Name: rs72975916
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.

rs72975916

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:127972910 (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=0.111493 (29511/264690, TOPMED)
T=0.123692 (17329/140098, GnomAD)
T=0.13166 (2487/18890, ALFA) (+ 13 more)
T=0.0868 (556/6404, 1000G_30x)
T=0.0873 (437/5008, 1000G)
T=0.1451 (650/4480, Estonian)
T=0.1565 (603/3854, ALSPAC)
T=0.1443 (535/3708, TWINSUK)
T=0.145 (145/998, GoNL)
T=0.157 (94/600, NorthernSweden)
T=0.107 (57/534, MGP)
T=0.134 (29/216, Qatari)
T=0.005 (1/214, Vietnamese)
C=0.48 (27/56, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.42 (5/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PTPRK : Intron Variant
Publications: 2 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	C=0.86834	T=0.13166
European	Sub	14286	C=0.85839	T=0.14161
African	Sub	2946	C=0.9036	T=0.0964
African Others	Sub	114	C=0.939	T=0.061
African American	Sub	2832	C=0.9022	T=0.0978
Asian	Sub	112	C=0.973	T=0.027
East Asian	Sub	86	C=0.98	T=0.02
Other Asian	Sub	26	C=0.96	T=0.04
Latin American 1	Sub	146	C=0.856	T=0.144
Latin American 2	Sub	610	C=0.934	T=0.066
South Asian	Sub	98	C=0.80	T=0.20
Other	Sub	692	C=0.861	T=0.139

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=0.888507	T=0.111493
gnomAD - Genomes	Global	Study-wide	140098	C=0.876308	T=0.123692
gnomAD - Genomes	European	Sub	75858	C=0.84812	T=0.15188
gnomAD - Genomes	African	Sub	41994	C=0.90258	T=0.09742
gnomAD - Genomes	American	Sub	13640	C=0.91012	T=0.08988
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9143	T=0.0857
gnomAD - Genomes	East Asian	Sub	3132	C=0.9978	T=0.0022
gnomAD - Genomes	Other	Sub	2150	C=0.9074	T=0.0926
Allele Frequency Aggregator	Total	Global	18890	C=0.86834	T=0.13166
Allele Frequency Aggregator	European	Sub	14286	C=0.85839	T=0.14161
Allele Frequency Aggregator	African	Sub	2946	C=0.9036	T=0.0964
Allele Frequency Aggregator	Other	Sub	692	C=0.861	T=0.139
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.934	T=0.066
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.856	T=0.144
Allele Frequency Aggregator	Asian	Sub	112	C=0.973	T=0.027
Allele Frequency Aggregator	South Asian	Sub	98	C=0.80	T=0.20
1000Genomes_30x	Global	Study-wide	6404	C=0.9132	T=0.0868
1000Genomes_30x	African	Sub	1786	C=0.9026	T=0.0974
1000Genomes_30x	Europe	Sub	1266	C=0.8649	T=0.1351
1000Genomes_30x	South Asian	Sub	1202	C=0.8752	T=0.1248
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.938	T=0.062
1000Genomes	Global	Study-wide	5008	C=0.9127	T=0.0873
1000Genomes	African	Sub	1322	C=0.9017	T=0.0983
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.8608	T=0.1392
1000Genomes	South Asian	Sub	978	C=0.873	T=0.127
1000Genomes	American	Sub	694	C=0.938	T=0.062
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8549	T=0.1451
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8435	T=0.1565
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8557	T=0.1443
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.855	T=0.145
Northern Sweden	ACPOP	Study-wide	600	C=0.843	T=0.157
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.893	T=0.107
Qatari	Global	Study-wide	216	C=0.866	T=0.134
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.995	T=0.005
SGDP_PRJ	Global	Study-wide	56	C=0.48	T=0.52
The Danish reference pan genome	Danish	Study-wide	40	C=0.82	T=0.17
Siberian	Global	Study-wide	12	C=0.42	T=0.58

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 6	NC_000006.12:g.127972910C>T
GRCh37.p13 chr 6	NC_000006.11:g.128294055C>T
GRCh38.p14 chr 6 alt locus HSCHR6_1_CTG8	NT_187556.1:g.318108C>T

Gene: PTPRK, protein tyrosine phosphatase receptor type K (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRK transcript variant 1	NM_001135648.3:c.4287+112… NM_001135648.3:c.4287+112G>A	N/A	Intron Variant
PTPRK transcript variant 3	NM_001291981.2:c.4335+112… NM_001291981.2:c.4335+112G>A	N/A	Intron Variant
PTPRK transcript variant 6	NM_001291984.2:c.4266+112… NM_001291984.2:c.4266+112G>A	N/A	Intron Variant
PTPRK transcript variant 2	NM_002844.4:c.4269+112G>A	N/A	Intron Variant
PTPRK transcript variant 4	NM_001291982.2:c.	N/A	Genic Downstream Transcript Variant
PTPRK transcript variant 5	NM_001291983.2:c.	N/A	Genic Downstream 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 6	NC_000006.12:g.127972910=	NC_000006.12:g.127972910C>T
GRCh37.p13 chr 6	NC_000006.11:g.128294055=	NC_000006.11:g.128294055C>T
GRCh38.p14 chr 6 alt locus HSCHR6_1_CTG8	NT_187556.1:g.318108=	NT_187556.1:g.318108C>T
PTPRK transcript variant 1	NM_001135648.1:c.4287+112=	NM_001135648.1:c.4287+112G>A
PTPRK transcript variant 1	NM_001135648.3:c.4287+112=	NM_001135648.3:c.4287+112G>A
PTPRK transcript variant 3	NM_001291981.2:c.4335+112=	NM_001291981.2:c.4335+112G>A
PTPRK transcript variant 6	NM_001291984.2:c.4266+112=	NM_001291984.2:c.4266+112G>A
PTPRK transcript variant 2	NM_002844.3:c.4269+112=	NM_002844.3:c.4269+112G>A
PTPRK transcript variant 2	NM_002844.4:c.4269+112=	NM_002844.4:c.4269+112G>A
PTPRK transcript variant X1	XM_005267081.1:c.4377+112=	XM_005267081.1:c.4377+112G>A
PTPRK transcript variant X2	XM_005267082.1:c.4341+112=	XM_005267082.1:c.4341+112G>A
PTPRK transcript variant X3	XM_005267083.1:c.4335+112=	XM_005267083.1:c.4335+112G>A
PTPRK transcript variant X4	XM_005267084.1:c.4323+112=	XM_005267084.1:c.4323+112G>A
PTPRK transcript variant X5	XM_005267085.1:c.4266+112=	XM_005267085.1:c.4266+112G>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#.

54 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss110898235	Feb 13, 2009 (130)
2	ILLUMINA-UK	ss116712291	Feb 14, 2009 (130)
3	COMPLETE_GENOMICS	ss162805358	Jul 04, 2010 (132)
4	COMPLETE_GENOMICS	ss167258879	Jul 04, 2010 (132)
5	BUSHMAN	ss202408269	Jul 04, 2010 (132)
6	1000GENOMES	ss222668176	Jul 14, 2010 (132)
7	1000GENOMES	ss233679275	Jul 15, 2010 (132)
8	TISHKOFF	ss559516393	Apr 25, 2013 (138)
9	SSMP	ss653747012	Apr 25, 2013 (138)
10	EVA-GONL	ss983489505	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1074025921	Aug 21, 2014 (142)
12	1000GENOMES	ss1322233056	Aug 21, 2014 (142)
13	DDI	ss1430892640	Apr 01, 2015 (144)
14	EVA_GENOME_DK	ss1581893963	Apr 01, 2015 (144)
15	EVA_DECODE	ss1593057167	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1616673096	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1659667129	Apr 01, 2015 (144)
18	EVA_MGP	ss1711142530	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1804666786	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1926733126	Feb 12, 2016 (147)
21	JJLAB	ss2024022587	Sep 14, 2016 (149)
22	ILLUMINA	ss2094965079	Dec 20, 2016 (150)
23	ILLUMINA	ss2095189798	Dec 20, 2016 (150)
24	USC_VALOUEV	ss2152216855	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2288305097	Dec 20, 2016 (150)
26	GNOMAD	ss2845015547	Nov 08, 2017 (151)
27	SWEGEN	ss2999936988	Nov 08, 2017 (151)
28	BIOINF_KMB_FNS_UNIBA	ss3025805436	Nov 08, 2017 (151)
29	CSHL	ss3347224722	Nov 08, 2017 (151)
30	ILLUMINA	ss3653187463	Oct 12, 2018 (152)
31	EGCUT_WGS	ss3667850481	Jul 13, 2019 (153)
32	EVA_DECODE	ss3718257987	Jul 13, 2019 (153)
33	ACPOP	ss3733974702	Jul 13, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3808814977	Jul 13, 2019 (153)
35	EVA	ss3830187799	Apr 26, 2020 (154)
36	SGDP_PRJ	ss3865687062	Apr 26, 2020 (154)
37	FSA-LAB	ss3984348256	Apr 26, 2021 (155)
38	FSA-LAB	ss3984348257	Apr 26, 2021 (155)
39	EVA	ss3986358408	Apr 26, 2021 (155)
40	VINODS	ss4025303797	Apr 26, 2021 (155)
41	TOPMED	ss4721538620	Apr 26, 2021 (155)
42	EVA	ss5237193216	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5270315455	Oct 13, 2022 (156)
44	EVA	ss5368946870	Oct 13, 2022 (156)
45	HUGCELL_USP	ss5467759285	Oct 13, 2022 (156)
46	EVA	ss5508706797	Oct 13, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5557244405	Oct 13, 2022 (156)
48	SANFORD_IMAGENETICS	ss5641471983	Oct 13, 2022 (156)
49	EVA	ss5800134244	Oct 13, 2022 (156)
50	EVA	ss5842974657	Oct 13, 2022 (156)
51	EVA	ss5848667255	Oct 13, 2022 (156)
52	EVA	ss5885914593	Oct 13, 2022 (156)
53	EVA	ss5970129061	Oct 13, 2022 (156)
54	EVA	ss5970129062	Oct 13, 2022 (156)
55	1000Genomes	NC_000006.11 - 128294055	Oct 12, 2018 (152)
56	1000Genomes_30x	NC_000006.12 - 127972910	Oct 13, 2022 (156)
57	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 128294055	Oct 12, 2018 (152)
58	Genetic variation in the Estonian population	NC_000006.11 - 128294055	Oct 12, 2018 (152)
59	The Danish reference pan genome	NC_000006.11 - 128294055	Apr 26, 2020 (154)
60	gnomAD - Genomes	NC_000006.12 - 127972910	Apr 26, 2021 (155)
61	Genome of the Netherlands Release 5	NC_000006.11 - 128294055	Apr 26, 2020 (154)
62	Medical Genome Project healthy controls from Spanish population	NC_000006.11 - 128294055	Apr 26, 2020 (154)
63	Northern Sweden	NC_000006.11 - 128294055	Jul 13, 2019 (153)
64	Qatari	NC_000006.11 - 128294055	Apr 26, 2020 (154)
65	SGDP_PRJ	NC_000006.11 - 128294055	Apr 26, 2020 (154)
66	Siberian	NC_000006.11 - 128294055	Apr 26, 2020 (154)
67	TopMed	NC_000006.12 - 127972910	Apr 26, 2021 (155)
68	UK 10K study - Twins	NC_000006.11 - 128294055	Oct 12, 2018 (152)
69	A Vietnamese Genetic Variation Database	NC_000006.11 - 128294055	Jul 13, 2019 (153)
70	ALFA	NC_000006.12 - 127972910	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)
rs73773978	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss110898235, ss116712291, ss162805358, ss167258879, ss202408269, ss1593057167, ss2094965079	NC_000006.10:128335747:C:T	NC_000006.12:127972909:C:T	(self)
34100575, 19002420, 13588729, 8058902, 8464440, 258290, 7259567, 8775056, 17704042, 4733209, 19002420, 4230995, ss222668176, ss233679275, ss559516393, ss653747012, ss983489505, ss1074025921, ss1322233056, ss1430892640, ss1581893963, ss1616673096, ss1659667129, ss1711142530, ss1804666786, ss1926733126, ss2024022587, ss2095189798, ss2152216855, ss2845015547, ss2999936988, ss3347224722, ss3653187463, ss3667850481, ss3733974702, ss3830187799, ss3865687062, ss3984348256, ss3984348257, ss3986358408, ss5368946870, ss5508706797, ss5641471983, ss5800134244, ss5842974657, ss5848667255, ss5970129061, ss5970129062	NC_000006.11:128294054:C:T	NC_000006.12:127972909:C:T	(self)
44770340, 240839096, 558916178, 2991732258, ss2288305097, ss3025805436, ss3718257987, ss3808814977, ss4721538620, ss5237193216, ss5270315455, ss5467759285, ss5557244405, ss5885914593	NC_000006.12:127972909:C:T	NC_000006.12:127972909:C:T	(self)
ss4025303797	NT_187556.1:318107:C:T	NC_000006.12:127972909:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs72975916

PMID	Title	Author	Year	Journal
22057235	Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease.	Trynka G et al.	2011	Nature genetics
23820479	THEMIS and PTPRK in celiac intestinal mucosa: coexpression in disease and after in vitro gliadin challenge.	Bondar C et al.	2014	European journal of human genetics

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

rs72975916