Name: rs906847
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.

rs906847

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:113761569 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.247403 (65485/264690, TOPMED)
T=0.246444 (34512/140040, GnomAD)
T=0.27465 (7761/28258, 14KJPN) (+ 16 more)
T=0.21488 (4059/18890, ALFA)
T=0.27092 (4540/16758, 8.3KJPN)
T=0.2761 (1768/6404, 1000G_30x)
T=0.2718 (1361/5008, 1000G)
T=0.1913 (857/4480, Estonian)
T=0.1502 (579/3854, ALSPAC)
T=0.1578 (585/3708, TWINSUK)
T=0.2457 (720/2930, KOREAN)
T=0.2615 (479/1832, Korea1K)
T=0.152 (152/998, GoNL)
T=0.210 (126/600, NorthernSweden)
T=0.189 (97/512, SGDP_PRJ)
T=0.282 (61/216, Qatari)
T=0.140 (30/214, Vietnamese)
T=0.25 (12/48, Siberian)
T=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZW10 : 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	18890	T=0.21488	C=0.78512
European	Sub	14286	T=0.17479	C=0.82521
African	Sub	2946	T=0.3971	C=0.6029
African Others	Sub	114	T=0.430	C=0.570
African American	Sub	2832	T=0.3958	C=0.6042
Asian	Sub	112	T=0.125	C=0.875
East Asian	Sub	86	T=0.14	C=0.86
Other Asian	Sub	26	T=0.08	C=0.92
Latin American 1	Sub	146	T=0.349	C=0.651
Latin American 2	Sub	610	T=0.231	C=0.769
South Asian	Sub	98	T=0.22	C=0.78
Other	Sub	692	T=0.237	C=0.763

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=0.247403	C=0.752597
gnomAD - Genomes	Global	Study-wide	140040	T=0.246444	C=0.753556
gnomAD - Genomes	European	Sub	75900	T=0.16917	C=0.83083
gnomAD - Genomes	African	Sub	41906	T=0.39760	C=0.60240
gnomAD - Genomes	American	Sub	13634	T=0.22525	C=0.77475
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.2849	C=0.7151
gnomAD - Genomes	East Asian	Sub	3128	T=0.1563	C=0.8437
gnomAD - Genomes	Other	Sub	2148	T=0.2342	C=0.7658
14KJPN	JAPANESE	Study-wide	28258	T=0.27465	C=0.72535
Allele Frequency Aggregator	Total	Global	18890	T=0.21488	C=0.78512
Allele Frequency Aggregator	European	Sub	14286	T=0.17479	C=0.82521
Allele Frequency Aggregator	African	Sub	2946	T=0.3971	C=0.6029
Allele Frequency Aggregator	Other	Sub	692	T=0.237	C=0.763
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.231	C=0.769
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.349	C=0.651
Allele Frequency Aggregator	Asian	Sub	112	T=0.125	C=0.875
Allele Frequency Aggregator	South Asian	Sub	98	T=0.22	C=0.78
8.3KJPN	JAPANESE	Study-wide	16758	T=0.27092	C=0.72908
1000Genomes_30x	Global	Study-wide	6404	T=0.2761	C=0.7239
1000Genomes_30x	African	Sub	1786	T=0.4054	C=0.5946
1000Genomes_30x	Europe	Sub	1266	T=0.1833	C=0.8167
1000Genomes_30x	South Asian	Sub	1202	T=0.2862	C=0.7138
1000Genomes_30x	East Asian	Sub	1170	T=0.1692	C=0.8308
1000Genomes_30x	American	Sub	980	T=0.276	C=0.724
1000Genomes	Global	Study-wide	5008	T=0.2718	C=0.7282
1000Genomes	African	Sub	1322	T=0.4100	C=0.5900
1000Genomes	East Asian	Sub	1008	T=0.1736	C=0.8264
1000Genomes	Europe	Sub	1006	T=0.1889	C=0.8111
1000Genomes	South Asian	Sub	978	T=0.278	C=0.722
1000Genomes	American	Sub	694	T=0.262	C=0.738
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1913	C=0.8087
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1502	C=0.8498
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1578	C=0.8422
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2457	C=0.7543
Korean Genome Project	KOREAN	Study-wide	1832	T=0.2615	C=0.7385
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.152	C=0.848
Northern Sweden	ACPOP	Study-wide	600	T=0.210	C=0.790
SGDP_PRJ	Global	Study-wide	512	T=0.189	C=0.811
Qatari	Global	Study-wide	216	T=0.282	C=0.718
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.140	C=0.860
Siberian	Global	Study-wide	48	T=0.25	C=0.75
The Danish reference pan genome	Danish	Study-wide	40	T=0.20	C=0.80

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 11	NC_000011.10:g.113761569T>C
GRCh37.p13 chr 11	NC_000011.9:g.113632291T>C

Gene: ZW10, zw10 kinetochore protein (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZW10 transcript	NM_004724.4:c.241-651A>G	N/A	Intron Variant
ZW10 transcript variant X1	XM_017018558.3:c.241-651A… XM_017018558.3:c.241-651A>G	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=	C
GRCh38.p14 chr 11	NC_000011.10:g.113761569=	NC_000011.10:g.113761569T>C
GRCh37.p13 chr 11	NC_000011.9:g.113632291=	NC_000011.9:g.113632291T>C
ZW10 transcript	NM_004724.3:c.241-651=	NM_004724.3:c.241-651A>G
ZW10 transcript	NM_004724.4:c.241-651=	NM_004724.4:c.241-651A>G
ZW10 transcript variant X1	XM_017018558.3:c.241-651=	XM_017018558.3:c.241-651A>G

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, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1340124	Oct 05, 2000 (86)
2	SC_JCM	ss3448204	Sep 28, 2001 (100)
3	SNP500CANCER	ss5606364	Jul 02, 2003 (116)
4	WI_SSAHASNP	ss12155037	Jul 11, 2003 (116)
5	SC_SNP	ss16120802	Feb 27, 2004 (120)
6	CSHL-HAPMAP	ss16538850	Feb 27, 2004 (120)
7	CSHL-HAPMAP	ss17432725	Feb 27, 2004 (120)
8	CSHL-HAPMAP	ss19211253	Feb 27, 2004 (120)
9	SSAHASNP	ss20778070	Apr 05, 2004 (121)
10	ABI	ss40017224	Mar 15, 2006 (126)
11	HGSV	ss78015509	Dec 07, 2007 (129)
12	BCMHGSC_JDW	ss88802997	Mar 24, 2008 (129)
13	HUMANGENOME_JCVI	ss97512677	Feb 06, 2009 (130)
14	BGI	ss106771705	Feb 06, 2009 (130)
15	1000GENOMES	ss111104784	Jan 25, 2009 (130)
16	1000GENOMES	ss115200089	Jan 25, 2009 (130)
17	ENSEMBL	ss132840486	Dec 01, 2009 (131)
18	ENSEMBL	ss137851183	Dec 01, 2009 (131)
19	GMI	ss156812438	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss168756406	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss170916786	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss175283049	Jul 04, 2010 (132)
23	BUSHMAN	ss203230747	Jul 04, 2010 (132)
24	BCM-HGSC-SUB	ss207534813	Jul 04, 2010 (132)
25	1000GENOMES	ss225470826	Jul 14, 2010 (132)
26	1000GENOMES	ss235725858	Jul 15, 2010 (132)
27	1000GENOMES	ss242322597	Jul 15, 2010 (132)
28	BL	ss255384883	May 09, 2011 (134)
29	GMI	ss281177353	May 04, 2012 (137)
30	GMI	ss286460815	Apr 25, 2013 (138)
31	PJP	ss291143318	May 09, 2011 (134)
32	TISHKOFF	ss562836728	Apr 25, 2013 (138)
33	SSMP	ss658360181	Apr 25, 2013 (138)
34	EVA-GONL	ss988980885	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1078058292	Aug 21, 2014 (142)
36	1000GENOMES	ss1343034285	Aug 21, 2014 (142)
37	DDI	ss1426766336	Apr 01, 2015 (144)
38	EVA_GENOME_DK	ss1575962996	Apr 01, 2015 (144)
39	EVA_DECODE	ss1598647014	Apr 01, 2015 (144)
40	EVA_UK10K_ALSPAC	ss1627499688	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1670493721	Apr 01, 2015 (144)
42	HAMMER_LAB	ss1807004466	Sep 08, 2015 (146)
43	WEILL_CORNELL_DGM	ss1932341978	Feb 12, 2016 (147)
44	GENOMED	ss1967463147	Jul 19, 2016 (147)
45	JJLAB	ss2026914953	Sep 14, 2016 (149)
46	USC_VALOUEV	ss2155227536	Dec 20, 2016 (150)
47	HUMAN_LONGEVITY	ss2185849395	Dec 20, 2016 (150)
48	SYSTEMSBIOZJU	ss2627932241	Nov 08, 2017 (151)
49	GRF	ss2699537769	Nov 08, 2017 (151)
50	GNOMAD	ss2904651042	Nov 08, 2017 (151)
51	SWEGEN	ss3008807497	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3027258232	Nov 08, 2017 (151)
53	CSHL	ss3349802830	Nov 08, 2017 (151)
54	URBANLAB	ss3649708812	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3676135240	Jul 13, 2019 (153)
56	EVA_DECODE	ss3692632336	Jul 13, 2019 (153)
57	ACPOP	ss3738554745	Jul 13, 2019 (153)
58	EVA	ss3749833313	Jul 13, 2019 (153)
59	PACBIO	ss3787072260	Jul 13, 2019 (153)
60	PACBIO	ss3792195735	Jul 13, 2019 (153)
61	PACBIO	ss3797078255	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3815163304	Jul 13, 2019 (153)
63	EVA	ss3832847503	Apr 26, 2020 (154)
64	EVA	ss3839986202	Apr 26, 2020 (154)
65	EVA	ss3845467926	Apr 26, 2020 (154)
66	SGDP_PRJ	ss3877172239	Apr 26, 2020 (154)
67	KRGDB	ss3925630798	Apr 26, 2020 (154)
68	KOGIC	ss3970781134	Apr 26, 2020 (154)
69	TOPMED	ss4900580189	Apr 26, 2021 (155)
70	TOMMO_GENOMICS	ss5203965475	Apr 26, 2021 (155)
71	1000G_HIGH_COVERAGE	ss5288961379	Oct 16, 2022 (156)
72	EVA	ss5402353168	Oct 16, 2022 (156)
73	HUGCELL_USP	ss5483944523	Oct 16, 2022 (156)
74	EVA	ss5510528143	Oct 16, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5585477324	Oct 16, 2022 (156)
76	SANFORD_IMAGENETICS	ss5652106104	Oct 16, 2022 (156)
77	TOMMO_GENOMICS	ss5752434996	Oct 16, 2022 (156)
78	YY_MCH	ss5812791089	Oct 16, 2022 (156)
79	EVA	ss5837252924	Oct 16, 2022 (156)
80	EVA	ss5850158042	Oct 16, 2022 (156)
81	EVA	ss5921726707	Oct 16, 2022 (156)
82	EVA	ss5943437041	Oct 16, 2022 (156)
83	EVA	ss5980703631	Oct 16, 2022 (156)
84	1000Genomes	NC_000011.9 - 113632291	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000011.10 - 113761569	Oct 16, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 113632291	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000011.9 - 113632291	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000011.9 - 113632291	Apr 26, 2020 (154)
89	gnomAD - Genomes	NC_000011.10 - 113761569	Apr 26, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000011.9 - 113632291	Apr 26, 2020 (154)
91	KOREAN population from KRGDB	NC_000011.9 - 113632291	Apr 26, 2020 (154)
92	Korean Genome Project	NC_000011.10 - 113761569	Apr 26, 2020 (154)
93	Northern Sweden	NC_000011.9 - 113632291	Jul 13, 2019 (153)
94	Qatari	NC_000011.9 - 113632291	Apr 26, 2020 (154)
95	SGDP_PRJ	NC_000011.9 - 113632291	Apr 26, 2020 (154)
96	Siberian	NC_000011.9 - 113632291	Apr 26, 2020 (154)
97	8.3KJPN	NC_000011.9 - 113632291	Apr 26, 2021 (155)
98	14KJPN	NC_000011.10 - 113761569	Oct 16, 2022 (156)
99	TopMed	NC_000011.10 - 113761569	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000011.9 - 113632291	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000011.9 - 113632291	Jul 13, 2019 (153)
102	ALFA	NC_000011.10 - 113761569	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
ss78015509, ss88802997, ss111104784, ss115200089, ss168756406, ss170916786, ss175283049, ss203230747, ss207534813, ss255384883, ss281177353, ss286460815, ss291143318, ss1598647014	NC_000011.8:113137500:T:C	NC_000011.10:113761568:T:C	(self)
55618992, 30872664, 21873488, 2742484, 13777426, 32808192, 11839610, 14383908, 29189219, 7743890, 61934782, 30872664, 6852007, ss225470826, ss235725858, ss242322597, ss562836728, ss658360181, ss988980885, ss1078058292, ss1343034285, ss1426766336, ss1575962996, ss1627499688, ss1670493721, ss1807004466, ss1932341978, ss1967463147, ss2026914953, ss2155227536, ss2627932241, ss2699537769, ss2904651042, ss3008807497, ss3349802830, ss3676135240, ss3738554745, ss3749833313, ss3787072260, ss3792195735, ss3797078255, ss3832847503, ss3839986202, ss3877172239, ss3925630798, ss5203965475, ss5402353168, ss5510528143, ss5652106104, ss5837252924, ss5943437041, ss5980703631	NC_000011.9:113632290:T:C	NC_000011.10:113761568:T:C	(self)
73003259, 392461187, 27159135, 86272100, 116125845, 2330338317, ss2185849395, ss3027258232, ss3649708812, ss3692632336, ss3815163304, ss3845467926, ss3970781134, ss4900580189, ss5288961379, ss5483944523, ss5585477324, ss5752434996, ss5812791089, ss5850158042, ss5921726707	NC_000011.10:113761568:T:C	NC_000011.10:113761568:T:C	(self)
ss12155037	NT_033899.5:17175969:T:C	NC_000011.10:113761568:T:C	(self)
ss16120802, ss16538850, ss17432725, ss19211253, ss20778070	NT_033899.6:17176077:T:C	NC_000011.10:113761568:T:C	(self)
ss1340124, ss3448204, ss5606364, ss40017224, ss97512677, ss106771705, ss132840486, ss137851183, ss156812438	NT_033899.8:17194706:T:C	NC_000011.10:113761568: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 rs906847

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

rs906847