976680, 15734426, 31860462, 8486694, 67675111, 33792216, 7497263, ss226151424, ss242728260, ss563629520, ss659229352, ss990324393, ss1079036163, ss1347970340, ss1427169571, ss1630146752, ss1673140785, ss1807582817, ss1933692496, ss1959496791, ss1967767740, ss2027605095, ss2155970340, ss2628292171, ss2700345739, ss2918925181, ss3010916719, ss3021502936, ss3651888776, ss3678179953, ss3739691815, ss3751385768, ss3879843482, ss3928680747, ss5209705804, ss5237525481, ss5410366484, ss5510950227, ss5624322852, ss5654642945, ss5839388651, ss5847423316, ss5946058294, ss5979416624	NC_000013.10:41526349:C:T	NC_000013.11:40952213:C:T	(self)
79877901, 428886122, 964180, 95334820, 159596004, 8914331454, ss2195812678, ss3725389274, ss3771742711, ss3816717492, ss4944050346, ss5293512924, ss5487898696, ss5592351966, ss5761497716, ss5814055212, ss5850701424, ss5924853202	NC_000013.11:40952213:C:T	NC_000013.11:40952213:C:T	(self)
ss154713696, ss161593110	NT_024524.14:22506349:C:T	NC_000013.11:40952213: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 rs60129138

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

rs60129138