Name: rs10134508
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.

rs10134508

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:58885102 (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=0.492187 (130277/264690, TOPMED)
T=0.477835 (66853/139908, GnomAD)
T=0.42752 (37430/87552, ALFA) (+ 19 more)
T=0.32451 (9170/28258, 14KJPN)
T=0.32834 (5503/16760, 8.3KJPN)
C=0.4525 (2898/6404, 1000G_30x)
C=0.4603 (2305/5008, 1000G)
T=0.3478 (1558/4480, Estonian)
T=0.4245 (1636/3854, ALSPAC)
T=0.4234 (1570/3708, TWINSUK)
T=0.3099 (908/2930, KOREAN)
T=0.4571 (949/2076, HGDP_Stanford)
C=0.4554 (857/1882, HapMap)
T=0.3248 (595/1832, Korea1K)
T=0.426 (425/998, GoNL)
T=0.372 (223/600, NorthernSweden)
C=0.300 (114/380, SGDP_PRJ)
T=0.491 (106/216, Qatari)
T=0.402 (86/214, Vietnamese)
T=0.36 (30/84, Ancient Sardinia)
T=0.40 (16/40, GENOME_DK)
C=0.39 (7/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01500 : 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	87552	C=0.57248	T=0.42752
European	Sub	74680	C=0.59586	T=0.40414
African	Sub	4518	C=0.3796	T=0.6204
African Others	Sub	170	C=0.300	T=0.700
African American	Sub	4348	C=0.3827	T=0.6173
Asian	Sub	234	C=0.577	T=0.423
East Asian	Sub	192	C=0.594	T=0.406
Other Asian	Sub	42	C=0.50	T=0.50
Latin American 1	Sub	252	C=0.528	T=0.472
Latin American 2	Sub	1226	C=0.4168	T=0.5832
South Asian	Sub	4950	C=0.4570	T=0.5430
Other	Sub	1692	C=0.5124	T=0.4876

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=0.507813	T=0.492187
gnomAD - Genomes	Global	Study-wide	139908	C=0.522165	T=0.477835
gnomAD - Genomes	European	Sub	75788	C=0.60576	T=0.39424
gnomAD - Genomes	African	Sub	41914	C=0.39123	T=0.60877
gnomAD - Genomes	American	Sub	13618	C=0.46079	T=0.53921
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.4630	T=0.5370
gnomAD - Genomes	East Asian	Sub	3116	C=0.5712	T=0.4288
gnomAD - Genomes	Other	Sub	2150	C=0.5372	T=0.4628
Allele Frequency Aggregator	Total	Global	87552	C=0.57248	T=0.42752
Allele Frequency Aggregator	European	Sub	74680	C=0.59586	T=0.40414
Allele Frequency Aggregator	South Asian	Sub	4950	C=0.4570	T=0.5430
Allele Frequency Aggregator	African	Sub	4518	C=0.3796	T=0.6204
Allele Frequency Aggregator	Other	Sub	1692	C=0.5124	T=0.4876
Allele Frequency Aggregator	Latin American 2	Sub	1226	C=0.4168	T=0.5832
Allele Frequency Aggregator	Latin American 1	Sub	252	C=0.528	T=0.472
Allele Frequency Aggregator	Asian	Sub	234	C=0.577	T=0.423
14KJPN	JAPANESE	Study-wide	28258	C=0.67549	T=0.32451
8.3KJPN	JAPANESE	Study-wide	16760	C=0.67166	T=0.32834
1000Genomes_30x	Global	Study-wide	6404	C=0.4525	T=0.5475
1000Genomes_30x	African	Sub	1786	C=0.3264	T=0.6736
1000Genomes_30x	Europe	Sub	1266	C=0.6074	T=0.3926
1000Genomes_30x	South Asian	Sub	1202	C=0.4052	T=0.5948
1000Genomes_30x	East Asian	Sub	1170	C=0.5795	T=0.4205
1000Genomes_30x	American	Sub	980	C=0.389	T=0.611
1000Genomes	Global	Study-wide	5008	C=0.4603	T=0.5397
1000Genomes	African	Sub	1322	C=0.3343	T=0.6657
1000Genomes	East Asian	Sub	1008	C=0.5853	T=0.4147
1000Genomes	Europe	Sub	1006	C=0.5984	T=0.4016
1000Genomes	South Asian	Sub	978	C=0.406	T=0.594
1000Genomes	American	Sub	694	C=0.395	T=0.605
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6522	T=0.3478
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5755	T=0.4245
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5766	T=0.4234
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6901	T=0.3099
HGDP-CEPH-db Supplement 1	Global	Study-wide	2076	C=0.5429	T=0.4571
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	468	C=0.703	T=0.297
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	412	C=0.483	T=0.517
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	C=0.563	T=0.437
HGDP-CEPH-db Supplement 1	Europe	Sub	320	C=0.697	T=0.303
HGDP-CEPH-db Supplement 1	Africa	Sub	240	C=0.446	T=0.554
HGDP-CEPH-db Supplement 1	America	Sub	216	C=0.282	T=0.718
HGDP-CEPH-db Supplement 1	Oceania	Sub	70	C=0.16	T=0.84
HapMap	Global	Study-wide	1882	C=0.4554	T=0.5446
HapMap	American	Sub	764	C=0.499	T=0.501
HapMap	African	Sub	692	C=0.316	T=0.684
HapMap	Asian	Sub	252	C=0.615	T=0.385
HapMap	Europe	Sub	174	C=0.586	T=0.414
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6752	T=0.3248
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.574	T=0.426
Northern Sweden	ACPOP	Study-wide	600	C=0.628	T=0.372
SGDP_PRJ	Global	Study-wide	380	C=0.300	T=0.700
Qatari	Global	Study-wide	216	C=0.509	T=0.491
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.598	T=0.402
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	84	C=0.64	T=0.36
The Danish reference pan genome	Danish	Study-wide	40	C=0.60	T=0.40
Siberian	Global	Study-wide	18	C=0.39	T=0.61

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 14	NC_000014.9:g.58885102C>T
GRCh37.p13 chr 14	NC_000014.8:g.59351820C>T

Gene: LINC01500, long intergenic non-protein coding RNA 1500 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01500 transcript	NR_110547.1: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	C=	T
GRCh38.p14 chr 14	NC_000014.9:g.58885102=	NC_000014.9:g.58885102C>T
GRCh37.p13 chr 14	NC_000014.8:g.59351820=	NC_000014.8:g.59351820C>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#.

89 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13993382	Dec 05, 2003 (119)
2	ABI	ss43584748	Mar 15, 2006 (126)
3	ILLUMINA	ss66871827	Nov 29, 2006 (127)
4	ILLUMINA	ss66950434	Nov 29, 2006 (127)
5	ILLUMINA	ss68078989	Dec 12, 2006 (127)
6	ILLUMINA	ss70467323	May 24, 2008 (130)
7	ILLUMINA	ss70988700	May 16, 2007 (127)
8	ILLUMINA	ss75896130	Dec 06, 2007 (129)
9	KRIBB_YJKIM	ss84910740	Dec 15, 2007 (130)
10	1000GENOMES	ss108376963	Jan 23, 2009 (130)
11	ILLUMINA-UK	ss118507221	Feb 14, 2009 (130)
12	ENSEMBL	ss137025802	Dec 01, 2009 (131)
13	ILLUMINA	ss152580666	Dec 01, 2009 (131)
14	GMI	ss155860809	Dec 01, 2009 (131)
15	ILLUMINA	ss159111327	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss168144844	Jul 04, 2010 (132)
17	ILLUMINA	ss169728482	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss171190498	Jul 04, 2010 (132)
19	BUSHMAN	ss200136306	Jul 04, 2010 (132)
20	1000GENOMES	ss211525976	Jul 14, 2010 (132)
21	1000GENOMES	ss226596249	Jul 14, 2010 (132)
22	1000GENOMES	ss236561363	Jul 15, 2010 (132)
23	1000GENOMES	ss242991417	Jul 15, 2010 (132)
24	GMI	ss282023314	May 04, 2012 (137)
25	PJP	ss291610853	May 09, 2011 (134)
26	ILLUMINA	ss536580459	Sep 08, 2015 (146)
27	TISHKOFF	ss564123505	Apr 25, 2013 (138)
28	SSMP	ss659804976	Apr 25, 2013 (138)
29	ILLUMINA	ss832624086	Jul 13, 2019 (153)
30	EVA-GONL	ss991199132	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1079695150	Aug 21, 2014 (142)
32	1000GENOMES	ss1351206054	Aug 21, 2014 (142)
33	DDI	ss1427440535	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1577286930	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1631840456	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1674834489	Apr 01, 2015 (144)
37	EVA_DECODE	ss1695200105	Apr 01, 2015 (144)
38	EVA_SVP	ss1713448351	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1807945973	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1934574521	Feb 12, 2016 (147)
41	GENOMED	ss1967974796	Jul 19, 2016 (147)
42	JJLAB	ss2028065399	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2156440801	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2202396540	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2628522710	Nov 08, 2017 (151)
46	GRF	ss2700866764	Nov 08, 2017 (151)
47	ILLUMINA	ss2710801685	Nov 08, 2017 (151)
48	GNOMAD	ss2928268936	Nov 08, 2017 (151)
49	SWEGEN	ss3012283414	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3027858478	Nov 08, 2017 (151)
51	CSHL	ss3350830346	Nov 08, 2017 (151)
52	ILLUMINA	ss3627229874	Oct 12, 2018 (152)
53	ILLUMINA	ss3638053343	Oct 12, 2018 (152)
54	ILLUMINA	ss3639040209	Oct 12, 2018 (152)
55	ILLUMINA	ss3639829452	Oct 12, 2018 (152)
56	ILLUMINA	ss3643039791	Oct 12, 2018 (152)
57	ILLUMINA	ss3643879984	Oct 12, 2018 (152)
58	URBANLAB	ss3650218371	Oct 12, 2018 (152)
59	EGCUT_WGS	ss3679533746	Jul 13, 2019 (153)
60	EVA_DECODE	ss3696778411	Jul 13, 2019 (153)
61	ACPOP	ss3740426321	Jul 13, 2019 (153)
62	EVA	ss3752383596	Jul 13, 2019 (153)
63	PACBIO	ss3787678727	Jul 13, 2019 (153)
64	PACBIO	ss3792715344	Jul 13, 2019 (153)
65	PACBIO	ss3797599560	Jul 13, 2019 (153)
66	KHV_HUMAN_GENOMES	ss3817716604	Jul 13, 2019 (153)
67	EVA	ss3833946048	Apr 27, 2020 (154)
68	EVA	ss3840566722	Apr 27, 2020 (154)
69	EVA	ss3846055864	Apr 27, 2020 (154)
70	HGDP	ss3847505061	Apr 27, 2020 (154)
71	SGDP_PRJ	ss3881613742	Apr 27, 2020 (154)
72	KRGDB	ss3930636405	Apr 27, 2020 (154)
73	KOGIC	ss3975026447	Apr 27, 2020 (154)
74	EVA	ss3985682709	Apr 26, 2021 (155)
75	EVA	ss4017672818	Apr 26, 2021 (155)
76	TOPMED	ss4972393293	Apr 26, 2021 (155)
77	TOMMO_GENOMICS	ss5213459595	Apr 26, 2021 (155)
78	1000G_HIGH_COVERAGE	ss5296401135	Oct 16, 2022 (156)
79	EVA	ss5415586834	Oct 16, 2022 (156)
80	HUGCELL_USP	ss5490426282	Oct 16, 2022 (156)
81	EVA	ss5511258843	Oct 16, 2022 (156)
82	1000G_HIGH_COVERAGE	ss5596774191	Oct 16, 2022 (156)
83	SANFORD_IMAGENETICS	ss5656322716	Oct 16, 2022 (156)
84	TOMMO_GENOMICS	ss5766327439	Oct 16, 2022 (156)
85	YY_MCH	ss5814796324	Oct 16, 2022 (156)
86	EVA	ss5841176893	Oct 16, 2022 (156)
87	EVA	ss5851054090	Oct 16, 2022 (156)
88	EVA	ss5901542903	Oct 16, 2022 (156)
89	EVA	ss5947756647	Oct 16, 2022 (156)
90	1000Genomes	NC_000014.8 - 59351820	Oct 12, 2018 (152)
91	1000Genomes_30x	NC_000014.9 - 58885102	Oct 16, 2022 (156)
92	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 59351820	Oct 12, 2018 (152)
93	Genetic variation in the Estonian population	NC_000014.8 - 59351820	Oct 12, 2018 (152)
94	The Danish reference pan genome	NC_000014.8 - 59351820	Apr 27, 2020 (154)
95	gnomAD - Genomes	NC_000014.9 - 58885102	Apr 26, 2021 (155)
96	Genome of the Netherlands Release 5	NC_000014.8 - 59351820	Apr 27, 2020 (154)
97	HGDP-CEPH-db Supplement 1	NC_000014.7 - 58421573	Apr 27, 2020 (154)
98	HapMap	NC_000014.9 - 58885102	Apr 27, 2020 (154)
99	KOREAN population from KRGDB	NC_000014.8 - 59351820	Apr 27, 2020 (154)
100	Korean Genome Project	NC_000014.9 - 58885102	Apr 27, 2020 (154)
101	Northern Sweden	NC_000014.8 - 59351820	Jul 13, 2019 (153)
102	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000014.8 - 59351820	Apr 26, 2021 (155)
103	Qatari	NC_000014.8 - 59351820	Apr 27, 2020 (154)
104	SGDP_PRJ	NC_000014.8 - 59351820	Apr 27, 2020 (154)
105	Siberian	NC_000014.8 - 59351820	Apr 27, 2020 (154)
106	8.3KJPN	NC_000014.8 - 59351820	Apr 26, 2021 (155)
107	14KJPN	NC_000014.9 - 58885102	Oct 16, 2022 (156)
108	TopMed	NC_000014.9 - 58885102	Apr 26, 2021 (155)
109	UK 10K study - Twins	NC_000014.8 - 59351820	Oct 12, 2018 (152)
110	A Vietnamese Genetic Variation Database	NC_000014.8 - 59351820	Jul 13, 2019 (153)
111	ALFA	NC_000014.9 - 58885102	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)
rs58439437	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
182953, ss108376963, ss118507221, ss168144844, ss171190498, ss200136306, ss211525976, ss282023314, ss291610853, ss1695200105, ss1713448351, ss3639040209, ss3639829452, ss3643039791, ss3643879984, ss3847505061	NC_000014.7:58421572:C:T	NC_000014.9:58885101:C:T	(self)
64194363, 35659852, 25271994, 3624527, 15928803, 37813799, 13711186, 908636, 16616451, 33630722, 8957155, 71428902, 35659852, 7933869, ss226596249, ss236561363, ss242991417, ss536580459, ss564123505, ss659804976, ss832624086, ss991199132, ss1079695150, ss1351206054, ss1427440535, ss1577286930, ss1631840456, ss1674834489, ss1807945973, ss1934574521, ss1967974796, ss2028065399, ss2156440801, ss2628522710, ss2700866764, ss2710801685, ss2928268936, ss3012283414, ss3350830346, ss3627229874, ss3638053343, ss3679533746, ss3740426321, ss3752383596, ss3787678727, ss3792715344, ss3797599560, ss3833946048, ss3840566722, ss3881613742, ss3930636405, ss3985682709, ss4017672818, ss5213459595, ss5415586834, ss5511258843, ss5656322716, ss5841176893, ss5947756647	NC_000014.8:59351819:C:T	NC_000014.9:58885101:C:T	(self)
84300126, 452637761, 1155392, 31404448, 100164543, 187938952, 6289865830, ss2202396540, ss3027858478, ss3650218371, ss3696778411, ss3817716604, ss3846055864, ss3975026447, ss4972393293, ss5296401135, ss5490426282, ss5596774191, ss5766327439, ss5814796324, ss5851054090, ss5901542903	NC_000014.9:58885101:C:T	NC_000014.9:58885101:C:T	(self)
ss13993382	NT_026437.10:39271860:C:T	NC_000014.9:58885101:C:T	(self)
ss43584748, ss66871827, ss66950434, ss68078989, ss70467323, ss70988700, ss75896130, ss84910740, ss137025802, ss152580666, ss155860809, ss159111327, ss169728482	NT_026437.12:40351819:C:T	NC_000014.9:58885101:C: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 rs10134508

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

rs10134508