Name: rs7533391
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.

rs7533391

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113841637 (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=0.231478 (61270/264690, TOPMED)
T=0.240719 (32692/135810, GnomAD)
T=0.07050 (1992/28256, 14KJPN) (+ 15 more)
T=0.26282 (4960/18872, ALFA)
T=0.07303 (1224/16760, 8.3KJPN)
T=0.2158 (1382/6404, 1000G_30x)
T=0.2179 (1091/5008, 1000G)
T=0.2500 (1116/4464, Estonian)
T=0.3124 (1204/3854, ALSPAC)
T=0.3034 (1125/3708, TWINSUK)
T=0.0870 (254/2918, KOREAN)
T=0.0655 (120/1832, Korea1K)
T=0.303 (302/998, GoNL)
T=0.282 (168/596, NorthernSweden)
C=0.386 (85/220, SGDP_PRJ)
T=0.324 (70/216, Qatari)
T=0.35 (14/40, GENOME_DK)
C=0.44 (14/32, 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	18872	C=0.73718	T=0.26282
European	Sub	14268	C=0.70276	T=0.29724
African	Sub	2946	C=0.8995	T=0.1005
African Others	Sub	114	C=0.982	T=0.018
African American	Sub	2832	C=0.8962	T=0.1038
Asian	Sub	112	C=0.857	T=0.143
East Asian	Sub	86	C=0.88	T=0.12
Other Asian	Sub	26	C=0.77	T=0.23
Latin American 1	Sub	146	C=0.712	T=0.288
Latin American 2	Sub	610	C=0.762	T=0.238
South Asian	Sub	98	C=0.57	T=0.43
Other	Sub	692	C=0.743	T=0.257

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	C=0.768522	T=0.231478
gnomAD - Genomes	Global	Study-wide	135810	C=0.759281	T=0.240719
gnomAD - Genomes	European	Sub	74122	C=0.69048	T=0.30952
gnomAD - Genomes	African	Sub	40042	C=0.88839	T=0.11161
gnomAD - Genomes	American	Sub	13180	C=0.74476	T=0.25524
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.6828	T=0.3172
gnomAD - Genomes	East Asian	Sub	3082	C=0.8984	T=0.1016
gnomAD - Genomes	Other	Sub	2068	C=0.7331	T=0.2669
14KJPN	JAPANESE	Study-wide	28256	C=0.92950	T=0.07050
Allele Frequency Aggregator	Total	Global	18872	C=0.73718	T=0.26282
Allele Frequency Aggregator	European	Sub	14268	C=0.70276	T=0.29724
Allele Frequency Aggregator	African	Sub	2946	C=0.8995	T=0.1005
Allele Frequency Aggregator	Other	Sub	692	C=0.743	T=0.257
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.762	T=0.238
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.712	T=0.288
Allele Frequency Aggregator	Asian	Sub	112	C=0.857	T=0.143
Allele Frequency Aggregator	South Asian	Sub	98	C=0.57	T=0.43
8.3KJPN	JAPANESE	Study-wide	16760	C=0.92697	T=0.07303
1000Genomes_30x	Global	Study-wide	6404	C=0.7842	T=0.2158
1000Genomes_30x	African	Sub	1786	C=0.9334	T=0.0666
1000Genomes_30x	Europe	Sub	1266	C=0.6596	T=0.3404
1000Genomes_30x	South Asian	Sub	1202	C=0.5923	T=0.4077
1000Genomes_30x	East Asian	Sub	1170	C=0.8974	T=0.1026
1000Genomes_30x	American	Sub	980	C=0.773	T=0.227
1000Genomes	Global	Study-wide	5008	C=0.7821	T=0.2179
1000Genomes	African	Sub	1322	C=0.9327	T=0.0673
1000Genomes	East Asian	Sub	1008	C=0.8988	T=0.1012
1000Genomes	Europe	Sub	1006	C=0.6561	T=0.3439
1000Genomes	South Asian	Sub	978	C=0.588	T=0.412
1000Genomes	American	Sub	694	C=0.782	T=0.218
Genetic variation in the Estonian population	Estonian	Study-wide	4464	C=0.7500	T=0.2500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6876	T=0.3124
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6966	T=0.3034
KOREAN population from KRGDB	KOREAN	Study-wide	2918	C=0.9130	T=0.0870
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9345	T=0.0655
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.697	T=0.303
Northern Sweden	ACPOP	Study-wide	596	C=0.718	T=0.282
SGDP_PRJ	Global	Study-wide	220	C=0.386	T=0.614
Qatari	Global	Study-wide	216	C=0.676	T=0.324
The Danish reference pan genome	Danish	Study-wide	40	C=0.65	T=0.35
Siberian	Global	Study-wide	32	C=0.44	T=0.56

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.113841637C>T
GRCh37.p13 chr 1	NC_000001.10:g.114384259C>T
PTPN22 RefSeqGene	NG_011432.1:g.35117G>A

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.916-3017… NM_001193431.2:c.916-3017G>A	N/A	Intron Variant
PTPN22 transcript variant 4	NM_001308297.1:c.844-3017… NM_001308297.1:c.844-3017G>A	N/A	Intron Variant
PTPN22 transcript variant 2	NM_012411.5:c.751-3017G>A	N/A	Intron Variant
PTPN22 transcript variant 1	NM_015967.8:c.916-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X1	XM_011541221.2:c.838-3017… XM_011541221.2:c.838-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X2	XM_011541222.2:c.916-3017… XM_011541222.2:c.916-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X6	XM_011541223.3:c.916-3017… XM_011541223.3:c.916-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X9	XM_011541225.3:c.844-3017… XM_011541225.3:c.844-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X7	XM_017001005.3:c.571-3017… XM_017001005.3:c.571-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X8	XM_017001006.2:c.916-2994… XM_017001006.2:c.916-2994G>A	N/A	Intron Variant
PTPN22 transcript variant X3	XM_047417630.1:c.766-3017… XM_047417630.1:c.766-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X4	XM_047417631.1:c.844-3017… XM_047417631.1:c.844-3017G>A	N/A	Intron Variant
PTPN22 transcript variant X5	XM_047417632.1:c.838-3017… XM_047417632.1:c.838-3017G>A	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	C=	T
GRCh38.p14 chr 1	NC_000001.11:g.113841637=	NC_000001.11:g.113841637C>T
GRCh37.p13 chr 1	NC_000001.10:g.114384259=	NC_000001.10:g.114384259C>T
PTPN22 RefSeqGene	NG_011432.1:g.35117=	NG_011432.1:g.35117G>A
PTPN22 transcript variant 3	NM_001193431.1:c.916-3017=	NM_001193431.1:c.916-3017G>A
PTPN22 transcript variant 3	NM_001193431.2:c.916-3017=	NM_001193431.2:c.916-3017G>A
PTPN22 transcript variant 4	NM_001308297.1:c.844-3017=	NM_001308297.1:c.844-3017G>A
PTPN22 transcript variant 2	NM_012411.4:c.751-3017=	NM_012411.4:c.751-3017G>A
PTPN22 transcript variant 2	NM_012411.5:c.751-3017=	NM_012411.5:c.751-3017G>A
PTPN22 transcript variant 1	NM_015967.5:c.916-3017=	NM_015967.5:c.916-3017G>A
PTPN22 transcript variant 1	NM_015967.8:c.916-3017=	NM_015967.8:c.916-3017G>A
PTPN22 transcript variant X1	XM_005270738.1:c.844-3017=	XM_005270738.1:c.844-3017G>A
PTPN22 transcript variant X1	XM_011541221.2:c.838-3017=	XM_011541221.2:c.838-3017G>A
PTPN22 transcript variant X2	XM_011541222.2:c.916-3017=	XM_011541222.2:c.916-3017G>A
PTPN22 transcript variant X6	XM_011541223.3:c.916-3017=	XM_011541223.3:c.916-3017G>A
PTPN22 transcript variant X9	XM_011541225.3:c.844-3017=	XM_011541225.3:c.844-3017G>A
PTPN22 transcript variant X7	XM_017001005.3:c.571-3017=	XM_017001005.3:c.571-3017G>A
PTPN22 transcript variant X8	XM_017001006.2:c.916-2994=	XM_017001006.2:c.916-2994G>A
PTPN22 transcript variant X3	XM_047417630.1:c.766-3017=	XM_047417630.1:c.766-3017G>A
PTPN22 transcript variant X4	XM_047417631.1:c.844-3017=	XM_047417631.1:c.844-3017G>A
PTPN22 transcript variant X5	XM_047417632.1:c.838-3017=	XM_047417632.1:c.838-3017G>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#.

56 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11384886	Jul 11, 2003 (116)
2	HGSV	ss77324832	Dec 06, 2007 (129)
3	BCMHGSC_JDW	ss87727475	Mar 23, 2008 (129)
4	BGI	ss106596202	Feb 05, 2009 (130)
5	ENSEMBL	ss138063510	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss165060324	Jul 04, 2010 (132)
7	BUSHMAN	ss198955260	Jul 04, 2010 (132)
8	1000GENOMES	ss238355030	Jul 15, 2010 (132)
9	BL	ss253397370	May 09, 2011 (134)
10	TISHKOFF	ss554595124	Apr 25, 2013 (138)
11	SSMP	ss648324291	Apr 25, 2013 (138)
12	EVA-GONL	ss975588501	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1068206260	Aug 21, 2014 (142)
14	1000GENOMES	ss1292502300	Aug 21, 2014 (142)
15	DDI	ss1425942610	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1574334452	Apr 01, 2015 (144)
17	EVA_DECODE	ss1584969380	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1601027396	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1644021429	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1794958689	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1918788656	Feb 12, 2016 (147)
22	GENOMED	ss1966845508	Jul 19, 2016 (147)
23	JJLAB	ss2019918736	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2147937569	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2165858181	Dec 20, 2016 (150)
26	GRF	ss2697867883	Nov 08, 2017 (151)
27	GNOMAD	ss2759761078	Nov 08, 2017 (151)
28	SWEGEN	ss2987467381	Nov 08, 2017 (151)
29	BIOINF_KMB_FNS_UNIBA	ss3023723917	Nov 08, 2017 (151)
30	CSHL	ss3343643188	Nov 08, 2017 (151)
31	URBANLAB	ss3646756582	Oct 11, 2018 (152)
32	EGCUT_WGS	ss3655556312	Jul 12, 2019 (153)
33	EVA_DECODE	ss3687565350	Jul 12, 2019 (153)
34	ACPOP	ss3727403756	Jul 12, 2019 (153)
35	EVA	ss3746693576	Jul 12, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3799696283	Jul 12, 2019 (153)
37	EVA	ss3826379125	Apr 25, 2020 (154)
38	EVA	ss3836581259	Apr 25, 2020 (154)
39	EVA	ss3841989705	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3849686069	Apr 25, 2020 (154)
41	KRGDB	ss3894784931	Apr 25, 2020 (154)
42	KOGIC	ss3945283242	Apr 25, 2020 (154)
43	TOPMED	ss4464226185	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5145760978	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5243670069	Oct 12, 2022 (156)
46	EVA	ss5321295290	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5444587436	Oct 12, 2022 (156)
48	EVA	ss5506003029	Oct 12, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5516694657	Oct 12, 2022 (156)
50	SANFORD_IMAGENETICS	ss5626332800	Oct 12, 2022 (156)
51	TOMMO_GENOMICS	ss5671053617	Oct 12, 2022 (156)
52	YY_MCH	ss5800946897	Oct 12, 2022 (156)
53	EVA	ss5832507586	Oct 12, 2022 (156)
54	EVA	ss5849074983	Oct 12, 2022 (156)
55	EVA	ss5909870774	Oct 12, 2022 (156)
56	EVA	ss5938200575	Oct 12, 2022 (156)
57	1000Genomes	NC_000001.10 - 114384259	Oct 11, 2018 (152)
58	1000Genomes_30x	NC_000001.11 - 113841637	Oct 12, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 114384259	Oct 11, 2018 (152)
60	Genetic variation in the Estonian population	NC_000001.10 - 114384259	Oct 11, 2018 (152)
61	The Danish reference pan genome	NC_000001.10 - 114384259	Apr 25, 2020 (154)
62	gnomAD - Genomes	NC_000001.11 - 113841637	Apr 25, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000001.10 - 114384259	Apr 25, 2020 (154)
64	KOREAN population from KRGDB	NC_000001.10 - 114384259	Apr 25, 2020 (154)
65	Korean Genome Project	NC_000001.11 - 113841637	Apr 25, 2020 (154)
66	Northern Sweden	NC_000001.10 - 114384259	Jul 12, 2019 (153)
67	Qatari	NC_000001.10 - 114384259	Apr 25, 2020 (154)
68	SGDP_PRJ	NC_000001.10 - 114384259	Apr 25, 2020 (154)
69	Siberian	NC_000001.10 - 114384259	Apr 25, 2020 (154)
70	8.3KJPN	NC_000001.10 - 114384259	Apr 25, 2021 (155)
71	14KJPN	NC_000001.11 - 113841637	Oct 12, 2022 (156)
72	TopMed	NC_000001.11 - 113841637	Apr 25, 2021 (155)
73	UK 10K study - Twins	NC_000001.10 - 114384259	Oct 11, 2018 (152)
74	ALFA	NC_000001.11 - 113841637	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
ss77324832	NC_000001.8:114096300:C:T	NC_000001.11:113841636:C:T	(self)
ss87727475, ss165060324, ss198955260, ss253397370, ss1584969380	NC_000001.9:114185781:C:T	NC_000001.11:113841636:C:T	(self)
3280739, 1815062, 1294560, 1671948, 789300, 1962325, 688621, 830586, 1703049, 453923, 3730285, 1815062, ss238355030, ss554595124, ss648324291, ss975588501, ss1068206260, ss1292502300, ss1425942610, ss1574334452, ss1601027396, ss1644021429, ss1794958689, ss1918788656, ss1966845508, ss2019918736, ss2147937569, ss2697867883, ss2759761078, ss2987467381, ss3343643188, ss3655556312, ss3727403756, ss3746693576, ss3826379125, ss3836581259, ss3849686069, ss3894784931, ss5145760978, ss5321295290, ss5506003029, ss5626332800, ss5832507586, ss5938200575	NC_000001.10:114384258:C:T	NC_000001.11:113841636:C:T	(self)
4220592, 23206890, 1661243, 4890721, 27832520, 12320877805, ss2165858181, ss3023723917, ss3646756582, ss3687565350, ss3799696283, ss3841989705, ss3945283242, ss4464226185, ss5243670069, ss5444587436, ss5516694657, ss5671053617, ss5800946897, ss5849074983, ss5909870774	NC_000001.11:113841636:C:T	NC_000001.11:113841636:C:T	(self)
ss11384886	NT_019273.15:4820062:C:T	NC_000001.11:113841636:C:T	(self)
ss106596202, ss138063510	NT_032977.9:84356176:C:T	NC_000001.11:113841636: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 rs7533391

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

rs7533391