Name: rs7139391
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.

rs7139391

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:73160143 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.447588 (118472/264690, TOPMED)
T=0.439740 (61524/139910, GnomAD)
C=0.35664 (10078/28258, 14KJPN) (+ 19 more)
T=0.42767 (11442/26754, ALFA)
C=0.35853 (6009/16760, 8.3KJPN)
C=0.4508 (2887/6404, 1000G_30x)
C=0.4445 (2226/5008, 1000G)
T=0.3790 (1698/4480, Estonian)
T=0.3570 (1376/3854, ALSPAC)
T=0.3376 (1252/3708, TWINSUK)
C=0.2829 (829/2930, KOREAN)
C=0.4355 (824/1892, HapMap)
C=0.2767 (507/1832, Korea1K)
T=0.4055 (455/1122, Daghestan)
T=0.367 (366/998, GoNL)
T=0.414 (259/626, Chileans)
T=0.398 (239/600, NorthernSweden)
C=0.285 (122/428, SGDP_PRJ)
T=0.380 (82/216, Qatari)
C=0.241 (51/212, Vietnamese)
T=0.25 (10/40, GENOME_DK)
C=0.42 (16/38, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	26754	C=0.57233	T=0.42767
European	Sub	15752	C=0.64087	T=0.35913
African	Sub	6256	C=0.4186	T=0.5814
African Others	Sub	210	C=0.381	T=0.619
African American	Sub	6046	C=0.4199	T=0.5801
Asian	Sub	162	C=0.198	T=0.802
East Asian	Sub	104	C=0.250	T=0.750
Other Asian	Sub	58	C=0.10	T=0.90
Latin American 1	Sub	292	C=0.658	T=0.342
Latin American 2	Sub	2770	C=0.5646	T=0.4354
South Asian	Sub	112	C=0.393	T=0.607
Other	Sub	1410	C=0.5433	T=0.4567

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=0.552412	T=0.447588
gnomAD - Genomes	Global	Study-wide	139910	C=0.560260	T=0.439740
gnomAD - Genomes	European	Sub	75800	C=0.63933	T=0.36067
gnomAD - Genomes	African	Sub	41894	C=0.42524	T=0.57476
gnomAD - Genomes	American	Sub	13622	C=0.58347	T=0.41653
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.6702	T=0.3298
gnomAD - Genomes	East Asian	Sub	3124	C=0.2446	T=0.7554
gnomAD - Genomes	Other	Sub	2150	C=0.5456	T=0.4544
14KJPN	JAPANESE	Study-wide	28258	C=0.35664	T=0.64336
Allele Frequency Aggregator	Total	Global	26754	C=0.57233	T=0.42767
Allele Frequency Aggregator	European	Sub	15752	C=0.64087	T=0.35913
Allele Frequency Aggregator	African	Sub	6256	C=0.4186	T=0.5814
Allele Frequency Aggregator	Latin American 2	Sub	2770	C=0.5646	T=0.4354
Allele Frequency Aggregator	Other	Sub	1410	C=0.5433	T=0.4567
Allele Frequency Aggregator	Latin American 1	Sub	292	C=0.658	T=0.342
Allele Frequency Aggregator	Asian	Sub	162	C=0.198	T=0.802
Allele Frequency Aggregator	South Asian	Sub	112	C=0.393	T=0.607
8.3KJPN	JAPANESE	Study-wide	16760	C=0.35853	T=0.64147
1000Genomes_30x	Global	Study-wide	6404	C=0.4508	T=0.5492
1000Genomes_30x	African	Sub	1786	C=0.4155	T=0.5845
1000Genomes_30x	Europe	Sub	1266	C=0.6280	T=0.3720
1000Genomes_30x	South Asian	Sub	1202	C=0.3852	T=0.6148
1000Genomes_30x	East Asian	Sub	1170	C=0.2658	T=0.7342
1000Genomes_30x	American	Sub	980	C=0.588	T=0.412
1000Genomes	Global	Study-wide	5008	C=0.4445	T=0.5555
1000Genomes	African	Sub	1322	C=0.4145	T=0.5855
1000Genomes	East Asian	Sub	1008	C=0.2659	T=0.7341
1000Genomes	Europe	Sub	1006	C=0.6292	T=0.3708
1000Genomes	South Asian	Sub	978	C=0.376	T=0.624
1000Genomes	American	Sub	694	C=0.589	T=0.411
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6210	T=0.3790
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6430	T=0.3570
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6624	T=0.3376
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2829	A=0.0000, G=0.0000, T=0.7171
HapMap	Global	Study-wide	1892	C=0.4355	T=0.5645
HapMap	American	Sub	770	C=0.455	T=0.545
HapMap	African	Sub	692	C=0.379	T=0.621
HapMap	Asian	Sub	254	C=0.390	T=0.610
HapMap	Europe	Sub	176	C=0.642	T=0.358
Korean Genome Project	KOREAN	Study-wide	1832	C=0.2767	T=0.7233
Genome-wide autozygosity in Daghestan	Global	Study-wide	1122	C=0.5945	T=0.4055
Genome-wide autozygosity in Daghestan	Daghestan	Sub	618	C=0.642	T=0.358
Genome-wide autozygosity in Daghestan	Near_East	Sub	142	C=0.634	T=0.366
Genome-wide autozygosity in Daghestan	Central Asia	Sub	120	C=0.408	T=0.592
Genome-wide autozygosity in Daghestan	Europe	Sub	108	C=0.676	T=0.324
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	C=0.32	T=0.68
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	C=0.75	T=0.25
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.633	T=0.367
Chileans	Chilean	Study-wide	626	C=0.586	T=0.414
Northern Sweden	ACPOP	Study-wide	600	C=0.602	T=0.398
SGDP_PRJ	Global	Study-wide	428	C=0.285	T=0.715
Qatari	Global	Study-wide	216	C=0.620	T=0.380
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.241	T=0.759
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Siberian	Global	Study-wide	38	C=0.42	T=0.58

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 13	NC_000013.11:g.73160143C>A
GRCh38.p14 chr 13	NC_000013.11:g.73160143C>G
GRCh38.p14 chr 13	NC_000013.11:g.73160143C>T
GRCh37.p13 chr 13	NC_000013.10:g.73734280C>A
GRCh37.p13 chr 13	NC_000013.10:g.73734280C>G
GRCh37.p13 chr 13	NC_000013.10:g.73734280C>T

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=	A	G	T
GRCh38.p14 chr 13	NC_000013.11:g.73160143=	NC_000013.11:g.73160143C>A	NC_000013.11:g.73160143C>G	NC_000013.11:g.73160143C>T
GRCh37.p13 chr 13	NC_000013.10:g.73734280=	NC_000013.10:g.73734280C>A	NC_000013.10:g.73734280C>G	NC_000013.10:g.73734280C>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#.

64 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10720441	Jul 11, 2003 (116)
2	SC_SNP	ss13294143	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss16629205	Feb 27, 2004 (120)
4	ABI	ss40334917	Mar 15, 2006 (126)
5	AFFY	ss76495466	Dec 07, 2007 (129)
6	BCMHGSC_JDW	ss89749084	Mar 24, 2008 (129)
7	ILLUMINA-UK	ss118841061	Dec 01, 2009 (131)
8	BUSHMAN	ss199388938	Jul 04, 2010 (142)
9	1000GENOMES	ss211428992	Jul 14, 2010 (132)
10	1000GENOMES	ss226270437	Jul 14, 2010 (132)
11	1000GENOMES	ss236320103	Jul 15, 2010 (132)
12	1000GENOMES	ss242800568	Jul 15, 2010 (132)
13	GMI	ss281779391	May 04, 2012 (137)
14	GMI	ss286736591	Apr 25, 2013 (138)
15	PJP	ss291476511	May 09, 2011 (134)
16	TISHKOFF	ss563760622	Apr 25, 2013 (138)
17	SSMP	ss659384695	Apr 25, 2013 (138)
18	EVA-GONL	ss990566668	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1079216656	Aug 21, 2014 (142)
20	1000GENOMES	ss1348851847	Aug 21, 2014 (142)
21	HAMMER_LAB	ss1397662754	Sep 08, 2015 (146)
22	DDI	ss1427240371	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1576894207	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1630611874	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1673605907	Apr 01, 2015 (144)
26	EVA_DECODE	ss1685096050	Apr 01, 2015 (144)
27	EVA_SVP	ss1713402567	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1807679105	Sep 08, 2015 (146)
29	WEILL_CORNELL_DGM	ss1933927206	Feb 12, 2016 (147)
30	GENOMED	ss1967824476	Jul 19, 2016 (147)
31	JJLAB	ss2027731904	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2156098561	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2197660085	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2628354262	Nov 08, 2017 (151)
35	GRF	ss2700486562	Nov 08, 2017 (151)
36	GNOMAD	ss2921468841	Nov 08, 2017 (151)
37	SWEGEN	ss3011284755	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3027684301	Nov 08, 2017 (151)
39	CSHL	ss3350534652	Nov 08, 2017 (151)
40	EGCUT_WGS	ss3678558269	Jul 13, 2019 (153)
41	EVA_DECODE	ss3695605852	Jul 13, 2019 (153)
42	ACPOP	ss3739890703	Jul 13, 2019 (153)
43	EVA	ss3751658918	Jul 13, 2019 (153)
44	PACBIO	ss3787506475	Jul 13, 2019 (153)
45	PACBIO	ss3792565911	Jul 13, 2019 (153)
46	PACBIO	ss3797449604	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3816990342	Jul 13, 2019 (153)
48	EVA	ss3833631369	Apr 27, 2020 (154)
49	SGDP_PRJ	ss3880306731	Apr 27, 2020 (154)
50	KRGDB	ss3929200581	Apr 27, 2020 (154)
51	KOGIC	ss3973861078	Apr 27, 2020 (154)
52	TOPMED	ss4952053482	Apr 26, 2021 (155)
53	TOMMO_GENOMICS	ss5210715763	Apr 26, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5294285436	Oct 16, 2022 (156)
55	EVA	ss5411782328	Oct 16, 2022 (156)
56	HUGCELL_USP	ss5488594306	Oct 16, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5593565758	Oct 16, 2022 (156)
58	SANFORD_IMAGENETICS	ss5655093686	Oct 16, 2022 (156)
59	TOMMO_GENOMICS	ss5762790193	Oct 16, 2022 (156)
60	YY_MCH	ss5814256594	Oct 16, 2022 (156)
61	EVA	ss5839697810	Oct 16, 2022 (156)
62	EVA	ss5850797815	Oct 16, 2022 (156)
63	EVA	ss5925735706	Oct 16, 2022 (156)
64	EVA	ss5946523191	Oct 16, 2022 (156)
65	1000Genomes	NC_000013.10 - 73734280	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000013.11 - 73160143	Oct 16, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 73734280	Oct 12, 2018 (152)
68	Chileans	NC_000013.10 - 73734280	Apr 27, 2020 (154)
69	Genome-wide autozygosity in Daghestan	NC_000013.9 - 72632281	Apr 27, 2020 (154)
70	Genetic variation in the Estonian population	NC_000013.10 - 73734280	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000013.10 - 73734280	Apr 27, 2020 (154)
72	gnomAD - Genomes	NC_000013.11 - 73160143	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000013.10 - 73734280	Apr 27, 2020 (154)
74	HapMap	NC_000013.11 - 73160143	Apr 27, 2020 (154)
75	KOREAN population from KRGDB	NC_000013.10 - 73734280	Apr 27, 2020 (154)
76	Korean Genome Project	NC_000013.11 - 73160143	Apr 27, 2020 (154)
77	Northern Sweden	NC_000013.10 - 73734280	Jul 13, 2019 (153)
78	Qatari	NC_000013.10 - 73734280	Apr 27, 2020 (154)
79	SGDP_PRJ	NC_000013.10 - 73734280	Apr 27, 2020 (154)
80	Siberian	NC_000013.10 - 73734280	Apr 27, 2020 (154)
81	8.3KJPN	NC_000013.10 - 73734280	Apr 26, 2021 (155)
82	14KJPN	NC_000013.11 - 73160143	Oct 16, 2022 (156)
83	TopMed	NC_000013.11 - 73160143	Apr 26, 2021 (155)
84	UK 10K study - Twins	NC_000013.10 - 73734280	Oct 12, 2018 (152)
85	A Vietnamese Genetic Variation Database	NC_000013.10 - 73734280	Jul 13, 2019 (153)
86	ALFA	NC_000013.11 - 73160143	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)
rs17372783	Dec 02, 2004 (124)
rs76790023	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
36377975, ss3929200581	NC_000013.10:73734279:C:A	NC_000013.11:73160142:C:A	(self)
36377975, ss3929200581	NC_000013.10:73734279:C:G	NC_000013.11:73160142:C:G	(self)
133317, ss76495466, ss89749084, ss118841061, ss199388938, ss211428992, ss281779391, ss286736591, ss291476511, ss1397662754, ss1685096050, ss1713402567	NC_000013.9:72632280:C:T	NC_000013.11:73160142:C:T	(self)
61749070, 34305881, 123918, 24296517, 3366662, 15314802, 36377975, 13175568, 15969136, 32323711, 8614915, 68685070, 34305881, 7619943, ss226270437, ss236320103, ss242800568, ss563760622, ss659384695, ss990566668, ss1079216656, ss1348851847, ss1427240371, ss1576894207, ss1630611874, ss1673605907, ss1807679105, ss1933927206, ss1967824476, ss2027731904, ss2156098561, ss2628354262, ss2700486562, ss2921468841, ss3011284755, ss3350534652, ss3678558269, ss3739890703, ss3751658918, ss3787506475, ss3792565911, ss3797449604, ss3833631369, ss3880306731, ss3929200581, ss5210715763, ss5411782328, ss5655093686, ss5839697810, ss5946523191	NC_000013.10:73734279:C:T	NC_000013.11:73160142:C:T	(self)
81091693, 435447877, 1026352, 30239079, 96627297, 167599140, 7226173710, ss2197660085, ss3027684301, ss3695605852, ss3816990342, ss3973861078, ss4952053482, ss5294285436, ss5488594306, ss5593565758, ss5762790193, ss5814256594, ss5850797815, ss5925735706	NC_000013.11:73160142:C:T	NC_000013.11:73160142:C:T	(self)
ss10720441, ss13294143	NT_024524.12:42308771:C:T	NC_000013.11:73160142:C:T	(self)
ss16629205	NT_024524.13:54714280:C:T	NC_000013.11:73160142:C:T	(self)
ss40334917	NT_024524.14:54714279:C:T	NC_000013.11:73160142: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 rs7139391

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

rs7139391