Name: rs5134
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.

rs5134

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:116831863 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.219272 (58039/264690, TOPMED)
C=0.208548 (29205/140040, GnomAD)
C=0.14736 (4164/28258, 14KJPN) (+ 15 more)
C=0.14113 (2666/18890, ALFA)
C=0.14751 (2472/16758, 8.3KJPN)
C=0.2459 (1575/6404, 1000G_30x)
C=0.2408 (1206/5008, 1000G)
C=0.0560 (251/4480, Estonian)
C=0.0457 (176/3854, ALSPAC)
C=0.0464 (172/3708, TWINSUK)
C=0.1403 (411/2930, KOREAN)
C=0.056 (56/998, GoNL)
C=0.040 (24/600, NorthernSweden)
C=0.139 (30/216, Qatari)
C=0.127 (27/212, Vietnamese)
T=0.353 (48/136, SGDP_PRJ)
C=0.05 (2/40, GENOME_DK)
T=0.45 (9/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: APOC3 : 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	T=0.85887	C=0.14113
European	Sub	14286	T=0.94421	C=0.05579
African	Sub	2946	T=0.4379	C=0.5621
African Others	Sub	114	T=0.281	C=0.719
African American	Sub	2832	T=0.4442	C=0.5558
Asian	Sub	112	T=0.884	C=0.116
East Asian	Sub	86	T=0.91	C=0.09
Other Asian	Sub	26	T=0.81	C=0.19
Latin American 1	Sub	146	T=0.815	C=0.185
Latin American 2	Sub	610	T=0.948	C=0.052
South Asian	Sub	98	T=0.94	C=0.06
Other	Sub	692	T=0.805	C=0.195

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	T=0.780728	C=0.219272
gnomAD - Genomes	Global	Study-wide	140040	T=0.791452	C=0.208548
gnomAD - Genomes	European	Sub	75910	T=0.95168	C=0.04832
gnomAD - Genomes	African	Sub	41880	T=0.44479	C=0.55521
gnomAD - Genomes	American	Sub	13654	T=0.90391	C=0.09609
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9527	C=0.0473
gnomAD - Genomes	East Asian	Sub	3126	T=0.8669	C=0.1331
gnomAD - Genomes	Other	Sub	2148	T=0.8138	C=0.1862
14KJPN	JAPANESE	Study-wide	28258	T=0.85264	C=0.14736
Allele Frequency Aggregator	Total	Global	18890	T=0.85887	C=0.14113
Allele Frequency Aggregator	European	Sub	14286	T=0.94421	C=0.05579
Allele Frequency Aggregator	African	Sub	2946	T=0.4379	C=0.5621
Allele Frequency Aggregator	Other	Sub	692	T=0.805	C=0.195
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.948	C=0.052
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.815	C=0.185
Allele Frequency Aggregator	Asian	Sub	112	T=0.884	C=0.116
Allele Frequency Aggregator	South Asian	Sub	98	T=0.94	C=0.06
8.3KJPN	JAPANESE	Study-wide	16758	T=0.85249	C=0.14751
1000Genomes_30x	Global	Study-wide	6404	T=0.7541	C=0.2459
1000Genomes_30x	African	Sub	1786	T=0.3499	C=0.6501
1000Genomes_30x	Europe	Sub	1266	T=0.9597	C=0.0403
1000Genomes_30x	South Asian	Sub	1202	T=0.9193	C=0.0807
1000Genomes_30x	East Asian	Sub	1170	T=0.8650	C=0.1350
1000Genomes_30x	American	Sub	980	T=0.890	C=0.110
1000Genomes	Global	Study-wide	5008	T=0.7592	C=0.2408
1000Genomes	African	Sub	1322	T=0.3427	C=0.6573
1000Genomes	East Asian	Sub	1008	T=0.8651	C=0.1349
1000Genomes	Europe	Sub	1006	T=0.9612	C=0.0388
1000Genomes	South Asian	Sub	978	T=0.917	C=0.083
1000Genomes	American	Sub	694	T=0.883	C=0.117
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9440	C=0.0560
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9543	C=0.0457
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9536	C=0.0464
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8597	C=0.1403
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.944	C=0.056
Northern Sweden	ACPOP	Study-wide	600	T=0.960	C=0.040
Qatari	Global	Study-wide	216	T=0.861	C=0.139
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.873	C=0.127
SGDP_PRJ	Global	Study-wide	136	T=0.353	C=0.647
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	C=0.05
Siberian	Global	Study-wide	20	T=0.45	C=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 11	NC_000011.10:g.116831863T>C
GRCh37.p13 chr 11	NC_000011.9:g.116702579T>C
APOC3 RefSeqGene	NG_008949.1:g.6956T>C

Gene: APOC3, apolipoprotein C3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
APOC3 transcript	NM_000040.3:c.180-901T>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	T=	C
GRCh38.p14 chr 11	NC_000011.10:g.116831863=	NC_000011.10:g.116831863T>C
GRCh37.p13 chr 11	NC_000011.9:g.116702579=	NC_000011.9:g.116702579T>C
APOC3 RefSeqGene	NG_008949.1:g.6956=	NG_008949.1:g.6956T>C
APOC3 transcript	NM_000040.1:c.180-901=	NM_000040.1:c.180-901T>C
APOC3 transcript	NM_000040.3:c.180-901=	NM_000040.3:c.180-901T>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#.

52 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss748175	Aug 11, 2000 (83)
2	KWOK	ss1974957	Oct 18, 2000 (87)
3	CSHL-HAPMAP	ss17420970	Feb 27, 2004 (120)
4	PARC	ss23145020	Sep 20, 2004 (126)
5	ABI	ss40081839	Mar 10, 2006 (126)
6	KRIBB_YJKIM	ss104796565	Feb 06, 2009 (130)
7	BUSHMAN	ss203260191	Jul 04, 2010 (132)
8	GMI	ss281185606	May 04, 2012 (137)
9	1000GENOMES	ss337011202	May 09, 2011 (134)
10	TISHKOFF	ss562850218	Apr 25, 2013 (138)
11	SSMP	ss658374247	Apr 25, 2013 (138)
12	EVA-GONL	ss989003816	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1078076173	Aug 21, 2014 (142)
14	1000GENOMES	ss1343124328	Aug 21, 2014 (142)
15	DDI	ss1426773802	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1575976543	Apr 01, 2015 (144)
17	EVA_DECODE	ss1598670638	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1627549381	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1670543414	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1807014120	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1932365909	Feb 12, 2016 (147)
22	JJLAB	ss2026926753	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2155240256	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2186035178	Dec 20, 2016 (150)
25	SYSTEMSBIOZJU	ss2627938069	Nov 08, 2017 (151)
26	GRF	ss2699551081	Nov 08, 2017 (151)
27	GNOMAD	ss2904901789	Nov 08, 2017 (151)
28	AFFY	ss2985600315	Nov 08, 2017 (151)
29	SWEGEN	ss3008843477	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3027264545	Nov 08, 2017 (151)
31	EGCUT_WGS	ss3676171584	Jul 13, 2019 (153)
32	EVA_DECODE	ss3692675894	Jul 13, 2019 (153)
33	ACPOP	ss3738574022	Jul 13, 2019 (153)
34	EVA	ss3749861121	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3815189850	Jul 13, 2019 (153)
36	EVA	ss3832858223	Apr 26, 2020 (154)
37	SGDP_PRJ	ss3877218594	Apr 26, 2020 (154)
38	KRGDB	ss3925680923	Apr 26, 2020 (154)
39	TOPMED	ss4901355678	Apr 26, 2021 (155)
40	TOMMO_GENOMICS	ss5204065112	Apr 26, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5289038376	Oct 16, 2022 (156)
42	EVA	ss5402499112	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5484014486	Oct 16, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5585593845	Oct 16, 2022 (156)
45	SANFORD_IMAGENETICS	ss5652149469	Oct 16, 2022 (156)
46	TOMMO_GENOMICS	ss5752564340	Oct 16, 2022 (156)
47	YY_MCH	ss5812809888	Oct 16, 2022 (156)
48	EVA	ss5837283489	Oct 16, 2022 (156)
49	EVA	ss5850166547	Oct 16, 2022 (156)
50	EVA	ss5921818112	Oct 16, 2022 (156)
51	EVA	ss5943483734	Oct 16, 2022 (156)
52	EVA	ss5980704879	Oct 16, 2022 (156)
53	1000Genomes	NC_000011.9 - 116702579	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000011.10 - 116831863	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 116702579	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000011.9 - 116702579	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000011.9 - 116702579	Apr 26, 2020 (154)
58	gnomAD - Genomes	NC_000011.10 - 116831863	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000011.9 - 116702579	Apr 26, 2020 (154)
60	KOREAN population from KRGDB	NC_000011.9 - 116702579	Apr 26, 2020 (154)
61	Northern Sweden	NC_000011.9 - 116702579	Jul 13, 2019 (153)
62	Qatari	NC_000011.9 - 116702579	Apr 26, 2020 (154)
63	SGDP_PRJ	NC_000011.9 - 116702579	Apr 26, 2020 (154)
64	Siberian	NC_000011.9 - 116702579	Apr 26, 2020 (154)
65	8.3KJPN	NC_000011.9 - 116702579	Apr 26, 2021 (155)
66	14KJPN	NC_000011.10 - 116831863	Oct 16, 2022 (156)
67	TopMed	NC_000011.10 - 116831863	Apr 26, 2021 (155)
68	UK 10K study - Twins	NC_000011.9 - 116702579	Oct 12, 2018 (152)
69	A Vietnamese Genetic Variation Database	NC_000011.9 - 116702579	Jul 13, 2019 (153)
70	ALFA	NC_000011.10 - 116831863	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)
rs2283266	May 23, 2006 (127)
rs12721087	Mar 10, 2006 (126)
rs17251312	Mar 10, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss203260191, ss281185606, ss1598670638	NC_000011.8:116207788:T:C	NC_000011.10:116831862:T:C	(self)
55712064, 30927046, 21909832, 2751323, 13799879, 32858317, 11858887, 14407839, 29235574, 7756610, 62034419, 30927046, 6862980, ss337011202, ss562850218, ss658374247, ss989003816, ss1078076173, ss1343124328, ss1426773802, ss1575976543, ss1627549381, ss1670543414, ss1807014120, ss1932365909, ss2026926753, ss2155240256, ss2627938069, ss2699551081, ss2904901789, ss2985600315, ss3008843477, ss3676171584, ss3738574022, ss3749861121, ss3832858223, ss3877218594, ss3925680923, ss5204065112, ss5402499112, ss5652149469, ss5837283489, ss5943483734, ss5980704879	NC_000011.9:116702578:T:C	NC_000011.10:116831862:T:C	(self)
73119780, 393103825, 86401444, 116901334, 9730276441, ss2186035178, ss3027264545, ss3692675894, ss3815189850, ss4901355678, ss5289038376, ss5484014486, ss5585593845, ss5752564340, ss5812809888, ss5850166547, ss5921818112	NC_000011.10:116831862:T:C	NC_000011.10:116831862:T:C	(self)
ss17420970	NT_033899.6:20246365:T:C	NC_000011.10:116831862:T:C	(self)
ss748175, ss1974957, ss23145020, ss40081839, ss104796565	NT_033899.8:20264994:T:C	NC_000011.10:116831862:T: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 rs5134

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

rs5134