Name: rs6729869
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.

rs6729869

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:34060127 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.371801 (98412/264690, TOPMED)
A=0.366436 (51263/139896, GnomAD)
T=0.35618 (10065/28258, 14KJPN) (+ 18 more)
A=0.36210 (6840/18890, ALFA)
T=0.35710 (5985/16760, 8.3KJPN)
A=0.3971 (2543/6404, 1000G_30x)
A=0.4044 (2025/5008, 1000G)
A=0.3431 (1537/4480, Estonian)
A=0.3586 (1382/3854, ALSPAC)
A=0.3732 (1384/3708, TWINSUK)
T=0.3191 (935/2930, KOREAN)
T=0.3275 (600/1832, Korea1K)
A=0.352 (351/998, GoNL)
A=0.413 (248/600, NorthernSweden)
A=0.420 (137/326, HapMap)
T=0.338 (108/320, SGDP_PRJ)
A=0.481 (104/216, Qatari)
T=0.370 (80/216, Vietnamese)
T=0.45 (18/40, GENOME_DK)
T=0.42 (16/38, Siberian)
A=0.44 (16/36, Ancient Sardinia)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01317 : Intron Variant
LOC105374456 : Intron Variant
Publications: 2 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	T=0.63790	A=0.36210
European	Sub	14286	T=0.63622	A=0.36378
African	Sub	2946	T=0.6565	A=0.3435
African Others	Sub	114	T=0.702	A=0.298
African American	Sub	2832	T=0.6547	A=0.3453
Asian	Sub	112	T=0.455	A=0.545
East Asian	Sub	86	T=0.38	A=0.62
Other Asian	Sub	26	T=0.69	A=0.31
Latin American 1	Sub	146	T=0.644	A=0.356
Latin American 2	Sub	610	T=0.649	A=0.351
South Asian	Sub	98	T=0.61	A=0.39
Other	Sub	692	T=0.616	A=0.384

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	T=0.628199	A=0.371801
gnomAD - Genomes	Global	Study-wide	139896	T=0.633564	A=0.366436
gnomAD - Genomes	European	Sub	75822	T=0.62682	A=0.37318
gnomAD - Genomes	African	Sub	41870	T=0.66659	A=0.33341
gnomAD - Genomes	American	Sub	13608	T=0.64859	A=0.35141
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.5665	A=0.4335
gnomAD - Genomes	East Asian	Sub	3130	T=0.3751	A=0.6249
gnomAD - Genomes	Other	Sub	2142	T=0.6130	A=0.3870
14KJPN	JAPANESE	Study-wide	28258	T=0.35618	A=0.64382
Allele Frequency Aggregator	Total	Global	18890	T=0.63790	A=0.36210
Allele Frequency Aggregator	European	Sub	14286	T=0.63622	A=0.36378
Allele Frequency Aggregator	African	Sub	2946	T=0.6565	A=0.3435
Allele Frequency Aggregator	Other	Sub	692	T=0.616	A=0.384
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.649	A=0.351
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.644	A=0.356
Allele Frequency Aggregator	Asian	Sub	112	T=0.455	A=0.545
Allele Frequency Aggregator	South Asian	Sub	98	T=0.61	A=0.39
8.3KJPN	JAPANESE	Study-wide	16760	T=0.35710	A=0.64290
1000Genomes_30x	Global	Study-wide	6404	T=0.6029	A=0.3971
1000Genomes_30x	African	Sub	1786	T=0.6971	A=0.3029
1000Genomes_30x	Europe	Sub	1266	T=0.6082	A=0.3918
1000Genomes_30x	South Asian	Sub	1202	T=0.6231	A=0.3769
1000Genomes_30x	East Asian	Sub	1170	T=0.3795	A=0.6205
1000Genomes_30x	American	Sub	980	T=0.666	A=0.334
1000Genomes	Global	Study-wide	5008	T=0.5956	A=0.4044
1000Genomes	African	Sub	1322	T=0.6944	A=0.3056
1000Genomes	East Asian	Sub	1008	T=0.3819	A=0.6181
1000Genomes	Europe	Sub	1006	T=0.6044	A=0.3956
1000Genomes	South Asian	Sub	978	T=0.620	A=0.380
1000Genomes	American	Sub	694	T=0.671	A=0.329
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.6569	A=0.3431
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6414	A=0.3586
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6268	A=0.3732
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3191	A=0.6809
Korean Genome Project	KOREAN	Study-wide	1832	T=0.3275	A=0.6725
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.648	A=0.352
Northern Sweden	ACPOP	Study-wide	600	T=0.587	A=0.413
HapMap	Global	Study-wide	326	T=0.580	A=0.420
HapMap	American	Sub	120	T=0.583	A=0.417
HapMap	African	Sub	118	T=0.686	A=0.314
HapMap	Asian	Sub	88	T=0.43	A=0.57
SGDP_PRJ	Global	Study-wide	320	T=0.338	A=0.662
Qatari	Global	Study-wide	216	T=0.519	A=0.481
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.370	A=0.630
The Danish reference pan genome	Danish	Study-wide	40	T=0.45	A=0.55
Siberian	Global	Study-wide	38	T=0.42	A=0.58
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	36	T=0.56	A=0.44

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 2	NC_000002.12:g.34060127T>A
GRCh37.p13 chr 2	NC_000002.11:g.34285194T>A

Gene: LINC01317, long intergenic non-protein coding RNA 1317 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01317 transcript	NR_126403.1:n.	N/A	Intron Variant

Gene: LOC105374456, uncharacterized LOC105374456 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374456 transcript	XR_939954.2: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	T=	A
GRCh38.p14 chr 2	NC_000002.12:g.34060127=	NC_000002.12:g.34060127T>A
GRCh37.p13 chr 2	NC_000002.11:g.34285194=	NC_000002.11:g.34285194T>A

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#.

83 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9952796	Jul 11, 2003 (116)
2	WUGSC_SSAHASNP	ss14499487	Dec 05, 2003 (119)
3	PERLEGEN	ss14885744	Dec 05, 2003 (119)
4	PERLEGEN	ss24149975	Sep 20, 2004 (123)
5	ABI	ss41711179	Mar 15, 2006 (126)
6	AFFY	ss65944513	Dec 01, 2006 (127)
7	CSHL-HAPMAP	ss68386789	Jan 12, 2007 (127)
8	BCMHGSC_JDW	ss91112846	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss97026175	Feb 05, 2009 (130)
10	BGI	ss106080408	Feb 05, 2009 (130)
11	1000GENOMES	ss109389717	Jan 24, 2009 (130)
12	1000GENOMES	ss110053852	Jan 24, 2009 (130)
13	ENSEMBL	ss138418114	Dec 01, 2009 (131)
14	ENSEMBL	ss139353377	Dec 01, 2009 (131)
15	GMI	ss156887689	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss163276655	Jul 04, 2010 (132)
17	BUSHMAN	ss200252032	Jul 04, 2010 (132)
18	1000GENOMES	ss219161025	Jul 14, 2010 (132)
19	1000GENOMES	ss231105872	Jul 14, 2010 (132)
20	1000GENOMES	ss238674364	Jul 15, 2010 (132)
21	GMI	ss276411790	May 04, 2012 (137)
22	PJP	ss292541117	May 09, 2011 (134)
23	TISHKOFF	ss555463517	Apr 25, 2013 (138)
24	SSMP	ss649046935	Apr 25, 2013 (138)
25	EVA-GONL	ss976667065	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1068991081	Aug 21, 2014 (142)
27	1000GENOMES	ss1296596746	Aug 21, 2014 (142)
28	DDI	ss1428529444	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1578812436	Apr 01, 2015 (144)
30	EVA_DECODE	ss1586074600	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1603175625	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1646169658	Apr 01, 2015 (144)
33	HAMMER_LAB	ss1796526845	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1919899632	Feb 12, 2016 (147)
35	GENOMED	ss1968733205	Jul 19, 2016 (147)
36	JJLAB	ss2020479426	Sep 14, 2016 (149)
37	ILLUMINA	ss2094805897	Dec 20, 2016 (150)
38	ILLUMINA	ss2095089356	Dec 20, 2016 (150)
39	USC_VALOUEV	ss2148524446	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2228946261	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2624753187	Nov 08, 2017 (151)
42	GRF	ss2703085446	Nov 08, 2017 (151)
43	GNOMAD	ss2771664955	Nov 08, 2017 (151)
44	AFFY	ss2985790207	Nov 08, 2017 (151)
45	SWEGEN	ss2989253671	Nov 08, 2017 (151)
46	ILLUMINA	ss3021958020	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3024006006	Nov 08, 2017 (151)
48	CSHL	ss3344154555	Nov 08, 2017 (151)
49	URBANLAB	ss3647001608	Oct 11, 2018 (152)
50	ILLUMINA	ss3652387826	Oct 11, 2018 (152)
51	EGCUT_WGS	ss3657211802	Jul 13, 2019 (153)
52	EVA_DECODE	ss3703587105	Jul 13, 2019 (153)
53	ILLUMINA	ss3725773080	Jul 13, 2019 (153)
54	ACPOP	ss3728301046	Jul 13, 2019 (153)
55	ILLUMINA	ss3744473945	Jul 13, 2019 (153)
56	EVA	ss3756565543	Jul 13, 2019 (153)
57	PACBIO	ss3783824524	Jul 13, 2019 (153)
58	PACBIO	ss3789418322	Jul 13, 2019 (153)
59	PACBIO	ss3794291102	Jul 13, 2019 (153)
60	KHV_HUMAN_GENOMES	ss3800943368	Jul 13, 2019 (153)
61	EVA	ss3826905768	Apr 25, 2020 (154)
62	EVA	ss3836860765	Apr 25, 2020 (154)
63	EVA	ss3842275542	Apr 25, 2020 (154)
64	SGDP_PRJ	ss3851944520	Apr 25, 2020 (154)
65	KRGDB	ss3897371356	Apr 25, 2020 (154)
66	KOGIC	ss3947453295	Apr 25, 2020 (154)
67	EVA	ss3984883944	Apr 26, 2021 (155)
68	TOPMED	ss4500093609	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5150643011	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5247512419	Oct 13, 2022 (156)
71	HUGCELL_USP	ss5447766254	Oct 13, 2022 (156)
72	EVA	ss5506349833	Oct 13, 2022 (156)
73	1000G_HIGH_COVERAGE	ss5522436758	Oct 13, 2022 (156)
74	SANFORD_IMAGENETICS	ss5624441222	Oct 13, 2022 (156)
75	SANFORD_IMAGENETICS	ss5628431848	Oct 13, 2022 (156)
76	TOMMO_GENOMICS	ss5679060521	Oct 13, 2022 (156)
77	YY_MCH	ss5802069616	Oct 13, 2022 (156)
78	EVA	ss5819886595	Oct 13, 2022 (156)
79	EVA	ss5847862706	Oct 13, 2022 (156)
80	EVA	ss5852459342	Oct 13, 2022 (156)
81	EVA	ss5929721899	Oct 13, 2022 (156)
82	EVA	ss5954640093	Oct 13, 2022 (156)
83	EVA	ss5979562072	Oct 13, 2022 (156)
84	1000Genomes	NC_000002.11 - 34285194	Oct 11, 2018 (152)
85	1000Genomes_30x	NC_000002.12 - 34060127	Oct 13, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 34285194	Oct 11, 2018 (152)
87	Genetic variation in the Estonian population	NC_000002.11 - 34285194	Oct 11, 2018 (152)
88	The Danish reference pan genome	NC_000002.11 - 34285194	Apr 25, 2020 (154)
89	gnomAD - Genomes	NC_000002.12 - 34060127	Apr 26, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000002.11 - 34285194	Apr 25, 2020 (154)
91	HapMap	NC_000002.12 - 34060127	Apr 25, 2020 (154)
92	KOREAN population from KRGDB	NC_000002.11 - 34285194	Apr 25, 2020 (154)
93	Korean Genome Project	NC_000002.12 - 34060127	Apr 25, 2020 (154)
94	Northern Sweden	NC_000002.11 - 34285194	Jul 13, 2019 (153)
95	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000002.11 - 34285194	Apr 26, 2021 (155)
96	Qatari	NC_000002.11 - 34285194	Apr 25, 2020 (154)
97	SGDP_PRJ	NC_000002.11 - 34285194	Apr 25, 2020 (154)
98	Siberian	NC_000002.11 - 34285194	Apr 25, 2020 (154)
99	8.3KJPN	NC_000002.11 - 34285194	Apr 26, 2021 (155)
100	14KJPN	NC_000002.12 - 34060127	Oct 13, 2022 (156)
101	TopMed	NC_000002.12 - 34060127	Apr 26, 2021 (155)
102	UK 10K study - Twins	NC_000002.11 - 34285194	Oct 11, 2018 (152)
103	A Vietnamese Genetic Variation Database	NC_000002.11 - 34285194	Jul 13, 2019 (153)
104	ALFA	NC_000002.12 - 34060127	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss91112846, ss109389717, ss110053852, ss163276655, ss200252032, ss276411790, ss292541117, ss1586074600	NC_000002.10:34138697:T:A	NC_000002.12:34060126:T:A	(self)
7521781, 4177669, 2950050, 4987534, 1835076, 4548750, 1585911, 109871, 1941562, 3961500, 1040800, 8612318, 4177669, 908026, ss219161025, ss231105872, ss238674364, ss555463517, ss649046935, ss976667065, ss1068991081, ss1296596746, ss1428529444, ss1578812436, ss1603175625, ss1646169658, ss1796526845, ss1919899632, ss1968733205, ss2020479426, ss2094805897, ss2095089356, ss2148524446, ss2624753187, ss2703085446, ss2771664955, ss2985790207, ss2989253671, ss3021958020, ss3344154555, ss3652387826, ss3657211802, ss3728301046, ss3744473945, ss3756565543, ss3783824524, ss3789418322, ss3794291102, ss3826905768, ss3836860765, ss3851944520, ss3897371356, ss3984883944, ss5150643011, ss5506349833, ss5624441222, ss5628431848, ss5819886595, ss5847862706, ss5954640093, ss5979562072	NC_000002.11:34285193:T:A	NC_000002.12:34060126:T:A	(self)
9962693, 53415392, 1767692, 3831296, 12897625, 303916488, 4722524726, ss2228946261, ss3024006006, ss3647001608, ss3703587105, ss3725773080, ss3800943368, ss3842275542, ss3947453295, ss4500093609, ss5247512419, ss5447766254, ss5522436758, ss5679060521, ss5802069616, ss5852459342, ss5929721899	NC_000002.12:34060126:T:A	NC_000002.12:34060126:T:A	(self)
ss9952796	NT_022184.12:13101126:T:A	NC_000002.12:34060126:T:A	(self)
ss14499487	NT_022184.13:13101126:T:A	NC_000002.12:34060126:T:A	(self)
ss14885744, ss24149975, ss41711179, ss65944513, ss68386789, ss97026175, ss106080408, ss138418114, ss139353377, ss156887689	NT_022184.15:13107080:T:A	NC_000002.12:34060126:T:A	(self)

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

2 citations for rs6729869

PMID	Title	Author	Year	Journal
19421330	Genome-wide association study of young-onset hypertension in the Han Chinese population of Taiwan.	Yang HC et al.	2009	PloS one
22479346	Identification of IGF1, SLC4A4, WWOX, and SFMBT1 as hypertension susceptibility genes in Han Chinese with a genome-wide gene-based association study.	Yang HC et al.	2012	PloS one

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

rs6729869