Name: rs10487113
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.

rs10487113

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:90469584 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.187298 (49576/264690, TOPMED)
T=0.183933 (25762/140062, GnomAD)
T=0.32479 (9178/28258, 14KJPN) (+ 19 more)
T=0.17470 (3300/18890, ALFA)
T=0.32402 (5430/16758, 8.3KJPN)
T=0.1993 (1276/6404, 1000G_30x)
T=0.1999 (1001/5008, 1000G)
T=0.1583 (709/4480, Estonian)
T=0.1606 (619/3854, ALSPAC)
T=0.1650 (612/3708, TWINSUK)
T=0.2811 (823/2928, KOREAN)
T=0.2582 (473/1832, Korea1K)
T=0.171 (171/998, GoNL)
T=0.152 (91/600, NorthernSweden)
T=0.002 (1/534, MGP)
T=0.220 (51/232, HapMap)
T=0.218 (47/216, Qatari)
T=0.178 (37/208, Vietnamese)
G=0.438 (77/176, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
G=0.50 (7/14, Siberian)
T=0.50 (7/14, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PTTG1IP2 : 2KB Upstream 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	18890	G=0.82530	T=0.17470
European	Sub	14286	G=0.83081	T=0.16919
African	Sub	2946	G=0.8089	T=0.1911
African Others	Sub	114	G=0.825	T=0.175
African American	Sub	2832	G=0.8083	T=0.1917
Asian	Sub	112	G=0.804	T=0.196
East Asian	Sub	86	G=0.78	T=0.22
Other Asian	Sub	26	G=0.88	T=0.12
Latin American 1	Sub	146	G=0.801	T=0.199
Latin American 2	Sub	610	G=0.795	T=0.205
South Asian	Sub	98	G=0.83	T=0.17
Other	Sub	692	G=0.816	T=0.184

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=0.812702	T=0.187298
gnomAD - Genomes	Global	Study-wide	140062	G=0.816067	T=0.183933
gnomAD - Genomes	European	Sub	75872	G=0.82753	T=0.17247
gnomAD - Genomes	African	Sub	41956	G=0.81709	T=0.18291
gnomAD - Genomes	American	Sub	13640	G=0.78006	T=0.21994
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.7249	T=0.2751
gnomAD - Genomes	East Asian	Sub	3128	G=0.7730	T=0.2270
gnomAD - Genomes	Other	Sub	2144	G=0.8237	T=0.1763
14KJPN	JAPANESE	Study-wide	28258	G=0.67521	T=0.32479
Allele Frequency Aggregator	Total	Global	18890	G=0.82530	T=0.17470
Allele Frequency Aggregator	European	Sub	14286	G=0.83081	T=0.16919
Allele Frequency Aggregator	African	Sub	2946	G=0.8089	T=0.1911
Allele Frequency Aggregator	Other	Sub	692	G=0.816	T=0.184
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.795	T=0.205
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.801	T=0.199
Allele Frequency Aggregator	Asian	Sub	112	G=0.804	T=0.196
Allele Frequency Aggregator	South Asian	Sub	98	G=0.83	T=0.17
8.3KJPN	JAPANESE	Study-wide	16758	G=0.67598	T=0.32402
1000Genomes_30x	Global	Study-wide	6404	G=0.8007	T=0.1993
1000Genomes_30x	African	Sub	1786	G=0.7928	T=0.2072
1000Genomes_30x	Europe	Sub	1266	G=0.7852	T=0.2148
1000Genomes_30x	South Asian	Sub	1202	G=0.8577	T=0.1423
1000Genomes_30x	East Asian	Sub	1170	G=0.7812	T=0.2188
1000Genomes_30x	American	Sub	980	G=0.789	T=0.211
1000Genomes	Global	Study-wide	5008	G=0.8001	T=0.1999
1000Genomes	African	Sub	1322	G=0.7859	T=0.2141
1000Genomes	East Asian	Sub	1008	G=0.7827	T=0.2173
1000Genomes	Europe	Sub	1006	G=0.7883	T=0.2117
1000Genomes	South Asian	Sub	978	G=0.862	T=0.138
1000Genomes	American	Sub	694	G=0.782	T=0.218
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8417	T=0.1583
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8394	T=0.1606
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8350	T=0.1650
KOREAN population from KRGDB	KOREAN	Study-wide	2928	G=0.7189	T=0.2811
Korean Genome Project	KOREAN	Study-wide	1832	G=0.7418	T=0.2582
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.829	T=0.171
Northern Sweden	ACPOP	Study-wide	600	G=0.848	T=0.152
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.998	T=0.002
HapMap	Global	Study-wide	232	G=0.780	T=0.220
HapMap	African	Sub	118	G=0.780	T=0.220
HapMap	American	Sub	114	G=0.781	T=0.219
Qatari	Global	Study-wide	216	G=0.782	T=0.218
A Vietnamese Genetic Variation Database	Global	Study-wide	208	G=0.822	T=0.178
SGDP_PRJ	Global	Study-wide	176	G=0.438	T=0.562
The Danish reference pan genome	Danish	Study-wide	40	G=0.85	T=0.15
Siberian	Global	Study-wide	14	G=0.50	T=0.50

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 7	NC_000007.14:g.90469584G>T
GRCh37.p13 chr 7	NC_000007.13:g.90098898G>T

Gene: PTTG1IP2, PTTG1IP family member 2 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
PTTG1IP2 transcript	NM_001365443.2:c.	N/A	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=	T
GRCh38.p14 chr 7	NC_000007.14:g.90469584=	NC_000007.14:g.90469584G>T
GRCh37.p13 chr 7	NC_000007.13:g.90098898=	NC_000007.13:g.90098898G>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#.

63 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss14873598	Dec 05, 2003 (119)
2	BROAD	ss28518572	Oct 08, 2004 (124)
3	CSHL-HAPMAP	ss68423266	Jan 12, 2007 (127)
4	BCMHGSC_JDW	ss93726041	Mar 25, 2008 (129)
5	BGI	ss104449538	Dec 01, 2009 (131)
6	ILLUMINA-UK	ss116190757	Feb 14, 2009 (130)
7	COMPLETE_GENOMICS	ss162519571	Jul 04, 2010 (132)
8	COMPLETE_GENOMICS	ss166847892	Jul 04, 2010 (132)
9	1000GENOMES	ss212076853	Jul 14, 2010 (132)
10	1000GENOMES	ss223199055	Jul 14, 2010 (132)
11	1000GENOMES	ss234071825	Jul 15, 2010 (132)
12	1000GENOMES	ss241008496	Jul 15, 2010 (132)
13	BL	ss254508786	May 09, 2011 (134)
14	GMI	ss279434289	May 04, 2012 (137)
15	TISHKOFF	ss560147333	Apr 25, 2013 (138)
16	SSMP	ss654548012	Apr 25, 2013 (138)
17	EVA-GONL	ss984528398	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1074787594	Aug 21, 2014 (142)
19	1000GENOMES	ss1326096428	Aug 21, 2014 (142)
20	DDI	ss1431206063	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1582302539	Apr 01, 2015 (144)
22	EVA_DECODE	ss1594105217	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1618673256	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1661667289	Apr 01, 2015 (144)
25	EVA_MGP	ss1711171086	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1805107908	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1927790494	Feb 12, 2016 (147)
28	GENOMED	ss1970758602	Jul 19, 2016 (147)
29	JJLAB	ss2024578101	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2152799150	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2295699437	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2626780976	Nov 08, 2017 (151)
33	GRF	ss2708505460	Nov 08, 2017 (151)
34	GNOMAD	ss2856051710	Nov 08, 2017 (151)
35	SWEGEN	ss3001609719	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3026082678	Nov 08, 2017 (151)
37	CSHL	ss3347726572	Nov 08, 2017 (151)
38	EGCUT_WGS	ss3669365141	Jul 13, 2019 (153)
39	EVA_DECODE	ss3720184496	Jul 13, 2019 (153)
40	ACPOP	ss3734851893	Jul 13, 2019 (153)
41	EVA	ss3766853225	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3810027137	Jul 13, 2019 (153)
43	EVA	ss3830695370	Apr 26, 2020 (154)
44	EVA	ss3838846254	Apr 26, 2020 (154)
45	EVA	ss3844301120	Apr 26, 2020 (154)
46	SGDP_PRJ	ss3867858168	Apr 26, 2020 (154)
47	KRGDB	ss3915124214	Apr 26, 2020 (154)
48	KOGIC	ss3962066061	Apr 26, 2020 (154)
49	TOPMED	ss4754372408	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5184379230	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5273818427	Oct 13, 2022 (156)
52	EVA	ss5375111039	Oct 13, 2022 (156)
53	HUGCELL_USP	ss5470810048	Oct 13, 2022 (156)
54	EVA	ss5509044879	Oct 13, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5562488481	Oct 13, 2022 (156)
56	SANFORD_IMAGENETICS	ss5643469361	Oct 13, 2022 (156)
57	TOMMO_GENOMICS	ss5725003458	Oct 13, 2022 (156)
58	YY_MCH	ss5808874474	Oct 13, 2022 (156)
59	EVA	ss5823175327	Oct 13, 2022 (156)
60	EVA	ss5855999130	Oct 13, 2022 (156)
61	EVA	ss5859844594	Oct 13, 2022 (156)
62	EVA	ss5972647173	Oct 13, 2022 (156)
63	EVA	ss5980448463	Oct 13, 2022 (156)
64	1000Genomes	NC_000007.13 - 90098898	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000007.14 - 90469584	Oct 13, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 90098898	Oct 12, 2018 (152)
67	Genetic variation in the Estonian population	NC_000007.13 - 90098898	Oct 12, 2018 (152)
68	The Danish reference pan genome	NC_000007.13 - 90098898	Apr 26, 2020 (154)
69	gnomAD - Genomes	NC_000007.14 - 90469584	Apr 26, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000007.13 - 90098898	Apr 26, 2020 (154)
71	HapMap	NC_000007.14 - 90469584	Apr 26, 2020 (154)
72	KOREAN population from KRGDB	NC_000007.13 - 90098898	Apr 26, 2020 (154)
73	Korean Genome Project	NC_000007.14 - 90469584	Apr 26, 2020 (154)
74	Medical Genome Project healthy controls from Spanish population	NC_000007.13 - 90098898	Apr 26, 2020 (154)
75	Northern Sweden	NC_000007.13 - 90098898	Jul 13, 2019 (153)
76	Qatari	NC_000007.13 - 90098898	Apr 26, 2020 (154)
77	SGDP_PRJ	NC_000007.13 - 90098898	Apr 26, 2020 (154)
78	Siberian	NC_000007.13 - 90098898	Apr 26, 2020 (154)
79	8.3KJPN	NC_000007.13 - 90098898	Apr 26, 2021 (155)
80	14KJPN	NC_000007.14 - 90469584	Oct 13, 2022 (156)
81	TopMed	NC_000007.14 - 90469584	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000007.13 - 90098898	Oct 12, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000007.13 - 90098898	Jul 13, 2019 (153)
84	ALFA	NC_000007.14 - 90469584	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)
rs17863433	Dec 02, 2004 (124)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss93726041, ss116190757, ss162519571, ss166847892, ss212076853, ss254508786, ss279434289, ss1594105217	NC_000007.12:89936833:G:T	NC_000007.14:90469583:G:T	(self)
38101514, 21201763, 15103389, 8467478, 9467056, 22301608, 286846, 8136758, 9832424, 19875148, 5315504, 42348537, 21201763, 4729427, ss223199055, ss234071825, ss241008496, ss560147333, ss654548012, ss984528398, ss1074787594, ss1326096428, ss1431206063, ss1582302539, ss1618673256, ss1661667289, ss1711171086, ss1805107908, ss1927790494, ss1970758602, ss2024578101, ss2152799150, ss2626780976, ss2708505460, ss2856051710, ss3001609719, ss3347726572, ss3669365141, ss3734851893, ss3766853225, ss3830695370, ss3838846254, ss3867858168, ss3915124214, ss5184379230, ss5375111039, ss5509044879, ss5643469361, ss5823175327, ss5972647173, ss5980448463	NC_000007.13:90098897:G:T	NC_000007.14:90469583:G:T	(self)
50014416, 268812398, 3443836, 18444062, 58840562, 591749967, 6153813972, ss2295699437, ss3026082678, ss3720184496, ss3810027137, ss3844301120, ss3962066061, ss4754372408, ss5273818427, ss5470810048, ss5562488481, ss5725003458, ss5808874474, ss5855999130, ss5859844594	NC_000007.14:90469583:G:T	NC_000007.14:90469583:G:T	(self)
ss14873598, ss28518572, ss68423266, ss104449538	NT_007933.15:28131740:G:T	NC_000007.14:90469583:G: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 rs10487113

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

rs10487113