Name: rs12136321
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.

rs12136321

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:13605685 (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>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.05411 (1529/28258, 14KJPN)
C=0.00229 (42/18304, ALFA)
C=0.05686 (953/16760, 8.3KJPN) (+ 14 more)
C=0.0522 (334/6404, 1000G_30x)
C=0.0493 (247/5008, 1000G)
C=0.0029 (13/4480, Estonian)
C=0.0047 (18/3854, ALSPAC)
C=0.0027 (10/3708, TWINSUK)
C=0.0756 (221/2922, KOREAN)
C=0.0688 (126/1832, Korea1K)
C=0.004 (4/998, GoNL)
C=0.012 (7/600, NorthernSweden)
C=0.060 (13/216, Qatari)
T=0.50 (25/50, SGDP_PRJ)
C=0.50 (25/50, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PDPN : 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	18304	T=0.99771	A=0.00000, C=0.00229
European	Sub	14148	T=0.99781	A=0.00000, C=0.00219
African	Sub	2570	T=0.9969	A=0.0000, C=0.0031
African Others	Sub	104	T=1.000	A=0.000, C=0.000
African American	Sub	2466	T=0.9968	A=0.0000, C=0.0032
Asian	Sub	94	T=0.99	A=0.00, C=0.01
East Asian	Sub	70	T=1.00	A=0.00, C=0.00
Other Asian	Sub	24	T=0.96	A=0.00, C=0.04
Latin American 1	Sub	140	T=1.000	A=0.000, C=0.000
Latin American 2	Sub	594	T=1.000	A=0.000, C=0.000
South Asian	Sub	96	T=1.00	A=0.00, C=0.00
Other	Sub	662	T=0.997	A=0.000, C=0.003

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
14KJPN	JAPANESE	Study-wide	28258	T=0.94589	C=0.05411
Allele Frequency Aggregator	Total	Global	18304	T=0.99771	A=0.00000, C=0.00229
Allele Frequency Aggregator	European	Sub	14148	T=0.99781	A=0.00000, C=0.00219
Allele Frequency Aggregator	African	Sub	2570	T=0.9969	A=0.0000, C=0.0031
Allele Frequency Aggregator	Other	Sub	662	T=0.997	A=0.000, C=0.003
Allele Frequency Aggregator	Latin American 2	Sub	594	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	140	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	96	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	Asian	Sub	94	T=0.99	A=0.00, C=0.01
8.3KJPN	JAPANESE	Study-wide	16760	T=0.94314	C=0.05686
1000Genomes_30x	Global	Study-wide	6404	T=0.9478	C=0.0522
1000Genomes_30x	African	Sub	1786	T=0.9076	C=0.0924
1000Genomes_30x	Europe	Sub	1266	T=0.9866	C=0.0134
1000Genomes_30x	South Asian	Sub	1202	T=0.9351	C=0.0649
1000Genomes_30x	East Asian	Sub	1170	T=0.9470	C=0.0530
1000Genomes_30x	American	Sub	980	T=0.988	C=0.012
1000Genomes	Global	Study-wide	5008	T=0.9507	C=0.0493
1000Genomes	African	Sub	1322	T=0.9092	C=0.0908
1000Genomes	East Asian	Sub	1008	T=0.9514	C=0.0486
1000Genomes	Europe	Sub	1006	T=0.9871	C=0.0129
1000Genomes	South Asian	Sub	978	T=0.943	C=0.057
1000Genomes	American	Sub	694	T=0.987	C=0.013
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9971	C=0.0029
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9953	C=0.0047
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9973	C=0.0027
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9244	C=0.0756
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9312	C=0.0688
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.996	C=0.004
Northern Sweden	ACPOP	Study-wide	600	T=0.988	C=0.012
Qatari	Global	Study-wide	216	T=0.940	C=0.060
SGDP_PRJ	Global	Study-wide	50	T=0.50	C=0.50
Siberian	Global	Study-wide	2	T=0.5	C=0.5

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.13605685T>A
GRCh38.p14 chr 1	NC_000001.11:g.13605685T>C
GRCh37.p13 chr 1	NC_000001.10:g.13932180T>A
GRCh37.p13 chr 1	NC_000001.10:g.13932180T>C

Gene: PDPN, podoplanin (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PDPN transcript variant 3	NM_001006624.2:c.-59-1488… NM_001006624.2:c.-59-1488T>A	N/A	Intron Variant
PDPN transcript variant 4	NM_001006625.2:c.-59-1488… NM_001006625.2:c.-59-1488T>A	N/A	Intron Variant
PDPN transcript variant 5	NM_001385053.1:c.-59-1488… NM_001385053.1:c.-59-1488T>A	N/A	Intron Variant
PDPN transcript variant 1	NM_006474.5:c.68-1488T>A	N/A	Intron Variant
PDPN transcript variant 2	NM_198389.2:c.296-1488T>A	N/A	Intron Variant
PDPN transcript variant X1	XM_006710295.2:c.-59-1488… XM_006710295.2:c.-59-1488T>A	N/A	Intron Variant
PDPN transcript variant X2	XM_024451404.2:c.-59-1488… XM_024451404.2:c.-59-1488T>A	N/A	Intron Variant
PDPN transcript variant X3	XM_047434471.1:c.-59-1488… XM_047434471.1:c.-59-1488T>A	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=	A	C
GRCh38.p14 chr 1	NC_000001.11:g.13605685=	NC_000001.11:g.13605685T>A	NC_000001.11:g.13605685T>C
GRCh37.p13 chr 1	NC_000001.10:g.13932180=	NC_000001.10:g.13932180T>A	NC_000001.10:g.13932180T>C
PDPN transcript variant 3	NM_001006624.1:c.-59-1488=	NM_001006624.1:c.-59-1488T>A	NM_001006624.1:c.-59-1488T>C
PDPN transcript variant 3	NM_001006624.2:c.-59-1488=	NM_001006624.2:c.-59-1488T>A	NM_001006624.2:c.-59-1488T>C
PDPN transcript variant 4	NM_001006625.1:c.-59-1488=	NM_001006625.1:c.-59-1488T>A	NM_001006625.1:c.-59-1488T>C
PDPN transcript variant 4	NM_001006625.2:c.-59-1488=	NM_001006625.2:c.-59-1488T>A	NM_001006625.2:c.-59-1488T>C
PDPN transcript variant 5	NM_001385053.1:c.-59-1488=	NM_001385053.1:c.-59-1488T>A	NM_001385053.1:c.-59-1488T>C
PDPN transcript variant 1	NM_006474.4:c.296-1488=	NM_006474.4:c.296-1488T>A	NM_006474.4:c.296-1488T>C
PDPN transcript variant 1	NM_006474.5:c.68-1488=	NM_006474.5:c.68-1488T>A	NM_006474.5:c.68-1488T>C
PDPN transcript variant 2	NM_198389.2:c.296-1488=	NM_198389.2:c.296-1488T>A	NM_198389.2:c.296-1488T>C
PDPN transcript variant X1	XM_005245723.1:c.-59-1488=	XM_005245723.1:c.-59-1488T>A	XM_005245723.1:c.-59-1488T>C
PDPN transcript variant X1	XM_006710295.2:c.-59-1488=	XM_006710295.2:c.-59-1488T>A	XM_006710295.2:c.-59-1488T>C
PDPN transcript variant X2	XM_024451404.2:c.-59-1488=	XM_024451404.2:c.-59-1488T>A	XM_024451404.2:c.-59-1488T>C
PDPN transcript variant X3	XM_047434471.1:c.-59-1488=	XM_047434471.1:c.-59-1488T>A	XM_047434471.1:c.-59-1488T>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#.

42 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18280356	Feb 28, 2004 (120)
2	COMPLETE_GENOMICS	ss163089359	Jul 04, 2010 (132)
3	GMI	ss275720850	May 04, 2012 (137)
4	1000GENOMES	ss328425350	May 09, 2011 (134)
5	TISHKOFF	ss553812313	Apr 25, 2013 (138)
6	SSMP	ss647587179	Apr 25, 2013 (138)
7	EVA-GONL	ss974871032	Aug 21, 2014 (142)
8	JMKIDD_LAB	ss1067679554	Aug 21, 2014 (142)
9	1000GENOMES	ss1289745161	Aug 21, 2014 (142)
10	EVA_DECODE	ss1584228190	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1599576527	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1642570560	Apr 01, 2015 (144)
13	HAMMER_LAB	ss1793927873	Sep 08, 2015 (146)
14	WEILL_CORNELL_DGM	ss1918073650	Feb 12, 2016 (147)
15	USC_VALOUEV	ss2147548523	Dec 20, 2016 (150)
16	HUMAN_LONGEVITY	ss2160163014	Dec 20, 2016 (150)
17	GRF	ss2697449232	Nov 08, 2017 (151)
18	ILLUMINA	ss2710666097	Nov 08, 2017 (151)
19	GNOMAD	ss2751819670	Nov 08, 2017 (151)
20	SWEGEN	ss2986333077	Nov 08, 2017 (151)
21	EGCUT_WGS	ss3654419419	Jul 12, 2019 (153)
22	EVA_DECODE	ss3686196981	Jul 12, 2019 (153)
23	EVA_DECODE	ss3686196982	Jul 12, 2019 (153)
24	ACPOP	ss3726804541	Jul 12, 2019 (153)
25	EVA	ss3745847909	Jul 12, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3798869193	Jul 12, 2019 (153)
27	SGDP_PRJ	ss3848241892	Apr 25, 2020 (154)
28	KRGDB	ss3893132472	Apr 25, 2020 (154)
29	KOGIC	ss3943865567	Apr 25, 2020 (154)
30	TOPMED	ss4439756176	Apr 25, 2021 (155)
31	TOPMED	ss4439756177	Apr 25, 2021 (155)
32	TOMMO_GENOMICS	ss5142569205	Apr 25, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5241245406	Oct 12, 2022 (156)
34	EVA	ss5316863353	Oct 12, 2022 (156)
35	HUGCELL_USP	ss5442430216	Oct 12, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5513032587	Oct 12, 2022 (156)
37	SANFORD_IMAGENETICS	ss5624962606	Oct 12, 2022 (156)
38	TOMMO_GENOMICS	ss5666906301	Oct 12, 2022 (156)
39	YY_MCH	ss5800342378	Oct 12, 2022 (156)
40	EVA	ss5831562691	Oct 12, 2022 (156)
41	EVA	ss5907105379	Oct 12, 2022 (156)
42	EVA	ss5936781517	Oct 12, 2022 (156)
43	1000Genomes	NC_000001.10 - 13932180	Oct 11, 2018 (152)
44	1000Genomes_30x	NC_000001.11 - 13605685	Oct 12, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 13932180	Oct 11, 2018 (152)
46	Genetic variation in the Estonian population	NC_000001.10 - 13932180	Oct 11, 2018 (152)
47	gnomAD - Genomes Submission ignored due to conflicting rows: Row 2986482 (NC_000001.11:13605684:T:A 1/140124) Row 2986483 (NC_000001.11:13605684:T:C 4125/140112)	-	Apr 25, 2021 (155)
48	gnomAD - Genomes Submission ignored due to conflicting rows: Row 2986482 (NC_000001.11:13605684:T:A 1/140124) Row 2986483 (NC_000001.11:13605684:T:C 4125/140112)	-	Apr 25, 2021 (155)
49	Genome of the Netherlands Release 5	NC_000001.10 - 13932180	Apr 25, 2020 (154)
50	KOREAN population from KRGDB	NC_000001.10 - 13932180	Apr 25, 2020 (154)
51	Korean Genome Project	NC_000001.11 - 13605685	Apr 25, 2020 (154)
52	Northern Sweden	NC_000001.10 - 13932180	Jul 12, 2019 (153)
53	Qatari	NC_000001.10 - 13932180	Apr 25, 2020 (154)
54	SGDP_PRJ	NC_000001.10 - 13932180	Apr 25, 2020 (154)
55	Siberian	NC_000001.10 - 13932180	Apr 25, 2020 (154)
56	8.3KJPN	NC_000001.10 - 13932180	Apr 25, 2021 (155)
57	14KJPN	NC_000001.11 - 13605685	Oct 12, 2022 (156)
58	TopMed Submission ignored due to conflicting rows: Row 3362511 (NC_000001.11:13605684:T:A 2/264690) Row 3362512 (NC_000001.11:13605684:T:C 8459/264690)	-	Apr 25, 2021 (155)
59	TopMed Submission ignored due to conflicting rows: Row 3362511 (NC_000001.11:13605684:T:A 2/264690) Row 3362512 (NC_000001.11:13605684:T:C 8459/264690)	-	Apr 25, 2021 (155)
60	UK 10K study - Twins	NC_000001.10 - 13932180	Oct 11, 2018 (152)
61	ALFA	NC_000001.11 - 13605685	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
137307176, ss3686196981, ss4439756176	NC_000001.11:13605684:T:A	NC_000001.11:13605684:T:A	(self)
ss163089359, ss275720850, ss1584228190	NC_000001.9:13804766:T:C	NC_000001.11:13605684:T:C	(self)
423222, 218051, 157667, 94107, 309866, 89406, 115580, 258872, 64877, 538512, 218051, ss328425350, ss553812313, ss647587179, ss974871032, ss1067679554, ss1289745161, ss1599576527, ss1642570560, ss1793927873, ss1918073650, ss2147548523, ss2697449232, ss2710666097, ss2751819670, ss2986333077, ss3654419419, ss3726804541, ss3745847909, ss3848241892, ss3893132472, ss5142569205, ss5316863353, ss5624962606, ss5831562691, ss5936781517	NC_000001.10:13932179:T:C	NC_000001.11:13605684:T:C	(self)
558522, 243568, 743405, 137307176, ss2160163014, ss3686196982, ss3798869193, ss3943865567, ss4439756177, ss5241245406, ss5442430216, ss5513032587, ss5666906301, ss5800342378, ss5907105379	NC_000001.11:13605684:T:C	NC_000001.11:13605684:T:C	(self)
ss18280356	NT_004873.15:309344:T:C	NC_000001.11:13605684: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 rs12136321

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

rs12136321