Name: rs6960142
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.

rs6960142

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:39465725 (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 / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.058846 (15576/264690, TOPMED)
T=0.061133 (8574/140252, GnomAD)
T=0.00004 (1/28258, 14KJPN) (+ 19 more)
T=0.00000 (0/16758, 8.3KJPN)
T=0.1118 (796/7118, ALFA)
T=0.0448 (287/6404, 1000G_30x)
T=0.0463 (232/5008, 1000G)
T=0.1107 (496/4480, Estonian)
T=0.0880 (339/3854, ALSPAC)
T=0.1001 (371/3708, TWINSUK)
T=0.0000 (0/2930, KOREAN)
A=0.0000 (0/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.075 (75/998, GoNL)
T=0.077 (46/600, NorthernSweden)
T=0.045 (25/554, SGDP_PRJ)
T=0.027 (9/330, HapMap)
T=0.065 (14/216, Qatari)
T=0.000 (0/216, Vietnamese)
T=0.00 (0/84, Ancient Sardinia)
T=0.02 (1/56, Siberian)
T=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: POU6F2 : 3 Prime UTR Variant
LOC105375238 : 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	7118	T=0.1118	A=0.0000, C=0.8882
European	Sub	6750	T=0.1141	A=0.0000, C=0.8859
African	Sub	134	T=0.045	A=0.000, C=0.955
African Others	Sub	6	T=0.0	A=0.0, C=1.0
African American	Sub	128	T=0.047	A=0.000, C=0.953
Asian	Sub	4	T=0.0	A=0.0, C=1.0
East Asian	Sub	2	T=0.0	A=0.0, C=1.0
Other Asian	Sub	2	T=0.0	A=0.0, C=1.0
Latin American 1	Sub	0	T=0	A=0, C=0
Latin American 2	Sub	2	T=1.0	A=0.0, C=0.0
South Asian	Sub	6	T=0.3	A=0.0, C=0.7
Other	Sub	222	T=0.072	A=0.000, C=0.928

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=0.058846	C=0.941154
gnomAD - Genomes	Global	Study-wide	140252	T=0.061133	C=0.938867
gnomAD - Genomes	European	Sub	75948	T=0.08611	C=0.91389
gnomAD - Genomes	African	Sub	42046	T=0.01767	C=0.98233
gnomAD - Genomes	American	Sub	13656	T=0.04723	C=0.95277
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.1502	C=0.8498
gnomAD - Genomes	East Asian	Sub	3134	T=0.0013	C=0.9987
gnomAD - Genomes	Other	Sub	2146	T=0.0666	C=0.9334
14KJPN	JAPANESE	Study-wide	28258	T=0.00004	C=0.99996
8.3KJPN	JAPANESE	Study-wide	16758	T=0.00000	C=1.00000
Allele Frequency Aggregator	Total	Global	7118	T=0.1118	A=0.0000, C=0.8882
Allele Frequency Aggregator	European	Sub	6750	T=0.1141	A=0.0000, C=0.8859
Allele Frequency Aggregator	Other	Sub	222	T=0.072	A=0.000, C=0.928
Allele Frequency Aggregator	African	Sub	134	T=0.045	A=0.000, C=0.955
Allele Frequency Aggregator	South Asian	Sub	6	T=0.3	A=0.0, C=0.7
Allele Frequency Aggregator	Asian	Sub	4	T=0.0	A=0.0, C=1.0
Allele Frequency Aggregator	Latin American 2	Sub	2	T=1.0	A=0.0, C=0.0
Allele Frequency Aggregator	Latin American 1	Sub	0	T=0	A=0, C=0
1000Genomes_30x	Global	Study-wide	6404	T=0.0448	C=0.9552
1000Genomes_30x	African	Sub	1786	T=0.0017	C=0.9983
1000Genomes_30x	Europe	Sub	1266	T=0.0845	C=0.9155
1000Genomes_30x	South Asian	Sub	1202	T=0.1040	C=0.8960
1000Genomes_30x	East Asian	Sub	1170	T=0.0000	C=1.0000
1000Genomes_30x	American	Sub	980	T=0.053	C=0.947
1000Genomes	Global	Study-wide	5008	T=0.0463	C=0.9537
1000Genomes	African	Sub	1322	T=0.0023	C=0.9977
1000Genomes	East Asian	Sub	1008	T=0.0000	C=1.0000
1000Genomes	Europe	Sub	1006	T=0.0855	C=0.9145
1000Genomes	South Asian	Sub	978	T=0.110	C=0.890
1000Genomes	American	Sub	694	T=0.050	C=0.950
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1107	C=0.8893
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0880	C=0.9120
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1001	C=0.8999
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0000	A=0.0000, C=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0000	C=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.075	C=0.925
Northern Sweden	ACPOP	Study-wide	600	T=0.077	C=0.923
SGDP_PRJ	Global	Study-wide	554	T=0.045	C=0.955
HapMap	Global	Study-wide	330	T=0.027	C=0.973
HapMap	African	Sub	120	T=0.000	C=1.000
HapMap	American	Sub	120	T=0.075	C=0.925
HapMap	Asian	Sub	90	T=0.00	C=1.00
Qatari	Global	Study-wide	216	T=0.065	C=0.935
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.000	C=1.000
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	84	T=0.00	C=1.00
Siberian	Global	Study-wide	56	T=0.02	C=0.98
The Danish reference pan genome	Danish	Study-wide	40	T=0.05	C=0.95

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.39465725T>A
GRCh38.p14 chr 7	NC_000007.14:g.39465725T>C
GRCh37.p13 chr 7	NC_000007.13:g.39505324T>A
GRCh37.p13 chr 7	NC_000007.13:g.39505324T>C
POU6F2 RefSeqGene	NG_016022.2:g.492848T>A
POU6F2 RefSeqGene	NG_016022.2:g.492848T>C

Gene: POU6F2, POU class 6 homeobox 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
POU6F2 transcript variant 2	NM_001166018.2:c.*1039=	N/A	3 Prime UTR Variant
POU6F2 transcript variant 1	NM_007252.4:c.*1039=	N/A	3 Prime UTR Variant
POU6F2 transcript variant 3	NM_001370959.1:c.*1039=	N/A	3 Prime UTR Variant
POU6F2 transcript variant X1	XM_047419843.1:c.*1039=	N/A	3 Prime UTR Variant
POU6F2 transcript variant X2	XM_047419845.1:c.*1039=	N/A	3 Prime UTR Variant

Gene: LOC105375238, uncharacterized LOC105375238 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105375238 transcript variant X2	XR_927186.2:n.	N/A	Intron Variant
LOC105375238 transcript variant X1	XR_927185.2:n.	N/A	Genic Downstream 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	T=	A	C
GRCh38.p14 chr 7	NC_000007.14:g.39465725=	NC_000007.14:g.39465725T>A	NC_000007.14:g.39465725T>C
GRCh37.p13 chr 7	NC_000007.13:g.39505324=	NC_000007.13:g.39505324T>A	NC_000007.13:g.39505324T>C
POU6F2 RefSeqGene	NG_016022.2:g.492848=	NG_016022.2:g.492848T>A	NG_016022.2:g.492848T>C
POU6F2 transcript variant 1	NM_007252.4:c.*1039=	NM_007252.4:c.*1039T>A	NM_007252.4:c.*1039T>C
POU6F2 transcript variant 2	NM_001166018.2:c.*1039=	NM_001166018.2:c.*1039T>A	NM_001166018.2:c.*1039T>C
POU6F2 transcript variant 3	NM_001370959.1:c.*1039=	NM_001370959.1:c.*1039T>A	NM_001370959.1:c.*1039T>C
POU6F2 transcript variant X2	XM_047419845.1:c.*1039=	XM_047419845.1:c.*1039T>A	XM_047419845.1:c.*1039T>C
POU6F2 transcript variant X1	XM_047419843.1:c.*1039=	XM_047419843.1:c.*1039T>A	XM_047419843.1:c.*1039T>C

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#.

77 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10382640	Jul 11, 2003 (116)
2	WUGSC_SSAHASNP	ss14562092	Dec 05, 2003 (120)
3	SSAHASNP	ss22636555	Apr 05, 2004 (121)
4	ABI	ss44778907	Mar 15, 2006 (126)
5	HGSV	ss78943139	Dec 07, 2007 (129)
6	HUMANGENOME_JCVI	ss98259819	Feb 06, 2009 (130)
7	BGI	ss105521333	Feb 06, 2009 (130)
8	1000GENOMES	ss111854405	Jan 25, 2009 (130)
9	1000GENOMES	ss113627613	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss116040562	Feb 14, 2009 (130)
11	ENSEMBL	ss144396715	Dec 01, 2009 (131)
12	GMI	ss154672022	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss162243032	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss164055310	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166462103	Jul 04, 2010 (132)
16	BUSHMAN	ss203213756	Jul 04, 2010 (132)
17	BCM-HGSC-SUB	ss208020554	Jul 04, 2010 (132)
18	1000GENOMES	ss223026866	Jul 14, 2010 (132)
19	1000GENOMES	ss233938887	Jul 15, 2010 (132)
20	1000GENOMES	ss240901139	Jul 15, 2010 (132)
21	BL	ss254206736	May 09, 2011 (134)
22	GMI	ss279271900	May 04, 2012 (137)
23	GMI	ss285611669	Apr 25, 2013 (138)
24	PJP	ss294052478	May 09, 2011 (134)
25	TISHKOFF	ss559943807	Apr 25, 2013 (138)
26	SSMP	ss654302367	Apr 25, 2013 (138)
27	EVA-GONL	ss984178315	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1074534741	Aug 21, 2014 (142)
29	1000GENOMES	ss1324755321	Aug 21, 2014 (142)
30	DDI	ss1431095388	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1582162532	Apr 01, 2015 (144)
32	EVA_DECODE	ss1593750761	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1618014477	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1661008510	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1804963076	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1927421764	Feb 12, 2016 (147)
37	GENOMED	ss1970678303	Jul 19, 2016 (147)
38	JJLAB	ss2024392827	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2152588376	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2293281554	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2626684655	Nov 08, 2017 (151)
42	GRF	ss2708249783	Nov 08, 2017 (151)
43	GNOMAD	ss2852085877	Nov 08, 2017 (151)
44	SWEGEN	ss3000965782	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3025991292	Nov 08, 2017 (151)
46	CSHL	ss3347540697	Nov 08, 2017 (151)
47	URBANLAB	ss3648609924	Oct 12, 2018 (152)
48	EGCUT_WGS	ss3668886983	Jul 13, 2019 (153)
49	EVA_DECODE	ss3719509814	Jul 13, 2019 (153)
50	ACPOP	ss3734548186	Jul 13, 2019 (153)
51	EVA	ss3766446314	Jul 13, 2019 (153)
52	PACBIO	ss3785791356	Jul 13, 2019 (153)
53	PACBIO	ss3791097199	Jul 13, 2019 (153)
54	PACBIO	ss3795977071	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3809610424	Jul 13, 2019 (153)
56	EVA	ss3825718396	Apr 26, 2020 (154)
57	EVA	ss3830525645	Apr 26, 2020 (154)
58	EVA	ss3838750570	Apr 26, 2020 (154)
59	EVA	ss3844202369	Apr 26, 2020 (154)
60	SGDP_PRJ	ss3867073231	Apr 26, 2020 (154)
61	KRGDB	ss3914129710	Apr 26, 2020 (154)
62	KOGIC	ss3961281217	Apr 26, 2020 (154)
63	EVA	ss3985291615	Apr 26, 2021 (155)
64	TOPMED	ss4742735951	Apr 26, 2021 (155)
65	TOMMO_GENOMICS	ss5182732141	Apr 26, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5272549735	Oct 13, 2022 (156)
67	EVA	ss5372965609	Oct 13, 2022 (156)
68	HUGCELL_USP	ss5469759335	Oct 13, 2022 (156)
69	EVA	ss5508924063	Oct 13, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5560553935	Oct 13, 2022 (156)
71	SANFORD_IMAGENETICS	ss5642762453	Oct 13, 2022 (156)
72	TOMMO_GENOMICS	ss5722444761	Oct 13, 2022 (156)
73	YY_MCH	ss5808519660	Oct 13, 2022 (156)
74	EVA	ss5822694111	Oct 13, 2022 (156)
75	EVA	ss5855855138	Oct 13, 2022 (156)
76	EVA	ss5858532997	Oct 13, 2022 (156)
77	EVA	ss5971972072	Oct 13, 2022 (156)
78	1000Genomes	NC_000007.13 - 39505324	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000007.14 - 39465725	Oct 13, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 39505324	Oct 12, 2018 (152)
81	Genetic variation in the Estonian population	NC_000007.13 - 39505324	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000007.13 - 39505324	Apr 26, 2020 (154)
83	gnomAD - Genomes	NC_000007.14 - 39465725	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000007.13 - 39505324	Apr 26, 2020 (154)
85	HapMap	NC_000007.14 - 39465725	Apr 26, 2020 (154)
86	KOREAN population from KRGDB	NC_000007.13 - 39505324	Apr 26, 2020 (154)
87	Korean Genome Project	NC_000007.14 - 39465725	Apr 26, 2020 (154)
88	Northern Sweden	NC_000007.13 - 39505324	Jul 13, 2019 (153)
89	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000007.13 - 39505324	Apr 26, 2021 (155)
90	Qatari	NC_000007.13 - 39505324	Apr 26, 2020 (154)
91	SGDP_PRJ	NC_000007.13 - 39505324	Apr 26, 2020 (154)
92	Siberian	NC_000007.13 - 39505324	Apr 26, 2020 (154)
93	8.3KJPN	NC_000007.13 - 39505324	Apr 26, 2021 (155)
94	14KJPN	NC_000007.14 - 39465725	Oct 13, 2022 (156)
95	TopMed	NC_000007.14 - 39465725	Apr 26, 2021 (155)
96	UK 10K study - Twins	NC_000007.13 - 39505324	Oct 12, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000007.13 - 39505324	Jul 13, 2019 (153)
98	ALFA	NC_000007.14 - 39465725	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)
rs10356734	Feb 27, 2004 (120)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
21307104, ss3914129710	NC_000007.13:39505323:T:A	NC_000007.14:39465724:T:A	(self)
7356042198	NC_000007.14:39465724:T:A	NC_000007.14:39465724:T:A	(self)
ss78943139	NC_000007.11:39278563:T:C	NC_000007.14:39465724:T:C	(self)
ss111854405, ss113627613, ss116040562, ss162243032, ss164055310, ss166462103, ss203213756, ss208020554, ss254206736, ss279271900, ss285611669, ss294052478, ss1593750761	NC_000007.12:39471848:T:C	NC_000007.14:39465724:T:C	(self)
36712202, 20472621, 14625231, 8327471, 9131186, 21307104, 7833051, 517542, 9463694, 19090211, 5104730, 40701448, 20472621, 4562833, ss223026866, ss233938887, ss240901139, ss559943807, ss654302367, ss984178315, ss1074534741, ss1324755321, ss1431095388, ss1582162532, ss1618014477, ss1661008510, ss1804963076, ss1927421764, ss1970678303, ss2024392827, ss2152588376, ss2626684655, ss2708249783, ss2852085877, ss3000965782, ss3347540697, ss3668886983, ss3734548186, ss3766446314, ss3785791356, ss3791097199, ss3795977071, ss3825718396, ss3830525645, ss3838750570, ss3867073231, ss3914129710, ss3985291615, ss5182732141, ss5372965609, ss5508924063, ss5642762453, ss5822694111, ss5971972072	NC_000007.13:39505323:T:C	NC_000007.14:39465724:T:C	(self)
48079870, 258809848, 3383447, 17659218, 56281865, 580113510, 7356042198, ss2293281554, ss3025991292, ss3648609924, ss3719509814, ss3809610424, ss3844202369, ss3961281217, ss4742735951, ss5272549735, ss5469759335, ss5560553935, ss5722444761, ss5808519660, ss5855855138, ss5858532997	NC_000007.14:39465724:T:C	NC_000007.14:39465724:T:C	(self)
ss10382640	NT_007819.13:38797439:T:C	NC_000007.14:39465724:T:C	(self)
ss14562092, ss22636555	NT_007819.14:38797439:T:C	NC_000007.14:39465724:T:C	(self)
ss44778907, ss98259819, ss105521333, ss144396715, ss154672022	NT_007819.17:39495323:T:C	NC_000007.14:39465724:T:C	(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 rs6960142

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

rs6960142