Name: rs2358816
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.

rs2358816

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113876746 (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 / A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.191447 (50674/264690, TOPMED)
T=0.183178 (25453/138952, GnomAD)
A=0.37624 (10631/28256, 14KJPN) (+ 16 more)
T=0.19468 (3614/18564, ALFA)
A=0.38025 (6373/16760, 8.3KJPN)
T=0.2505 (1604/6404, 1000G_30x)
T=0.2588 (1296/5008, 1000G)
T=0.2408 (1079/4480, Estonian)
T=0.2120 (817/3854, ALSPAC)
T=0.2025 (751/3708, TWINSUK)
A=0.3352 (982/2930, KOREAN)
A=0.3357 (615/1832, Korea1K)
T=0.034 (34/998, GoNL)
T=0.203 (122/600, NorthernSweden)
T=0.248 (77/310, HapMap)
A=0.355 (83/234, SGDP_PRJ)
T=0.250 (54/216, Qatari)
A=0.481 (101/210, Vietnamese)
A=0.43 (13/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: AP4B1-AS1 : Intron Variant
BCL2L15 : 500B Downstream 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18564	A=0.80532	C=0.00000, T=0.19468
European	Sub	14022	A=0.78462	C=0.00000, T=0.21538
African	Sub	2886	A=0.9529	C=0.0000, T=0.0471
African Others	Sub	114	A=0.991	C=0.000, T=0.009
African American	Sub	2772	A=0.9513	C=0.0000, T=0.0487
Asian	Sub	112	A=0.455	C=0.000, T=0.545
East Asian	Sub	86	A=0.38	C=0.00, T=0.62
Other Asian	Sub	26	A=0.69	C=0.00, T=0.31
Latin American 1	Sub	146	A=0.767	C=0.000, T=0.233
Latin American 2	Sub	610	A=0.646	C=0.000, T=0.354
South Asian	Sub	98	A=0.86	C=0.00, T=0.14
Other	Sub	690	A=0.807	C=0.000, T=0.193

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=0.808553	T=0.191447
gnomAD - Genomes	Global	Study-wide	138952	A=0.816822	T=0.183178
gnomAD - Genomes	European	Sub	75318	A=0.77991	T=0.22009
gnomAD - Genomes	African	Sub	41570	A=0.94246	T=0.05754
gnomAD - Genomes	American	Sub	13520	A=0.73891	T=0.26109
gnomAD - Genomes	Ashkenazi Jewish	Sub	3310	A=0.8057	T=0.1943
gnomAD - Genomes	East Asian	Sub	3098	A=0.3906	T=0.6094
gnomAD - Genomes	Other	Sub	2136	A=0.8020	T=0.1980
14KJPN	JAPANESE	Study-wide	28256	A=0.37624	T=0.62376
Allele Frequency Aggregator	Total	Global	18564	A=0.80532	C=0.00000, T=0.19468
Allele Frequency Aggregator	European	Sub	14022	A=0.78462	C=0.00000, T=0.21538
Allele Frequency Aggregator	African	Sub	2886	A=0.9529	C=0.0000, T=0.0471
Allele Frequency Aggregator	Other	Sub	690	A=0.807	C=0.000, T=0.193
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.646	C=0.000, T=0.354
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.767	C=0.000, T=0.233
Allele Frequency Aggregator	Asian	Sub	112	A=0.455	C=0.000, T=0.545
Allele Frequency Aggregator	South Asian	Sub	98	A=0.86	C=0.00, T=0.14
8.3KJPN	JAPANESE	Study-wide	16760	A=0.38025	T=0.61975
1000Genomes_30x	Global	Study-wide	6404	A=0.7495	T=0.2505
1000Genomes_30x	African	Sub	1786	A=0.9737	T=0.0263
1000Genomes_30x	Europe	Sub	1266	A=0.7717	T=0.2283
1000Genomes_30x	South Asian	Sub	1202	A=0.8128	T=0.1872
1000Genomes_30x	East Asian	Sub	1170	A=0.3795	T=0.6205
1000Genomes_30x	American	Sub	980	A=0.677	T=0.323
1000Genomes	Global	Study-wide	5008	A=0.7412	T=0.2588
1000Genomes	African	Sub	1322	A=0.9735	T=0.0265
1000Genomes	East Asian	Sub	1008	A=0.3839	T=0.6161
1000Genomes	Europe	Sub	1006	A=0.7714	T=0.2286
1000Genomes	South Asian	Sub	978	A=0.816	T=0.184
1000Genomes	American	Sub	694	A=0.669	T=0.331
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7592	T=0.2408
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7880	T=0.2120
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7975	T=0.2025
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.3352	G=0.0000, T=0.6648
Korean Genome Project	KOREAN	Study-wide	1832	A=0.3357	T=0.6643
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.966	T=0.034
Northern Sweden	ACPOP	Study-wide	600	A=0.797	T=0.203
HapMap	Global	Study-wide	310	A=0.752	T=0.248
HapMap	African	Sub	116	A=0.991	T=0.009
HapMap	American	Sub	108	A=0.787	T=0.213
HapMap	Asian	Sub	86	A=0.38	T=0.62
SGDP_PRJ	Global	Study-wide	234	A=0.355	T=0.645
Qatari	Global	Study-wide	216	A=0.750	T=0.250
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.481	T=0.519
Siberian	Global	Study-wide	30	A=0.43	T=0.57

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 1	NC_000001.11:g.113876746A>C
GRCh38.p14 chr 1	NC_000001.11:g.113876746A>G
GRCh38.p14 chr 1	NC_000001.11:g.113876746A>T
GRCh37.p13 chr 1	NC_000001.10:g.114419368A>C
GRCh37.p13 chr 1	NC_000001.10:g.114419368A>G
GRCh37.p13 chr 1	NC_000001.10:g.114419368A>T
PTPN22 RefSeqGene	NG_011432.1:g.8T>G
PTPN22 RefSeqGene	NG_011432.1:g.8T>C
PTPN22 RefSeqGene	NG_011432.1:g.8T>A

Gene: BCL2L15, BCL2 like 15 (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
BCL2L15 transcript	NM_001010922.3:c.	N/A	Downstream Transcript Variant

Gene: AP4B1-AS1, AP4B1 antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AP4B1-AS1 transcript variant 2	NR_037864.1:n.	N/A	Intron Variant
AP4B1-AS1 transcript variant 1	NR_125965.1:n.	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	A=	C	G	T
GRCh38.p14 chr 1	NC_000001.11:g.113876746=	NC_000001.11:g.113876746A>C	NC_000001.11:g.113876746A>G	NC_000001.11:g.113876746A>T
GRCh37.p13 chr 1	NC_000001.10:g.114419368=	NC_000001.10:g.114419368A>C	NC_000001.10:g.114419368A>G	NC_000001.10:g.114419368A>T
PTPN22 RefSeqGene	NG_011432.1:g.8=	NG_011432.1:g.8T>G	NG_011432.1:g.8T>C	NG_011432.1:g.8T>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, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3315157	Sep 28, 2001 (100)
2	ABI	ss41302310	Mar 13, 2006 (126)
3	1000GENOMES	ss108537828	Jan 23, 2009 (130)
4	GMI	ss155553206	Dec 01, 2009 (131)
5	ILLUMINA	ss161038725	Dec 01, 2009 (131)
6	1000GENOMES	ss230698860	Jul 14, 2010 (132)
7	1000GENOMES	ss238355075	Jul 15, 2010 (132)
8	GMI	ss275984890	May 04, 2012 (137)
9	GMI	ss284124211	Apr 25, 2013 (138)
10	ILLUMINA	ss479357731	Mar 15, 2016 (147)
11	SSMP	ss648324396	Apr 25, 2013 (138)
12	EVA-GONL	ss975588683	Aug 21, 2014 (142)
13	1000GENOMES	ss1292503037	Aug 21, 2014 (142)
14	EVA_DECODE	ss1584969566	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1601027789	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1644021822	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1918788810	Feb 12, 2016 (147)
18	JJLAB	ss2019918809	Sep 14, 2016 (149)
19	ILLUMINA	ss2094847394	Dec 20, 2016 (150)
20	ILLUMINA	ss2094972891	Dec 20, 2016 (150)
21	USC_VALOUEV	ss2147937682	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2165859891	Dec 20, 2016 (150)
23	SYSTEMSBIOZJU	ss2624469077	Nov 08, 2017 (151)
24	GRF	ss2697868004	Nov 08, 2017 (151)
25	ILLUMINA	ss2710680382	Nov 08, 2017 (151)
26	GNOMAD	ss2759763515	Nov 08, 2017 (151)
27	SWEGEN	ss2987467715	Nov 08, 2017 (151)
28	BIOINF_KMB_FNS_UNIBA	ss3023723965	Nov 08, 2017 (151)
29	CSHL	ss3343643269	Nov 08, 2017 (151)
30	ILLUMINA	ss3651455558	Oct 11, 2018 (152)
31	EGCUT_WGS	ss3655556634	Jul 12, 2019 (153)
32	EVA_DECODE	ss3687565752	Jul 12, 2019 (153)
33	ACPOP	ss3727403931	Jul 12, 2019 (153)
34	EVA	ss3746693793	Jul 12, 2019 (153)
35	PACBIO	ss3783524581	Jul 12, 2019 (153)
36	PACBIO	ss3789165571	Jul 12, 2019 (153)
37	PACBIO	ss3794038504	Jul 12, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3799696497	Jul 12, 2019 (153)
39	EVA	ss3826379220	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3849686446	Apr 25, 2020 (154)
41	KRGDB	ss3894785484	Apr 25, 2020 (154)
42	KOGIC	ss3945283695	Apr 25, 2020 (154)
43	TOPMED	ss4464233660	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5145762018	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5243670756	Oct 12, 2022 (156)
46	EVA	ss5321296528	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5444588057	Oct 12, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5516695634	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5626333116	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5671055029	Oct 12, 2022 (156)
51	YY_MCH	ss5800947055	Oct 12, 2022 (156)
52	EVA	ss5832507845	Oct 12, 2022 (156)
53	EVA	ss5849075068	Oct 12, 2022 (156)
54	EVA	ss5909871530	Oct 12, 2022 (156)
55	EVA	ss5938200927	Oct 12, 2022 (156)
56	1000Genomes	NC_000001.10 - 114419368	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000001.11 - 113876746	Oct 12, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 114419368	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000001.10 - 114419368	Oct 11, 2018 (152)
60	gnomAD - Genomes	NC_000001.11 - 113876746	Apr 25, 2021 (155)
61	Genome of the Netherlands Release 5	NC_000001.10 - 114419368	Apr 25, 2020 (154)
62	HapMap	NC_000001.11 - 113876746	Apr 25, 2020 (154)
63	KOREAN population from KRGDB	NC_000001.10 - 114419368	Apr 25, 2020 (154)
64	Korean Genome Project	NC_000001.11 - 113876746	Apr 25, 2020 (154)
65	Northern Sweden	NC_000001.10 - 114419368	Jul 12, 2019 (153)
66	Qatari	NC_000001.10 - 114419368	Apr 25, 2020 (154)
67	SGDP_PRJ	NC_000001.10 - 114419368	Apr 25, 2020 (154)
68	Siberian	NC_000001.10 - 114419368	Apr 25, 2020 (154)
69	8.3KJPN	NC_000001.10 - 114419368	Apr 25, 2021 (155)
70	14KJPN	NC_000001.11 - 113876746	Oct 12, 2022 (156)
71	TopMed	NC_000001.11 - 113876746	Apr 25, 2021 (155)
72	UK 10K study - Twins	NC_000001.10 - 114419368	Oct 11, 2018 (152)
73	A Vietnamese Genetic Variation Database	NC_000001.10 - 114419368	Jul 12, 2019 (153)
74	ALFA	NC_000001.11 - 113876746	Apr 25, 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
7383361615	NC_000001.11:113876745:A:C	NC_000001.11:113876745:A:C	(self)
1962878, ss3894785484	NC_000001.10:114419367:A:G	NC_000001.11:113876745:A:G	(self)
ss108537828, ss275984890, ss284124211, ss1584969566, ss2094847394	NC_000001.9:114220890:A:T	NC_000001.11:113876745:A:T	(self)
3281517, 1815513, 1294882, 789481, 1962878, 688796, 830740, 1703426, 454036, 3731325, 1815513, 393026, ss230698860, ss238355075, ss648324396, ss975588683, ss1292503037, ss1601027789, ss1644021822, ss1918788810, ss2019918809, ss2094972891, ss2147937682, ss2624469077, ss2697868004, ss2710680382, ss2759763515, ss2987467715, ss3343643269, ss3651455558, ss3655556634, ss3727403931, ss3746693793, ss3783524581, ss3789165571, ss3794038504, ss3826379220, ss3849686446, ss3894785484, ss5145762018, ss5321296528, ss5626333116, ss5832507845, ss5938200927	NC_000001.10:114419367:A:T	NC_000001.11:113876745:A:T	(self)
4221569, 23213232, 158532, 1661696, 4892133, 27839995, 7383361615, ss2165859891, ss3023723965, ss3687565752, ss3799696497, ss3945283695, ss4464233660, ss5243670756, ss5444588057, ss5516695634, ss5671055029, ss5800947055, ss5849075068, ss5909871530	NC_000001.11:113876745:A:T	NC_000001.11:113876745:A:T	(self)
ss3315157, ss41302310, ss155553206, ss161038725, ss479357731	NT_032977.9:84391285:A:T	NC_000001.11:113876745:A: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 rs2358816

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

rs2358816