Name: rs894517
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.

rs894517

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:27201742 (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: G=0.265775 (70348/264690, TOPMED)
C=0.36227 (10237/28258, 14KJPN)
C=0.36031 (6038/16758, 8.3KJPN) (+ 16 more)
G=0.11961 (1653/13820, ALFA)
G=0.3203 (2051/6404, 1000G_30x)
G=0.3217 (1611/5008, 1000G)
G=0.2397 (1074/4480, Estonian)
G=0.2291 (883/3854, ALSPAC)
G=0.2287 (848/3708, TWINSUK)
C=0.4420 (1295/2930, KOREAN)
G=0.3206 (606/1890, HapMap)
G=0.251 (250/998, GoNL)
G=0.255 (153/600, NorthernSweden)
C=0.343 (118/344, SGDP_PRJ)
G=0.287 (62/216, Qatari)
C=0.500 (108/216, Vietnamese)
G=0.500 (108/216, Vietnamese)
G=0.30 (12/40, GENOME_DK)
C=0.38 (12/32, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BBOX1-AS1 : Intron Variant
LOC124902651 : 2KB Upstream 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	13820	C=0.88039	A=0.00000, G=0.11961, T=0.00000
European	Sub	11142	C=0.85927	A=0.00000, G=0.14073, T=0.00000
African	Sub	1874	C=0.9835	A=0.0000, G=0.0165, T=0.0000
African Others	Sub	86	C=0.98	A=0.00, G=0.02, T=0.00
African American	Sub	1788	C=0.9838	A=0.0000, G=0.0162, T=0.0000
Asian	Sub	26	C=0.92	A=0.00, G=0.08, T=0.00
East Asian	Sub	24	C=0.92	A=0.00, G=0.08, T=0.00
Other Asian	Sub	2	C=1.0	A=0.0, G=0.0, T=0.0
Latin American 1	Sub	62	C=1.00	A=0.00, G=0.00, T=0.00
Latin American 2	Sub	174	C=1.000	A=0.000, G=0.000, T=0.000
South Asian	Sub	56	C=1.00	A=0.00, G=0.00, T=0.00
Other	Sub	486	C=0.893	A=0.000, G=0.107, T=0.000

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=0.734225	G=0.265775
14KJPN	JAPANESE	Study-wide	28258	C=0.36227	G=0.63773
8.3KJPN	JAPANESE	Study-wide	16758	C=0.36031	G=0.63969
Allele Frequency Aggregator	Total	Global	13820	C=0.88039	A=0.00000, G=0.11961, T=0.00000
Allele Frequency Aggregator	European	Sub	11142	C=0.85927	A=0.00000, G=0.14073, T=0.00000
Allele Frequency Aggregator	African	Sub	1874	C=0.9835	A=0.0000, G=0.0165, T=0.0000
Allele Frequency Aggregator	Other	Sub	486	C=0.893	A=0.000, G=0.107, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	174	C=1.000	A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	62	C=1.00	A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	56	C=1.00	A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	26	C=0.92	A=0.00, G=0.08, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.6797	G=0.3203
1000Genomes_30x	African	Sub	1786	C=0.7637	G=0.2363
1000Genomes_30x	Europe	Sub	1266	C=0.7646	G=0.2354
1000Genomes_30x	South Asian	Sub	1202	C=0.7646	G=0.2354
1000Genomes_30x	East Asian	Sub	1170	C=0.4462	G=0.5538
1000Genomes_30x	American	Sub	980	C=0.592	G=0.408
1000Genomes	Global	Study-wide	5008	C=0.6783	G=0.3217
1000Genomes	African	Sub	1322	C=0.7655	G=0.2345
1000Genomes	East Asian	Sub	1008	C=0.4464	G=0.5536
1000Genomes	Europe	Sub	1006	C=0.7704	G=0.2296
1000Genomes	South Asian	Sub	978	C=0.769	G=0.231
1000Genomes	American	Sub	694	C=0.588	G=0.412
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7603	G=0.2397
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7709	G=0.2291
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7713	G=0.2287
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4420	A=0.0000, G=0.5580, T=0.0000
HapMap	Global	Study-wide	1890	C=0.6794	G=0.3206
HapMap	American	Sub	770	C=0.666	G=0.334
HapMap	African	Sub	690	C=0.793	G=0.207
HapMap	Asian	Sub	254	C=0.394	G=0.606
HapMap	Europe	Sub	176	C=0.705	G=0.295
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.749	G=0.251
Northern Sweden	ACPOP	Study-wide	600	C=0.745	G=0.255
SGDP_PRJ	Global	Study-wide	344	C=0.343	G=0.657
Qatari	Global	Study-wide	216	C=0.713	G=0.287
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.500	G=0.500
The Danish reference pan genome	Danish	Study-wide	40	C=0.70	G=0.30
Siberian	Global	Study-wide	32	C=0.38	G=0.62

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.27201742C>A
GRCh38.p14 chr 11	NC_000011.10:g.27201742C>G
GRCh38.p14 chr 11	NC_000011.10:g.27201742C>T
GRCh37.p13 chr 11	NC_000011.9:g.27223289C>A
GRCh37.p13 chr 11	NC_000011.9:g.27223289C>G
GRCh37.p13 chr 11	NC_000011.9:g.27223289C>T

Gene: BBOX1-AS1, BBOX1 antisense RNA 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BBOX1-AS1 transcript variant 1	NR_125766.1:n.	N/A	Intron Variant
BBOX1-AS1 transcript variant 2	NR_125767.1:n.	N/A	Intron Variant
BBOX1-AS1 transcript variant 3	NR_125768.1:n.	N/A	Intron Variant

Gene: LOC124902651, uncharacterized LOC124902651 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124902651 transcript variant X1	XR_007062631.1:n.	N/A	Upstream Transcript Variant
LOC124902651 transcript variant X2	XR_007062632.1:n.	N/A	Upstream 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	C=	A	G	T
GRCh38.p14 chr 11	NC_000011.10:g.27201742=	NC_000011.10:g.27201742C>A	NC_000011.10:g.27201742C>G	NC_000011.10:g.27201742C>T
GRCh37.p13 chr 11	NC_000011.9:g.27223289=	NC_000011.9:g.27223289C>A	NC_000011.9:g.27223289C>G	NC_000011.9:g.27223289C>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#.

75 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1324598	Oct 05, 2000 (86)
2	PERLEGEN	ss24149016	Sep 20, 2004 (123)
3	AFFY	ss66367488	Nov 30, 2006 (127)
4	PERLEGEN	ss69313727	May 17, 2007 (127)
5	AFFY	ss76091370	Dec 08, 2007 (130)
6	KRIBB_YJKIM	ss81443319	Dec 17, 2007 (130)
7	HGSV	ss81749472	Dec 15, 2007 (130)
8	BGI	ss102951369	Dec 01, 2009 (131)
9	1000GENOMES	ss110240112	Jan 24, 2009 (130)
10	1000GENOMES	ss114390993	Jan 25, 2009 (130)
11	GMI	ss156094725	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss168100148	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss169473757	Jul 04, 2010 (132)
14	AFFY	ss172473426	Jul 04, 2010 (132)
15	BUSHMAN	ss202530796	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss207650259	Jul 04, 2010 (132)
17	1000GENOMES	ss225162298	Jul 14, 2010 (132)
18	1000GENOMES	ss235498453	Jul 15, 2010 (132)
19	1000GENOMES	ss242143085	Jul 15, 2010 (132)
20	BL	ss255001008	May 09, 2011 (134)
21	GMI	ss280938050	May 04, 2012 (137)
22	GMI	ss286343594	Apr 25, 2013 (138)
23	PJP	ss291207957	May 09, 2011 (134)
24	TISHKOFF	ss562465367	Apr 25, 2013 (138)
25	SSMP	ss657955658	Apr 25, 2013 (138)
26	EVA-GONL	ss988343291	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1077603909	Aug 21, 2014 (142)
28	1000GENOMES	ss1340597680	Aug 21, 2014 (142)
29	DDI	ss1426582035	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1575610380	Apr 01, 2015 (144)
31	EVA_DECODE	ss1598019387	Apr 01, 2015 (144)
32	EVA_UK10K_ALSPAC	ss1626244549	Apr 01, 2015 (144)
33	EVA_UK10K_TWINSUK	ss1669238582	Apr 01, 2015 (144)
34	EVA_SVP	ss1713244018	Apr 01, 2015 (144)
35	WEILL_CORNELL_DGM	ss1931704837	Feb 12, 2016 (147)
36	GENOMED	ss1967327841	Jul 19, 2016 (147)
37	JJLAB	ss2026600089	Sep 14, 2016 (149)
38	ILLUMINA	ss2094790354	Dec 20, 2016 (150)
39	ILLUMINA	ss2095020988	Dec 20, 2016 (150)
40	USC_VALOUEV	ss2154888551	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2181164931	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2627772956	Nov 08, 2017 (151)
43	GRF	ss2699166252	Nov 08, 2017 (151)
44	GNOMAD	ss2897667076	Nov 08, 2017 (151)
45	AFFY	ss2984938131	Nov 08, 2017 (151)
46	AFFY	ss2985583195	Nov 08, 2017 (151)
47	SWEGEN	ss3007797164	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3027098554	Nov 08, 2017 (151)
49	CSHL	ss3349516357	Nov 08, 2017 (151)
50	ILLUMINA	ss3651683557	Oct 12, 2018 (152)
51	ILLUMINA	ss3653709980	Oct 12, 2018 (152)
52	EGCUT_WGS	ss3675199082	Jul 13, 2019 (153)
53	EVA_DECODE	ss3691454316	Jul 13, 2019 (153)
54	ACPOP	ss3738034221	Jul 13, 2019 (153)
55	EVA	ss3749093191	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3814444777	Jul 13, 2019 (153)
57	EVA	ss3832547131	Apr 26, 2020 (154)
58	EVA	ss3839824227	Apr 26, 2020 (154)
59	EVA	ss3845301568	Apr 26, 2020 (154)
60	SGDP_PRJ	ss3875904355	Apr 26, 2020 (154)
61	KRGDB	ss3924148527	Apr 26, 2020 (154)
62	TOPMED	ss4879318813	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5201214337	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5286822697	Oct 16, 2022 (156)
65	EVA	ss5398501929	Oct 16, 2022 (156)
66	HUGCELL_USP	ss5482080664	Oct 16, 2022 (156)
67	EVA	ss5510298195	Oct 16, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5582162754	Oct 16, 2022 (156)
69	SANFORD_IMAGENETICS	ss5650884487	Oct 16, 2022 (156)
70	TOMMO_GENOMICS	ss5748116313	Oct 16, 2022 (156)
71	YY_MCH	ss5812238496	Oct 16, 2022 (156)
72	EVA	ss5836431596	Oct 16, 2022 (156)
73	EVA	ss5849916128	Oct 16, 2022 (156)
74	EVA	ss5919310981	Oct 16, 2022 (156)
75	EVA	ss5942193300	Oct 16, 2022 (156)
76	1000Genomes	NC_000011.9 - 27223289	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000011.10 - 27201742	Oct 16, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 27223289	Oct 12, 2018 (152)
79	Genetic variation in the Estonian population	NC_000011.9 - 27223289	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000011.9 - 27223289	Apr 26, 2020 (154)
81	gnomAD - Genomes Submission ignored due to conflicting rows: Row 374761022 (NC_000011.10:27201741:C:A 1/140122) Row 374761023 (NC_000011.10:27201741:C:G 34614/140078) Row 374761024 (NC_000011.10:27201741:C:T 1/140122)	-	Apr 26, 2021 (155)
82	gnomAD - Genomes Submission ignored due to conflicting rows: Row 374761022 (NC_000011.10:27201741:C:A 1/140122) Row 374761023 (NC_000011.10:27201741:C:G 34614/140078) Row 374761024 (NC_000011.10:27201741:C:T 1/140122)	-	Apr 26, 2021 (155)
83	gnomAD - Genomes Submission ignored due to conflicting rows: Row 374761022 (NC_000011.10:27201741:C:A 1/140122) Row 374761023 (NC_000011.10:27201741:C:G 34614/140078) Row 374761024 (NC_000011.10:27201741:C:T 1/140122)	-	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000011.9 - 27223289	Apr 26, 2020 (154)
85	HapMap	NC_000011.10 - 27201742	Apr 26, 2020 (154)
86	KOREAN population from KRGDB	NC_000011.9 - 27223289	Apr 26, 2020 (154)
87	Northern Sweden	NC_000011.9 - 27223289	Jul 13, 2019 (153)
88	Qatari	NC_000011.9 - 27223289	Apr 26, 2020 (154)
89	SGDP_PRJ	NC_000011.9 - 27223289	Apr 26, 2020 (154)
90	Siberian	NC_000011.9 - 27223289	Apr 26, 2020 (154)
91	8.3KJPN	NC_000011.9 - 27223289	Apr 26, 2021 (155)
92	14KJPN	NC_000011.10 - 27201742	Oct 16, 2022 (156)
93	TopMed	NC_000011.10 - 27201742	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000011.9 - 27223289	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000011.9 - 27223289	Jul 13, 2019 (153)
96	ALFA	NC_000011.10 - 27201742	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)
rs56620496	May 24, 2008 (130)
rs58538756	May 24, 2008 (130)
rs61725997	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
31325921, ss3924148527	NC_000011.9:27223288:C:A	NC_000011.10:27201741:C:A	(self)
1338766926	NC_000011.10:27201741:C:A	NC_000011.10:27201741:C:A	(self)
ss66367488, ss76091370, ss81749472, ss110240112, ss114390993, ss168100148, ss169473757, ss172473426, ss202530796, ss207650259, ss255001008, ss280938050, ss286343594, ss291207957, ss1598019387, ss1713244018	NC_000011.8:27179864:C:G	NC_000011.10:27201741:C:G	(self)
53098273, 29496469, 20937330, 2499103, 13158847, 31325921, 11319086, 13746767, 27921335, 7404905, 59183644, 29496469, 6553988, ss225162298, ss235498453, ss242143085, ss562465367, ss657955658, ss988343291, ss1077603909, ss1340597680, ss1426582035, ss1575610380, ss1626244549, ss1669238582, ss1931704837, ss1967327841, ss2026600089, ss2094790354, ss2095020988, ss2154888551, ss2627772956, ss2699166252, ss2897667076, ss2984938131, ss2985583195, ss3007797164, ss3349516357, ss3651683557, ss3653709980, ss3675199082, ss3738034221, ss3749093191, ss3832547131, ss3839824227, ss3875904355, ss3924148527, ss5201214337, ss5398501929, ss5510298195, ss5650884487, ss5836431596, ss5942193300	NC_000011.9:27223288:C:G	NC_000011.10:27201741:C:G	(self)
69688689, 578139, 81953417, 94864469, 1338766926, ss2181164931, ss3027098554, ss3691454316, ss3814444777, ss3845301568, ss4879318813, ss5286822697, ss5482080664, ss5582162754, ss5748116313, ss5812238496, ss5849916128, ss5919310981	NC_000011.10:27201741:C:G	NC_000011.10:27201741:C:G	(self)
ss1324598, ss24149016, ss69313727, ss81443319, ss102951369, ss156094725	NT_009237.18:27163288:C:G	NC_000011.10:27201741:C:G	(self)
31325921, ss3924148527	NC_000011.9:27223288:C:T	NC_000011.10:27201741:C:T	(self)
1338766926	NC_000011.10:27201741:C:T	NC_000011.10:27201741: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 rs894517

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

rs894517