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dbSNP Short Genetic Variations

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.

rs10481625

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr9:8804761 (GRCh38.p12) 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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.26131 (32812/125568, TOPMED)
T=0.2595 (8015/30892, GnomAD)
T=0.244 (1223/5008, 1000G) (+ 3 more)
T=0.294 (1319/4480, Estonian)
T=0.290 (1116/3854, ALSPAC)
T=0.283 (1051/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTPRD : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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.p12 chr 9 NC_000009.12:g.8804761T>A
GRCh38.p12 chr 9 NC_000009.12:g.8804761T>C
GRCh38.p12 chr 9 NC_000009.12:g.8804761T>G
GRCh37.p13 chr 9 NC_000009.11:g.8804761T>A
GRCh37.p13 chr 9 NC_000009.11:g.8804761T>C
GRCh37.p13 chr 9 NC_000009.11:g.8804761T>G
PTPRD RefSeqGene NG_033963.1:g.1812963A>T
PTPRD RefSeqGene NG_033963.1:g.1812963A>G
PTPRD RefSeqGene NG_033963.1:g.1812963A>C
Gene: PTPRD, protein tyrosine phosphatase, receptor type D (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PTPRD transcript variant 1 NM_002839.3:c. N/A Intron Variant
PTPRD transcript variant 5 NM_001040712.2:c. N/A Genic Upstream Transcript Variant
PTPRD transcript variant 6 NM_001171025.1:c. N/A Genic Upstream Transcript Variant
PTPRD transcript variant 2 NM_130391.3:c. N/A Genic Upstream Transcript Variant
PTPRD transcript variant 3 NM_130392.3:c. N/A Genic Upstream Transcript Variant
PTPRD transcript variant 4 NM_130393.3:c. N/A Genic Upstream Transcript Variant
PTPRD transcript variant X10 XM_006716817.4:c. N/A Intron Variant
PTPRD transcript variant X25 XM_006716823.3:c. N/A Intron Variant
PTPRD transcript variant X27 XM_006716825.4:c. N/A Intron Variant
PTPRD transcript variant X29 XM_006716827.4:c. N/A Intron Variant
PTPRD transcript variant X41 XM_006716832.4:c. N/A Intron Variant
PTPRD transcript variant X42 XM_006716833.4:c. N/A Intron Variant
PTPRD transcript variant X43 XM_006716834.4:c. N/A Intron Variant
PTPRD transcript variant X46 XM_006716835.4:c. N/A Intron Variant
PTPRD transcript variant X49 XM_006716837.4:c. N/A Intron Variant
PTPRD transcript variant X26 XM_011517992.3:c. N/A Intron Variant
PTPRD transcript variant X1 XM_017014958.2:c. N/A Intron Variant
PTPRD transcript variant X2 XM_017014959.2:c. N/A Intron Variant
PTPRD transcript variant X3 XM_017014960.2:c. N/A Intron Variant
PTPRD transcript variant X4 XM_017014961.2:c. N/A Intron Variant
PTPRD transcript variant X5 XM_017014962.2:c. N/A Intron Variant
PTPRD transcript variant X6 XM_017014963.2:c. N/A Intron Variant
PTPRD transcript variant X7 XM_017014964.2:c. N/A Intron Variant
PTPRD transcript variant X8 XM_017014965.2:c. N/A Intron Variant
PTPRD transcript variant X9 XM_017014966.2:c. N/A Intron Variant
PTPRD transcript variant X11 XM_017014967.2:c. N/A Intron Variant
PTPRD transcript variant X12 XM_017014968.2:c. N/A Intron Variant
PTPRD transcript variant X13 XM_017014969.2:c. N/A Intron Variant
PTPRD transcript variant X14 XM_017014970.2:c. N/A Intron Variant
PTPRD transcript variant X16 XM_017014971.2:c. N/A Intron Variant
PTPRD transcript variant X17 XM_017014972.2:c. N/A Intron Variant
PTPRD transcript variant X18 XM_017014973.2:c. N/A Intron Variant
PTPRD transcript variant X19 XM_017014974.2:c. N/A Intron Variant
PTPRD transcript variant X20 XM_017014975.2:c. N/A Intron Variant
PTPRD transcript variant X21 XM_017014976.2:c. N/A Intron Variant
PTPRD transcript variant X22 XM_017014977.2:c. N/A Intron Variant
PTPRD transcript variant X23 XM_017014978.2:c. N/A Intron Variant
PTPRD transcript variant X24 XM_017014979.2:c. N/A Intron Variant
PTPRD transcript variant X28 XM_017014980.2:c. N/A Intron Variant
PTPRD transcript variant X30 XM_017014981.2:c. N/A Intron Variant
PTPRD transcript variant X31 XM_017014982.2:c. N/A Intron Variant
PTPRD transcript variant X32 XM_017014983.2:c. N/A Intron Variant
PTPRD transcript variant X33 XM_017014984.2:c. N/A Intron Variant
PTPRD transcript variant X34 XM_017014985.2:c. N/A Intron Variant
PTPRD transcript variant X35 XM_017014986.2:c. N/A Intron Variant
PTPRD transcript variant X36 XM_017014987.2:c. N/A Intron Variant
PTPRD transcript variant X37 XM_017014988.2:c. N/A Intron Variant
PTPRD transcript variant X38 XM_017014989.2:c. N/A Intron Variant
PTPRD transcript variant X39 XM_017014990.2:c. N/A Intron Variant
PTPRD transcript variant X40 XM_017014991.2:c. N/A Intron Variant
PTPRD transcript variant X44 XM_017014992.2:c. N/A Intron Variant
PTPRD transcript variant X45 XM_017014993.2:c. N/A Intron Variant
PTPRD transcript variant X47 XM_017014994.2:c. N/A Intron Variant
PTPRD transcript variant X48 XM_017014995.2:c. N/A Intron Variant
PTPRD transcript variant X15 XM_024447625.1:c. N/A Intron Variant
PTPRD transcript variant X50 XM_024447627.1:c. N/A Intron Variant
Help

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
Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.26131 C=0.73869
gnomAD - Genomes Global Study-wide 30892 T=0.2595 A=0.0001, G=0.0000, C=0.7404
gnomAD - Genomes European Sub 18450 T=0.2730 A=0.0000, G=0.0001, C=0.7269
gnomAD - Genomes African Sub 8710 T=0.243 A=0.000, G=0.000, C=0.757
gnomAD - Genomes East Asian Sub 1612 T=0.210 A=0.000, G=0.000, C=0.790
gnomAD - Genomes Other Sub 980 T=0.22 A=0.00, G=0.00, C=0.78
gnomAD - Genomes American Sub 838 T=0.27 A=0.00, G=0.00, C=0.73
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.27 A=0.00, G=0.00, C=0.73
1000Genomes Global Study-wide 5008 T=0.244 C=0.756
1000Genomes African Sub 1322 T=0.259 C=0.741
1000Genomes East Asian Sub 1008 T=0.200 C=0.800
1000Genomes Europe Sub 1006 T=0.268 C=0.732
1000Genomes South Asian Sub 978 T=0.26 C=0.74
1000Genomes American Sub 694 T=0.23 C=0.77
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.294 C=0.706
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.290 C=0.710
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.283 C=0.717
Help

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 G Note
GRCh38.p12 chr 9 NC_000009.12:...

NC_000009.12:g.8804761T=

NC_000009.12:...

NC_000009.12:g.8804761T>A

NC_000009.12:...

NC_000009.12:g.8804761T>C

NC_000009.12:...

NC_000009.12:g.8804761T>G

GRCh37.p13 chr 9 NC_000009.11:...

NC_000009.11:g.8804761T=

NC_000009.11:...

NC_000009.11:g.8804761T>A

NC_000009.11:...

NC_000009.11:g.8804761T>C

NC_000009.11:...

NC_000009.11:g.8804761T>G

PTPRD RefSeqGene NG_033963.1:g...

NG_033963.1:g.1812963A=

NG_033963.1:g...

NG_033963.1:g.1812963A>T

NG_033963.1:g...

NG_033963.1:g.1812963A>G

NG_033963.1:g...

NG_033963.1:g.1812963A>C

Help

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#.

73 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss14863353 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss17248352 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19776191 Feb 27, 2004 (120)
4 SSAHASNP ss22817555 Apr 05, 2004 (121)
5 ABI ss43386103 Mar 15, 2006 (126)
6 PERLEGEN ss69281524 May 17, 2007 (127)
7 HGSV ss77765412 Dec 07, 2007 (129)
8 HGSV ss84165577 Dec 15, 2007 (130)
9 HGSV ss86086807 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss94006505 Mar 25, 2008 (129)
11 HUMANGENOME_JCVI ss97704757 Feb 06, 2009 (130)
12 BGI ss105660093 Feb 06, 2009 (130)
13 1000GENOMES ss108574970 Jan 23, 2009 (130)
14 1000GENOMES ss114117044 Jan 25, 2009 (130)
15 ILLUMINA-UK ss115685815 Feb 14, 2009 (130)
16 ENSEMBL ss142913808 Dec 01, 2009 (131)
17 ENSEMBL ss143930704 Dec 01, 2009 (131)
18 GMI ss157157100 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss163763947 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss164464419 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss166116747 Jul 04, 2010 (132)
22 BUSHMAN ss200068502 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss206865956 Jul 04, 2010 (132)
24 1000GENOMES ss224110788 Jul 14, 2010 (132)
25 1000GENOMES ss234717275 Jul 15, 2010 (132)
26 1000GENOMES ss241513474 Jul 15, 2010 (132)
27 BL ss254035321 May 09, 2011 (134)
28 GMI ss280097241 May 04, 2012 (137)
29 GMI ss285965390 Apr 25, 2013 (138)
30 PJP ss294325186 May 09, 2011 (134)
31 ILLUMINA ss483257018 May 04, 2012 (137)
32 ILLUMINA ss485818779 May 04, 2012 (137)
33 ILLUMINA ss535474864 Sep 08, 2015 (146)
34 TISHKOFF ss561224829 Apr 25, 2013 (138)
35 SSMP ss655652575 Apr 25, 2013 (138)
36 ILLUMINA ss780209774 Sep 08, 2015 (146)
37 ILLUMINA ss782072002 Sep 08, 2015 (146)
38 ILLUMINA ss835694571 Sep 08, 2015 (146)
39 EVA-GONL ss986288749 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1076093288 Aug 21, 2014 (142)
41 1000GENOMES ss1332814587 Aug 21, 2014 (142)
42 DDI ss1431743162 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1582977757 Apr 01, 2015 (144)
44 EVA_DECODE ss1595915354 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1622208458 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1665202491 Apr 01, 2015 (144)
47 HAMMER_LAB ss1805869854 Sep 08, 2015 (146)
48 WEILL_CORNELL_DGM ss1929568855 Feb 12, 2016 (147)
49 ILLUMINA ss1959164464 Feb 12, 2016 (147)
50 GENOMED ss1971149728 Jul 19, 2016 (147)
51 JJLAB ss2025492890 Sep 14, 2016 (149)
52 USC_VALOUEV ss2153722354 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2309220354 Dec 20, 2016 (150)
54 TOPMED ss2479235436 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2627222714 Nov 08, 2017 (151)
56 ILLUMINA ss2634834636 Nov 08, 2017 (151)
57 GRF ss2709520272 Nov 08, 2017 (151)
58 GNOMAD ss2875186763 Nov 08, 2017 (151)
59 AFFY ss2985455603 Nov 08, 2017 (151)
60 AFFY ss2986099747 Nov 08, 2017 (151)
61 SWEGEN ss3004351862 Nov 08, 2017 (151)
62 ILLUMINA ss3022906802 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3026535036 Nov 08, 2017 (151)
64 CSHL ss3348513259 Nov 08, 2017 (151)
65 TOPMED ss3581475906 Nov 08, 2017 (151)
66 TOPMED ss3581475907 Nov 08, 2017 (151)
67 TOPMED ss3581475908 Nov 08, 2017 (151)
68 ILLUMINA ss3630209503 Oct 12, 2018 (152)
69 ILLUMINA ss3632728810 Oct 12, 2018 (152)
70 ILLUMINA ss3642673243 Oct 12, 2018 (152)
71 URBANLAB ss3649065209 Oct 12, 2018 (152)
72 ILLUMINA ss3653457260 Oct 12, 2018 (152)
73 ILLUMINA ss3654219630 Oct 12, 2018 (152)
74 1000Genomes NC_000009.11 - 8804761 Oct 12, 2018 (152)
75 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 8804761 Oct 12, 2018 (152)
76 Genetic variation in the Estonian population NC_000009.11 - 8804761 Oct 12, 2018 (152)
77 gnomAD - Genomes NC_000009.11 - 8804761 Oct 12, 2018 (152)
78 TopMed NC_000009.12 - 8804761 Oct 12, 2018 (152)
79 UK 10K study - Twins NC_000009.11 - 8804761 Oct 12, 2018 (152)
Help

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)
rs60075424 May 25, 2008 (130)
rs386480743 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77765412, ss84165577, ss86086807 NC_000009.9:8794760:T= NC_000009.12:8804760:T= (self)
ss94006505, ss108574970, ss114117044, ss115685815, ss163763947, ss164464419, ss166116747, ss200068502, ss206865956, ss254035321, ss280097241, ss285965390, ss294325186, ss485818779, ss1595915354 NC_000009.10:8794760:T= NC_000009.12:8804760:T= (self)
45040250, 25062561, 17825062, 215814518, 25062561, ss224110788, ss234717275, ss241513474, ss483257018, ss535474864, ss561224829, ss655652575, ss780209774, ss782072002, ss835694571, ss986288749, ss1076093288, ss1332814587, ss1431743162, ss1582977757, ss1622208458, ss1665202491, ss1805869854, ss1929568855, ss1959164464, ss1971149728, ss2025492890, ss2153722354, ss2479235436, ss2627222714, ss2634834636, ss2709520272, ss2875186763, ss2985455603, ss2986099747, ss3004351862, ss3022906802, ss3348513259, ss3630209503, ss3632728810, ss3642673243, ss3653457260, ss3654219630 NC_000009.11:8804760:T= NC_000009.12:8804760:T= (self)
405509400, ss2309220354, ss3026535036, ss3581475906, ss3581475907, ss3581475908, ss3649065209 NC_000009.12:8804760:T= NC_000009.12:8804760:T= (self)
ss14863353, ss17248352, ss19776191, ss22817555 NT_008413.16:8794760:T= NC_000009.12:8804760:T= (self)
ss43386103, ss69281524, ss97704757, ss105660093, ss142913808, ss143930704, ss157157100 NT_008413.18:8794760:T= NC_000009.12:8804760:T= (self)
215814518, ss2875186763 NC_000009.11:8804760:T>A NC_000009.12:8804760:T>A (self)
ss2309220354, ss3581475906 NC_000009.12:8804760:T>A NC_000009.12:8804760:T>A (self)
ss77765412, ss84165577, ss86086807 NC_000009.9:8794760:T>C NC_000009.12:8804760:T>C (self)
ss94006505, ss108574970, ss114117044, ss115685815, ss163763947, ss164464419, ss166116747, ss200068502, ss206865956, ss254035321, ss280097241, ss285965390, ss294325186, ss485818779, ss1595915354 NC_000009.10:8794760:T>C NC_000009.12:8804760:T>C (self)
45040250, 25062561, 17825062, 215814518, 25062561, ss224110788, ss234717275, ss241513474, ss483257018, ss535474864, ss561224829, ss655652575, ss780209774, ss782072002, ss835694571, ss986288749, ss1076093288, ss1332814587, ss1431743162, ss1582977757, ss1622208458, ss1665202491, ss1805869854, ss1929568855, ss1959164464, ss1971149728, ss2025492890, ss2153722354, ss2479235436, ss2627222714, ss2634834636, ss2709520272, ss2875186763, ss2985455603, ss2986099747, ss3004351862, ss3022906802, ss3348513259, ss3630209503, ss3632728810, ss3642673243, ss3653457260, ss3654219630 NC_000009.11:8804760:T>C NC_000009.12:8804760:T>C (self)
405509400, ss2309220354, ss3026535036, ss3581475907, ss3649065209 NC_000009.12:8804760:T>C NC_000009.12:8804760:T>C (self)
ss14863353, ss17248352, ss19776191, ss22817555 NT_008413.16:8794760:T>C NC_000009.12:8804760:T>C (self)
ss43386103, ss69281524, ss97704757, ss105660093, ss142913808, ss143930704, ss157157100 NT_008413.18:8794760:T>C NC_000009.12:8804760:T>C (self)
215814518, ss2875186763 NC_000009.11:8804760:T>G NC_000009.12:8804760:T>G (self)
ss2309220354, ss3581475908 NC_000009.12:8804760:T>G NC_000009.12:8804760:T>G (self)
Help

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

No publications for rs10481625

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.

Software version is: 2.0.1.post58+e54ea20