Name: rs1039151
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.

rs1039151

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99271625 (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>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.270369 (71564/264690, TOPMED)
T=0.257399 (35902/139480, GnomAD)
G=0.17496 (4944/28258, 14KJPN) (+ 16 more)
G=0.17291 (2898/16760, 8.3KJPN)
T=0.14005 (1966/14038, ALFA)
T=0.3863 (2474/6404, 1000G_30x)
T=0.4004 (2005/5008, 1000G)
T=0.2294 (1027/4476, Estonian)
T=0.2460 (948/3854, ALSPAC)
T=0.2344 (869/3708, TWINSUK)
G=0.2007 (588/2930, KOREAN)
G=0.1889 (346/1832, Korea1K)
T=0.236 (236/998, GoNL)
T=0.185 (111/600, NorthernSweden)
G=0.345 (96/278, SGDP_PRJ)
T=0.264 (57/216, Qatari)
G=0.207 (43/208, Vietnamese)
T=0.30 (12/40, GENOME_DK)
G=0.40 (8/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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	14038	G=0.85995	A=0.00000, T=0.14005
European	Sub	11234	G=0.84618	A=0.00000, T=0.15382
African	Sub	1842	G=0.9007	A=0.0000, T=0.0993
African Others	Sub	80	G=0.91	A=0.00, T=0.09
African American	Sub	1762	G=0.9001	A=0.0000, T=0.0999
Asian	Sub	6	G=0.5	A=0.0, T=0.5
East Asian	Sub	2	G=0.0	A=0.0, T=1.0
Other Asian	Sub	4	G=0.8	A=0.0, T=0.2
Latin American 1	Sub	76	G=1.00	A=0.00, T=0.00
Latin American 2	Sub	398	G=1.000	A=0.000, T=0.000
South Asian	Sub	26	G=0.92	A=0.00, T=0.08
Other	Sub	456	G=0.890	A=0.000, T=0.110

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=0.729631	T=0.270369
gnomAD - Genomes	Global	Study-wide	139480	G=0.742601	T=0.257399
gnomAD - Genomes	European	Sub	75590	G=0.76851	T=0.23149
gnomAD - Genomes	African	Sub	41720	G=0.71776	T=0.28224
gnomAD - Genomes	American	Sub	13592	G=0.80106	T=0.19894
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.7508	T=0.2492
gnomAD - Genomes	East Asian	Sub	3118	G=0.1966	T=0.8034
gnomAD - Genomes	Other	Sub	2142	G=0.7232	T=0.2768
14KJPN	JAPANESE	Study-wide	28258	G=0.17496	T=0.82504
8.3KJPN	JAPANESE	Study-wide	16760	G=0.17291	T=0.82709
Allele Frequency Aggregator	Total	Global	14038	G=0.85995	A=0.00000, T=0.14005
Allele Frequency Aggregator	European	Sub	11234	G=0.84618	A=0.00000, T=0.15382
Allele Frequency Aggregator	African	Sub	1842	G=0.9007	A=0.0000, T=0.0993
Allele Frequency Aggregator	Other	Sub	456	G=0.890	A=0.000, T=0.110
Allele Frequency Aggregator	Latin American 2	Sub	398	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	76	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	26	G=0.92	A=0.00, T=0.08
Allele Frequency Aggregator	Asian	Sub	6	G=0.5	A=0.0, T=0.5
1000Genomes_30x	Global	Study-wide	6404	G=0.6137	T=0.3863
1000Genomes_30x	African	Sub	1786	G=0.7503	T=0.2497
1000Genomes_30x	Europe	Sub	1266	G=0.7370	T=0.2630
1000Genomes_30x	South Asian	Sub	1202	G=0.5000	T=0.5000
1000Genomes_30x	East Asian	Sub	1170	G=0.2068	T=0.7932
1000Genomes_30x	American	Sub	980	G=0.831	T=0.169
1000Genomes	Global	Study-wide	5008	G=0.5996	T=0.4004
1000Genomes	African	Sub	1322	G=0.7504	T=0.2496
1000Genomes	East Asian	Sub	1008	G=0.2014	T=0.7986
1000Genomes	Europe	Sub	1006	G=0.7445	T=0.2555
1000Genomes	South Asian	Sub	978	G=0.501	T=0.499
1000Genomes	American	Sub	694	G=0.820	T=0.180
Genetic variation in the Estonian population	Estonian	Study-wide	4476	G=0.7706	T=0.2294
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7540	T=0.2460
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7656	T=0.2344
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2007	T=0.7993
Korean Genome Project	KOREAN	Study-wide	1832	G=0.1889	T=0.8111
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.764	T=0.236
Northern Sweden	ACPOP	Study-wide	600	G=0.815	T=0.185
SGDP_PRJ	Global	Study-wide	278	G=0.345	T=0.655
Qatari	Global	Study-wide	216	G=0.736	T=0.264
A Vietnamese Genetic Variation Database	Global	Study-wide	208	G=0.207	T=0.793
The Danish reference pan genome	Danish	Study-wide	40	G=0.70	T=0.30
Siberian	Global	Study-wide	20	G=0.40	T=0.60

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 4	NC_000004.12:g.99271625G>A
GRCh38.p14 chr 4	NC_000004.12:g.99271625G>T
GRCh37.p13 chr 4	NC_000004.11:g.100192782G>A
GRCh37.p13 chr 4	NC_000004.11:g.100192782G>T

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1:n.	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	G=	A	T
GRCh38.p14 chr 4	NC_000004.12:g.99271625=	NC_000004.12:g.99271625G>A	NC_000004.12:g.99271625G>T
GRCh37.p13 chr 4	NC_000004.11:g.100192782=	NC_000004.11:g.100192782G>A	NC_000004.11:g.100192782G>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#.

66 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1505486	Oct 05, 2000 (86)
2	SC_SNP	ss16031888	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss16996787	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss20189333	Feb 27, 2004 (120)
5	SSAHASNP	ss22062785	Apr 05, 2004 (123)
6	ABI	ss42200004	Mar 13, 2006 (126)
7	BCMHGSC_JDW	ss92703342	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss98986833	Feb 05, 2009 (130)
9	BGI	ss105848317	Feb 05, 2009 (130)
10	1000GENOMES	ss110291845	Jan 24, 2009 (130)
11	ENSEMBL	ss139782240	Dec 01, 2009 (131)
12	ENSEMBL	ss142888269	Dec 01, 2009 (131)
13	GMI	ss157650852	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss163917487	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166944081	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss206522313	Jul 04, 2010 (132)
17	1000GENOMES	ss210581947	Jul 14, 2010 (132)
18	1000GENOMES	ss221098816	Jul 14, 2010 (132)
19	1000GENOMES	ss232515164	Jul 14, 2010 (132)
20	1000GENOMES	ss239780141	Jul 15, 2010 (132)
21	GMI	ss277844466	May 04, 2012 (137)
22	GMI	ss284967901	Apr 25, 2013 (138)
23	PJP	ss293147544	May 09, 2011 (134)
24	TISHKOFF	ss557721274	Apr 25, 2013 (138)
25	SSMP	ss651525795	Apr 25, 2013 (138)
26	EVA-GONL	ss980450348	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1071787276	Aug 21, 2014 (142)
28	1000GENOMES	ss1310980609	Aug 21, 2014 (142)
29	EVA_GENOME_DK	ss1580687529	Apr 01, 2015 (144)
30	EVA_DECODE	ss1589954386	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1610736718	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1653730751	Apr 01, 2015 (144)
33	WEILL_CORNELL_DGM	ss1923690387	Feb 12, 2016 (147)
34	JJLAB	ss2022431166	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2150560337	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2265426907	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2625714517	Nov 08, 2017 (151)
38	GRF	ss2706037160	Nov 08, 2017 (151)
39	GNOMAD	ss2812856791	Nov 08, 2017 (151)
40	SWEGEN	ss2995210840	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3024990849	Nov 08, 2017 (151)
42	CSHL	ss3345861917	Nov 08, 2017 (151)
43	URBANLAB	ss3647802695	Oct 12, 2018 (152)
44	EGCUT_WGS	ss3663106695	Jul 13, 2019 (153)
45	EVA_DECODE	ss3712657235	Jul 13, 2019 (153)
46	ACPOP	ss3731422006	Jul 13, 2019 (153)
47	EVA	ss3762167280	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3805315711	Jul 13, 2019 (153)
49	EVA	ss3828703665	Apr 26, 2020 (154)
50	SGDP_PRJ	ss3859611042	Apr 26, 2020 (154)
51	KRGDB	ss3905888580	Apr 26, 2020 (154)
52	KOGIC	ss3954742635	Apr 26, 2020 (154)
53	TOPMED	ss4624647675	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5167079287	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5260289169	Oct 13, 2022 (156)
56	EVA	ss5350977588	Oct 13, 2022 (156)
57	HUGCELL_USP	ss5458931541	Oct 13, 2022 (156)
58	EVA	ss5507641592	Oct 13, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5541957427	Oct 13, 2022 (156)
60	SANFORD_IMAGENETICS	ss5635666000	Oct 13, 2022 (156)
61	TOMMO_GENOMICS	ss5701810781	Oct 13, 2022 (156)
62	YY_MCH	ss5805354149	Oct 13, 2022 (156)
63	EVA	ss5844424527	Oct 13, 2022 (156)
64	EVA	ss5854356061	Oct 13, 2022 (156)
65	EVA	ss5864677850	Oct 13, 2022 (156)
66	EVA	ss5964056718	Oct 13, 2022 (156)
67	1000Genomes	NC_000004.11 - 100192782	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000004.12 - 99271625	Oct 13, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100192782	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000004.11 - 100192782	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000004.11 - 100192782	Apr 26, 2020 (154)
72	gnomAD - Genomes	NC_000004.12 - 99271625	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000004.11 - 100192782	Apr 26, 2020 (154)
74	KOREAN population from KRGDB	NC_000004.11 - 100192782	Apr 26, 2020 (154)
75	Korean Genome Project	NC_000004.12 - 99271625	Apr 26, 2020 (154)
76	Northern Sweden	NC_000004.11 - 100192782	Jul 13, 2019 (153)
77	Qatari	NC_000004.11 - 100192782	Apr 26, 2020 (154)
78	SGDP_PRJ	NC_000004.11 - 100192782	Apr 26, 2020 (154)
79	Siberian	NC_000004.11 - 100192782	Apr 26, 2020 (154)
80	8.3KJPN	NC_000004.11 - 100192782	Apr 26, 2021 (155)
81	14KJPN	NC_000004.12 - 99271625	Oct 13, 2022 (156)
82	TopMed	NC_000004.12 - 99271625	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000004.11 - 100192782	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000004.11 - 100192782	Jul 13, 2019 (153)
85	ALFA	NC_000004.12 - 99271625	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)
rs13108898	Sep 24, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
4885539345, ss2265426907	NC_000004.12:99271624:G:A	NC_000004.12:99271624:G:A	(self)
ss92703342, ss110291845, ss163917487, ss166944081, ss206522313, ss210581947, ss277844466, ss284967901, ss293147544, ss1589954386	NC_000004.10:100411804:G:T	NC_000004.12:99271624:G:T	(self)
22422831, 12472976, 8844943, 6852468, 5513830, 13065974, 4706871, 5732317, 11628022, 3076691, 25048594, 12472976, 2744426, ss221098816, ss232515164, ss239780141, ss557721274, ss651525795, ss980450348, ss1071787276, ss1310980609, ss1580687529, ss1610736718, ss1653730751, ss1923690387, ss2022431166, ss2150560337, ss2625714517, ss2706037160, ss2812856791, ss2995210840, ss3345861917, ss3663106695, ss3731422006, ss3762167280, ss3828703665, ss3859611042, ss3905888580, ss5167079287, ss5350977588, ss5507641592, ss5635666000, ss5844424527, ss5964056718	NC_000004.11:100192781:G:T	NC_000004.12:99271624:G:T	(self)
29483362, 158839630, 11120636, 35647885, 462025231, 4885539345, ss2265426907, ss3024990849, ss3647802695, ss3712657235, ss3805315711, ss3954742635, ss4624647675, ss5260289169, ss5458931541, ss5541957427, ss5701810781, ss5805354149, ss5854356061, ss5864677850	NC_000004.12:99271624:G:T	NC_000004.12:99271624:G:T	(self)
ss16031888, ss16996787, ss20189333, ss22062785	NT_016354.16:24687485:G:T	NC_000004.12:99271624:G:T	(self)
ss1505486, ss42200004, ss98986833, ss105848317, ss139782240, ss142888269, ss157650852	NT_016354.19:24740502:G:T	NC_000004.12:99271624: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 rs1039151

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1039151