Name: rs7555354
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.

rs7555354

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113841809 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.206468 (54650/264690, TOPMED)
A=0.210234 (29418/139930, GnomAD)
A=0.07064 (1996/28256, 14KJPN) (+ 16 more)
A=0.24034 (4540/18890, ALFA)
A=0.07333 (1229/16760, 8.3KJPN)
A=0.1921 (1230/6404, 1000G_30x)
A=0.1951 (977/5008, 1000G)
A=0.2292 (1027/4480, Estonian)
A=0.2971 (1145/3854, ALSPAC)
A=0.2891 (1072/3708, TWINSUK)
A=0.0873 (255/2922, KOREAN)
A=0.0660 (121/1832, Korea1K)
A=0.278 (277/998, GoNL)
A=0.248 (149/600, NorthernSweden)
A=0.306 (66/216, Qatari)
A=0.193 (41/212, Vietnamese)
G=0.384 (76/198, SGDP_PRJ)
A=0.33 (13/40, GENOME_DK)
G=0.47 (14/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: AP4B1-AS1 : Intron Variant
PTPN22 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	G=0.75966	A=0.24034
European	Sub	14286	G=0.72148	A=0.27852
African	Sub	2946	G=0.9437	A=0.0563
African Others	Sub	114	G=1.000	A=0.000
African American	Sub	2832	G=0.9414	A=0.0586
Asian	Sub	112	G=0.857	A=0.143
East Asian	Sub	86	G=0.88	A=0.12
Other Asian	Sub	26	G=0.77	A=0.23
Latin American 1	Sub	146	G=0.753	A=0.247
Latin American 2	Sub	610	G=0.775	A=0.225
South Asian	Sub	98	G=0.57	A=0.43
Other	Sub	692	G=0.763	A=0.237

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=0.793532	A=0.206468
gnomAD - Genomes	Global	Study-wide	139930	G=0.789766	A=0.210234
gnomAD - Genomes	European	Sub	75770	G=0.71144	A=0.28856
gnomAD - Genomes	African	Sub	41936	G=0.93895	A=0.06105
gnomAD - Genomes	American	Sub	13624	G=0.76659	A=0.23341
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.7016	A=0.2984
gnomAD - Genomes	East Asian	Sub	3130	G=0.9006	A=0.0994
gnomAD - Genomes	Other	Sub	2146	G=0.7619	A=0.2381
14KJPN	JAPANESE	Study-wide	28256	G=0.92936	A=0.07064
Allele Frequency Aggregator	Total	Global	18890	G=0.75966	A=0.24034
Allele Frequency Aggregator	European	Sub	14286	G=0.72148	A=0.27852
Allele Frequency Aggregator	African	Sub	2946	G=0.9437	A=0.0563
Allele Frequency Aggregator	Other	Sub	692	G=0.763	A=0.237
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.775	A=0.225
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.753	A=0.247
Allele Frequency Aggregator	Asian	Sub	112	G=0.857	A=0.143
Allele Frequency Aggregator	South Asian	Sub	98	G=0.57	A=0.43
8.3KJPN	JAPANESE	Study-wide	16760	G=0.92667	A=0.07333
1000Genomes_30x	Global	Study-wide	6404	G=0.8079	A=0.1921
1000Genomes_30x	African	Sub	1786	G=0.9927	A=0.0073
1000Genomes_30x	Europe	Sub	1266	G=0.6746	A=0.3254
1000Genomes_30x	South Asian	Sub	1202	G=0.5948	A=0.4052
1000Genomes_30x	East Asian	Sub	1170	G=0.9034	A=0.0966
1000Genomes_30x	American	Sub	980	G=0.791	A=0.209
1000Genomes	Global	Study-wide	5008	G=0.8049	A=0.1951
1000Genomes	African	Sub	1322	G=0.9909	A=0.0091
1000Genomes	East Asian	Sub	1008	G=0.9058	A=0.0942
1000Genomes	Europe	Sub	1006	G=0.6730	A=0.3270
1000Genomes	South Asian	Sub	978	G=0.589	A=0.411
1000Genomes	American	Sub	694	G=0.800	A=0.200
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7708	A=0.2292
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7029	A=0.2971
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7109	A=0.2891
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9127	A=0.0873
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9340	A=0.0660
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.722	A=0.278
Northern Sweden	ACPOP	Study-wide	600	G=0.752	A=0.248
Qatari	Global	Study-wide	216	G=0.694	A=0.306
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.807	A=0.193
SGDP_PRJ	Global	Study-wide	198	G=0.384	A=0.616
The Danish reference pan genome	Danish	Study-wide	40	G=0.68	A=0.33
Siberian	Global	Study-wide	30	G=0.47	A=0.53

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.113841809G>A
GRCh37.p13 chr 1	NC_000001.10:g.114384431G>A
PTPN22 RefSeqGene	NG_011432.1:g.34945C>T

Gene: PTPN22, protein tyrosine phosphatase non-receptor type 22 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPN22 transcript variant 3	NM_001193431.2:c.916-3189… NM_001193431.2:c.916-3189C>T	N/A	Intron Variant
PTPN22 transcript variant 4	NM_001308297.1:c.844-3189… NM_001308297.1:c.844-3189C>T	N/A	Intron Variant
PTPN22 transcript variant 2	NM_012411.5:c.751-3189C>T	N/A	Intron Variant
PTPN22 transcript variant 1	NM_015967.8:c.916-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X1	XM_011541221.2:c.838-3189… XM_011541221.2:c.838-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X2	XM_011541222.2:c.916-3189… XM_011541222.2:c.916-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X6	XM_011541223.3:c.916-3189… XM_011541223.3:c.916-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X9	XM_011541225.3:c.844-3189… XM_011541225.3:c.844-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X7	XM_017001005.3:c.571-3189… XM_017001005.3:c.571-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X8	XM_017001006.2:c.916-3166… XM_017001006.2:c.916-3166C>T	N/A	Intron Variant
PTPN22 transcript variant X3	XM_047417630.1:c.766-3189… XM_047417630.1:c.766-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X4	XM_047417631.1:c.844-3189… XM_047417631.1:c.844-3189C>T	N/A	Intron Variant
PTPN22 transcript variant X5	XM_047417632.1:c.838-3189… XM_047417632.1:c.838-3189C>T	N/A	Intron Variant

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

Molecule type	Change	Amino acid[Codon]	SO Term
AP4B1-AS1 transcript variant 1	NR_125965.1:n.	N/A	Intron Variant
AP4B1-AS1 transcript variant 2	NR_037864.1:n.	N/A	Genic Upstream 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	G=	A
GRCh38.p14 chr 1	NC_000001.11:g.113841809=	NC_000001.11:g.113841809G>A
GRCh37.p13 chr 1	NC_000001.10:g.114384431=	NC_000001.10:g.114384431G>A
PTPN22 RefSeqGene	NG_011432.1:g.34945=	NG_011432.1:g.34945C>T
PTPN22 transcript variant 3	NM_001193431.1:c.916-3189=	NM_001193431.1:c.916-3189C>T
PTPN22 transcript variant 3	NM_001193431.2:c.916-3189=	NM_001193431.2:c.916-3189C>T
PTPN22 transcript variant 4	NM_001308297.1:c.844-3189=	NM_001308297.1:c.844-3189C>T
PTPN22 transcript variant 2	NM_012411.4:c.751-3189=	NM_012411.4:c.751-3189C>T
PTPN22 transcript variant 2	NM_012411.5:c.751-3189=	NM_012411.5:c.751-3189C>T
PTPN22 transcript variant 1	NM_015967.5:c.916-3189=	NM_015967.5:c.916-3189C>T
PTPN22 transcript variant 1	NM_015967.8:c.916-3189=	NM_015967.8:c.916-3189C>T
PTPN22 transcript variant X1	XM_005270738.1:c.844-3189=	XM_005270738.1:c.844-3189C>T
PTPN22 transcript variant X1	XM_011541221.2:c.838-3189=	XM_011541221.2:c.838-3189C>T
PTPN22 transcript variant X2	XM_011541222.2:c.916-3189=	XM_011541222.2:c.916-3189C>T
PTPN22 transcript variant X6	XM_011541223.3:c.916-3189=	XM_011541223.3:c.916-3189C>T
PTPN22 transcript variant X9	XM_011541225.3:c.844-3189=	XM_011541225.3:c.844-3189C>T
PTPN22 transcript variant X7	XM_017001005.3:c.571-3189=	XM_017001005.3:c.571-3189C>T
PTPN22 transcript variant X8	XM_017001006.2:c.916-3166=	XM_017001006.2:c.916-3166C>T
PTPN22 transcript variant X3	XM_047417630.1:c.766-3189=	XM_047417630.1:c.766-3189C>T
PTPN22 transcript variant X4	XM_047417631.1:c.844-3189=	XM_047417631.1:c.844-3189C>T
PTPN22 transcript variant X5	XM_047417632.1:c.838-3189=	XM_047417632.1:c.838-3189C>T

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, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11429617	Jul 11, 2003 (116)
2	HGSV	ss77669083	Dec 06, 2007 (129)
3	COMPLETE_GENOMICS	ss165060335	Jul 04, 2010 (132)
4	COMPLETE_GENOMICS	ss167019570	Jul 04, 2010 (132)
5	BUSHMAN	ss198955264	Jul 04, 2010 (132)
6	BL	ss253397374	May 09, 2011 (134)
7	1000GENOMES	ss328867756	May 09, 2011 (134)
8	TISHKOFF	ss554595128	Apr 25, 2013 (138)
9	SSMP	ss648324293	Apr 25, 2013 (138)
10	EVA-GONL	ss975588502	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1068206261	Aug 21, 2014 (142)
12	1000GENOMES	ss1292502307	Aug 21, 2014 (142)
13	DDI	ss1425942611	Apr 01, 2015 (144)
14	EVA_GENOME_DK	ss1574334453	Apr 01, 2015 (144)
15	EVA_DECODE	ss1584969382	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1601027399	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1644021432	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1918788658	Feb 12, 2016 (147)
19	GENOMED	ss1966845509	Jul 19, 2016 (147)
20	JJLAB	ss2019918737	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2147937570	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2165858200	Dec 20, 2016 (150)
23	GRF	ss2697867885	Nov 08, 2017 (151)
24	GNOMAD	ss2759761097	Nov 08, 2017 (151)
25	SWEGEN	ss2987467384	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3023723918	Nov 08, 2017 (151)
27	CSHL	ss3343643189	Nov 08, 2017 (151)
28	URBANLAB	ss3646756583	Oct 11, 2018 (152)
29	EGCUT_WGS	ss3655556313	Jul 12, 2019 (153)
30	EVA_DECODE	ss3687565351	Jul 12, 2019 (153)
31	ACPOP	ss3727403758	Jul 12, 2019 (153)
32	EVA	ss3746693577	Jul 12, 2019 (153)
33	KHV_HUMAN_GENOMES	ss3799696286	Jul 12, 2019 (153)
34	EVA	ss3826379126	Apr 25, 2020 (154)
35	EVA	ss3836581260	Apr 25, 2020 (154)
36	EVA	ss3841989706	Apr 25, 2020 (154)
37	SGDP_PRJ	ss3849686070	Apr 25, 2020 (154)
38	KRGDB	ss3894784935	Apr 25, 2020 (154)
39	KOGIC	ss3945283248	Apr 25, 2020 (154)
40	TOPMED	ss4464226232	Apr 25, 2021 (155)
41	TOMMO_GENOMICS	ss5145760986	Apr 25, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5243670072	Oct 12, 2022 (156)
43	EVA	ss5321295301	Oct 12, 2022 (156)
44	HUGCELL_USP	ss5444587441	Oct 12, 2022 (156)
45	EVA	ss5506003030	Oct 12, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5516694664	Oct 12, 2022 (156)
47	SANFORD_IMAGENETICS	ss5626332801	Oct 12, 2022 (156)
48	TOMMO_GENOMICS	ss5671053627	Oct 12, 2022 (156)
49	YY_MCH	ss5800946899	Oct 12, 2022 (156)
50	EVA	ss5832507588	Oct 12, 2022 (156)
51	EVA	ss5909870780	Oct 12, 2022 (156)
52	EVA	ss5938200578	Oct 12, 2022 (156)
53	1000Genomes	NC_000001.10 - 114384431	Oct 11, 2018 (152)
54	1000Genomes_30x	NC_000001.11 - 113841809	Oct 12, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 114384431	Oct 11, 2018 (152)
56	Genetic variation in the Estonian population	NC_000001.10 - 114384431	Oct 11, 2018 (152)
57	The Danish reference pan genome	NC_000001.10 - 114384431	Apr 25, 2020 (154)
58	gnomAD - Genomes	NC_000001.11 - 113841809	Apr 25, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000001.10 - 114384431	Apr 25, 2020 (154)
60	KOREAN population from KRGDB	NC_000001.10 - 114384431	Apr 25, 2020 (154)
61	Korean Genome Project	NC_000001.11 - 113841809	Apr 25, 2020 (154)
62	Northern Sweden	NC_000001.10 - 114384431	Jul 12, 2019 (153)
63	Qatari	NC_000001.10 - 114384431	Apr 25, 2020 (154)
64	SGDP_PRJ	NC_000001.10 - 114384431	Apr 25, 2020 (154)
65	Siberian	NC_000001.10 - 114384431	Apr 25, 2020 (154)
66	8.3KJPN	NC_000001.10 - 114384431	Apr 25, 2021 (155)
67	14KJPN	NC_000001.11 - 113841809	Oct 12, 2022 (156)
68	TopMed	NC_000001.11 - 113841809	Apr 25, 2021 (155)
69	UK 10K study - Twins	NC_000001.10 - 114384431	Oct 11, 2018 (152)
70	A Vietnamese Genetic Variation Database	NC_000001.10 - 114384431	Jul 12, 2019 (153)
71	ALFA	NC_000001.11 - 113841809	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
ss77669083	NC_000001.8:114096472:G:A	NC_000001.11:113841808:G:A	(self)
ss165060335, ss167019570, ss198955264, ss253397374, ss1584969382	NC_000001.9:114185953:G:A	NC_000001.11:113841808:G:A	(self)
3280746, 1815065, 1294561, 1671949, 789301, 1962329, 688623, 830588, 1703050, 453924, 3730293, 1815065, 392940, ss328867756, ss554595128, ss648324293, ss975588502, ss1068206261, ss1292502307, ss1425942611, ss1574334453, ss1601027399, ss1644021432, ss1918788658, ss1966845509, ss2019918737, ss2147937570, ss2697867885, ss2759761097, ss2987467384, ss3343643189, ss3655556313, ss3727403758, ss3746693577, ss3826379126, ss3836581260, ss3849686070, ss3894784935, ss5145760986, ss5321295301, ss5506003030, ss5626332801, ss5832507588, ss5938200578	NC_000001.10:114384430:G:A	NC_000001.11:113841808:G:A	(self)
4220599, 23206929, 1661249, 4890731, 27832567, 2602243674, ss2165858200, ss3023723918, ss3646756583, ss3687565351, ss3799696286, ss3841989706, ss3945283248, ss4464226232, ss5243670072, ss5444587441, ss5516694664, ss5671053627, ss5800946899, ss5909870780	NC_000001.11:113841808:G:A	NC_000001.11:113841808:G:A	(self)
ss11429617	NT_019273.15:4820234:G:A	NC_000001.11:113841808:G:A	(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 rs7555354

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

rs7555354