Name: rs17760268
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.

rs17760268

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:56533930 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.056523 (14961/264690, TOPMED)
T=0.056349 (7903/140252, GnomAD)
T=0.07366 (5808/78854, ALFA) (+ 18 more)
T=0.03541 (2787/78700, PAGE_STUDY)
T=0.0372 (238/6404, 1000G_30x)
T=0.0375 (188/5008, 1000G)
T=0.0464 (208/4480, Estonian)
T=0.0931 (359/3854, ALSPAC)
T=0.0863 (320/3708, TWINSUK)
T=0.0461 (96/2084, HGDP_Stanford)
T=0.0467 (54/1156, HapMap)
T=0.103 (103/998, GoNL)
T=0.064 (40/626, Chileans)
T=0.068 (41/600, NorthernSweden)
T=0.088 (19/216, Qatari)
T=0.31 (20/64, Ancient Sardinia)
T=0.07 (3/40, GENOME_DK)
C=0.50 (19/38, SGDP_PRJ)
T=0.50 (19/38, SGDP_PRJ)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC112268194 : Intron Variant
Publications: 1 citation
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	78854	C=0.92634	T=0.07366
European	Sub	61956	C=0.91722	T=0.08278
African	Sub	5638	C=0.9874	T=0.0126
African Others	Sub	182	C=1.000	T=0.000
African American	Sub	5456	C=0.9870	T=0.0130
Asian	Sub	272	C=1.000	T=0.000
East Asian	Sub	198	C=1.000	T=0.000
Other Asian	Sub	74	C=1.00	T=0.00
Latin American 1	Sub	400	C=0.943	T=0.058
Latin American 2	Sub	3384	C=0.9471	T=0.0529
South Asian	Sub	4972	C=0.9463	T=0.0537
Other	Sub	2232	C=0.9377	T=0.0623

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=0.943477	T=0.056523
gnomAD - Genomes	Global	Study-wide	140252	C=0.943651	T=0.056349
gnomAD - Genomes	European	Sub	75958	C=0.92094	T=0.07906
gnomAD - Genomes	African	Sub	42038	C=0.98363	T=0.01637
gnomAD - Genomes	American	Sub	13648	C=0.93281	T=0.06719
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9522	T=0.0478
gnomAD - Genomes	East Asian	Sub	3132	C=0.9990	T=0.0010
gnomAD - Genomes	Other	Sub	2152	C=0.9391	T=0.0609
Allele Frequency Aggregator	Total	Global	78854	C=0.92634	T=0.07366
Allele Frequency Aggregator	European	Sub	61956	C=0.91722	T=0.08278
Allele Frequency Aggregator	African	Sub	5638	C=0.9874	T=0.0126
Allele Frequency Aggregator	South Asian	Sub	4972	C=0.9463	T=0.0537
Allele Frequency Aggregator	Latin American 2	Sub	3384	C=0.9471	T=0.0529
Allele Frequency Aggregator	Other	Sub	2232	C=0.9377	T=0.0623
Allele Frequency Aggregator	Latin American 1	Sub	400	C=0.943	T=0.058
Allele Frequency Aggregator	Asian	Sub	272	C=1.000	T=0.000
The PAGE Study	Global	Study-wide	78700	C=0.96459	T=0.03541
The PAGE Study	AfricanAmerican	Sub	32516	C=0.98136	T=0.01864
The PAGE Study	Mexican	Sub	10808	C=0.94458	T=0.05542
The PAGE Study	Asian	Sub	8318	C=0.9992	T=0.0008
The PAGE Study	PuertoRican	Sub	7918	C=0.9365	T=0.0635
The PAGE Study	NativeHawaiian	Sub	4534	C=0.9727	T=0.0273
The PAGE Study	Cuban	Sub	4230	C=0.9038	T=0.0962
The PAGE Study	Dominican	Sub	3828	C=0.9376	T=0.0624
The PAGE Study	CentralAmerican	Sub	2450	C=0.9555	T=0.0445
The PAGE Study	SouthAmerican	Sub	1982	C=0.9591	T=0.0409
The PAGE Study	NativeAmerican	Sub	1260	C=0.9460	T=0.0540
The PAGE Study	SouthAsian	Sub	856	C=0.949	T=0.051
1000Genomes_30x	Global	Study-wide	6404	C=0.9628	T=0.0372
1000Genomes_30x	African	Sub	1786	C=0.9961	T=0.0039
1000Genomes_30x	Europe	Sub	1266	C=0.9155	T=0.0845
1000Genomes_30x	South Asian	Sub	1202	C=0.9517	T=0.0483
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.933	T=0.067
1000Genomes	Global	Study-wide	5008	C=0.9625	T=0.0375
1000Genomes	African	Sub	1322	C=0.9955	T=0.0045
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9165	T=0.0835
1000Genomes	South Asian	Sub	978	C=0.950	T=0.050
1000Genomes	American	Sub	694	C=0.929	T=0.071
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9536	T=0.0464
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9069	T=0.0931
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9137	T=0.0863
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	C=0.9539	T=0.0461
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	C=0.998	T=0.002
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	C=0.947	T=0.053
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	C=0.903	T=0.097
HGDP-CEPH-db Supplement 1	Europe	Sub	320	C=0.887	T=0.113
HGDP-CEPH-db Supplement 1	Africa	Sub	242	C=1.000	T=0.000
HGDP-CEPH-db Supplement 1	America	Sub	216	C=0.986	T=0.014
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	C=1.00	T=0.00
HapMap	Global	Study-wide	1156	C=0.9533	T=0.0467
HapMap	American	Sub	592	C=0.943	T=0.057
HapMap	African	Sub	300	C=0.997	T=0.003
HapMap	Europe	Sub	174	C=0.891	T=0.109
HapMap	Asian	Sub	90	C=1.00	T=0.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.897	T=0.103
Chileans	Chilean	Study-wide	626	C=0.936	T=0.064
Northern Sweden	ACPOP	Study-wide	600	C=0.932	T=0.068
Qatari	Global	Study-wide	216	C=0.912	T=0.088
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	64	C=0.69	T=0.31
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	T=0.07
SGDP_PRJ	Global	Study-wide	38	C=0.50	T=0.50
Siberian	Global	Study-wide	2	C=0.5	T=0.5

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 17	NC_000017.11:g.56533930C>T
GRCh37.p13 chr 17	NC_000017.10:g.54611291C>T

Gene: LOC112268194, uncharacterized LOC112268194 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC112268194 transcript	XR_002958121.1: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	C=	T
GRCh38.p14 chr 17	NC_000017.11:g.56533930=	NC_000017.11:g.56533930C>T
GRCh37.p13 chr 17	NC_000017.10:g.54611291=	NC_000017.10:g.54611291C>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#.

69 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24703436	Sep 20, 2004 (123)
2	AFFY	ss66230356	Dec 01, 2006 (127)
3	ILLUMINA	ss67193633	Dec 01, 2006 (127)
4	ILLUMINA	ss67578259	Dec 01, 2006 (127)
5	ILLUMINA	ss68186731	Dec 12, 2006 (127)
6	PERLEGEN	ss69198738	May 17, 2007 (127)
7	ILLUMINA	ss70671808	May 25, 2008 (130)
8	ILLUMINA	ss71234338	May 17, 2007 (127)
9	ILLUMINA	ss75713644	Dec 07, 2007 (129)
10	AFFY	ss76376356	Dec 08, 2007 (130)
11	HGSV	ss77755371	Dec 07, 2007 (129)
12	KRIBB_YJKIM	ss85403556	Dec 15, 2007 (130)
13	ILLUMINA	ss153717917	Dec 01, 2009 (131)
14	ILLUMINA	ss159326132	Dec 01, 2009 (131)
15	ILLUMINA	ss172892367	Jul 04, 2010 (132)
16	AFFY	ss173418076	Jul 04, 2010 (132)
17	1000GENOMES	ss237278132	Jul 15, 2010 (132)
18	ILLUMINA	ss536984361	Sep 08, 2015 (146)
19	ILLUMINA	ss832838152	Jul 13, 2019 (153)
20	EVA-GONL	ss993203624	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1081124105	Aug 21, 2014 (142)
22	1000GENOMES	ss1359027662	Aug 21, 2014 (142)
23	EVA_GENOME_DK	ss1578195490	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1635839512	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1678833545	Apr 01, 2015 (144)
26	EVA_DECODE	ss1697249985	Apr 01, 2015 (144)
27	EVA_SVP	ss1713589187	Apr 01, 2015 (144)
28	WEILL_CORNELL_DGM	ss1936665017	Feb 12, 2016 (147)
29	ILLUMINA	ss1959756176	Feb 12, 2016 (147)
30	JJLAB	ss2029108305	Sep 14, 2016 (149)
31	ILLUMINA	ss2094801533	Dec 20, 2016 (150)
32	ILLUMINA	ss2095075947	Dec 20, 2016 (150)
33	USC_VALOUEV	ss2157585638	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2217593955	Dec 20, 2016 (150)
35	GNOMAD	ss2950973363	Nov 08, 2017 (151)
36	SWEGEN	ss3015692765	Nov 08, 2017 (151)
37	ILLUMINA	ss3021790622	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3028376505	Nov 08, 2017 (151)
39	CSHL	ss3351785046	Nov 08, 2017 (151)
40	ILLUMINA	ss3627691084	Oct 12, 2018 (152)
41	ILLUMINA	ss3638167181	Oct 12, 2018 (152)
42	ILLUMINA	ss3639092249	Oct 12, 2018 (152)
43	ILLUMINA	ss3639854488	Oct 12, 2018 (152)
44	ILLUMINA	ss3643145145	Oct 12, 2018 (152)
45	ILLUMINA	ss3643903870	Oct 12, 2018 (152)
46	ILLUMINA	ss3652207939	Oct 12, 2018 (152)
47	ILLUMINA	ss3652207940	Oct 12, 2018 (152)
48	EGCUT_WGS	ss3682570300	Jul 13, 2019 (153)
49	EVA_DECODE	ss3700656050	Jul 13, 2019 (153)
50	ILLUMINA	ss3725630970	Jul 13, 2019 (153)
51	ACPOP	ss3742107390	Jul 13, 2019 (153)
52	EVA	ss3754779705	Jul 13, 2019 (153)
53	PAGE_CC	ss3771935106	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3820045812	Jul 13, 2019 (153)
55	EVA	ss3834914884	Apr 27, 2020 (154)
56	HGDP	ss3847566722	Apr 27, 2020 (154)
57	SGDP_PRJ	ss3885947874	Apr 27, 2020 (154)
58	EVA	ss3985796162	Apr 27, 2021 (155)
59	EVA	ss4017771874	Apr 27, 2021 (155)
60	TOPMED	ss5039298307	Apr 27, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5303467113	Oct 16, 2022 (156)
62	EVA	ss5428195601	Oct 16, 2022 (156)
63	HUGCELL_USP	ss5496480437	Oct 16, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5607352889	Oct 16, 2022 (156)
65	SANFORD_IMAGENETICS	ss5624399469	Oct 16, 2022 (156)
66	SANFORD_IMAGENETICS	ss5660289417	Oct 16, 2022 (156)
67	EVA	ss5834112890	Oct 16, 2022 (156)
68	EVA	ss5914308479	Oct 16, 2022 (156)
69	EVA	ss5951682199	Oct 16, 2022 (156)
70	1000Genomes	NC_000017.10 - 54611291	Oct 12, 2018 (152)
71	1000Genomes_30x	NC_000017.11 - 56533930	Oct 16, 2022 (156)
72	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 54611291	Oct 12, 2018 (152)
73	Chileans	NC_000017.10 - 54611291	Apr 27, 2020 (154)
74	Genetic variation in the Estonian population	NC_000017.10 - 54611291	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000017.10 - 54611291	Apr 27, 2020 (154)
76	gnomAD - Genomes	NC_000017.11 - 56533930	Apr 27, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000017.10 - 54611291	Apr 27, 2020 (154)
78	HGDP-CEPH-db Supplement 1	NC_000017.9 - 51966290	Apr 27, 2020 (154)
79	HapMap	NC_000017.11 - 56533930	Apr 27, 2020 (154)
80	Northern Sweden	NC_000017.10 - 54611291	Jul 13, 2019 (153)
81	The PAGE Study	NC_000017.11 - 56533930	Jul 13, 2019 (153)
82	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000017.10 - 54611291	Apr 27, 2021 (155)
83	Qatari	NC_000017.10 - 54611291	Apr 27, 2020 (154)
84	SGDP_PRJ	NC_000017.10 - 54611291	Apr 27, 2020 (154)
85	Siberian	NC_000017.10 - 54611291	Apr 27, 2020 (154)
86	TopMed	NC_000017.11 - 56533930	Apr 27, 2021 (155)
87	UK 10K study - Twins	NC_000017.10 - 54611291	Oct 12, 2018 (152)
88	ALFA	NC_000017.11 - 56533930	Apr 27, 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)
rs56480660	May 25, 2008 (130)
rs59898879	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
244614, ss77755371, ss1697249985, ss1713589187, ss3639092249, ss3639854488, ss3643145145, ss3643903870, ss3847566722	NC_000017.9:51966289:C:T	NC_000017.11:56533929:C:T	(self)
72283618, 40056331, 183274, 28308548, 4396212, 17851379, 15392255, 1022089, 18706939, 37964854, 10101992, 40056331, ss237278132, ss536984361, ss832838152, ss993203624, ss1081124105, ss1359027662, ss1578195490, ss1635839512, ss1678833545, ss1936665017, ss1959756176, ss2029108305, ss2094801533, ss2095075947, ss2157585638, ss2950973363, ss3015692765, ss3021790622, ss3351785046, ss3627691084, ss3638167181, ss3652207939, ss3652207940, ss3682570300, ss3742107390, ss3754779705, ss3834914884, ss3885947874, ss3985796162, ss4017771874, ss5428195601, ss5624399469, ss5660289417, ss5834112890, ss5951682199	NC_000017.10:54611290:C:T	NC_000017.11:56533929:C:T	(self)
94878824, 510045896, 1505025, 1156575, 254843969, 10471358344, ss2217593955, ss3028376505, ss3700656050, ss3725630970, ss3771935106, ss3820045812, ss5039298307, ss5303467113, ss5496480437, ss5607352889, ss5914308479	NC_000017.11:56533929:C:T	NC_000017.11:56533929:C:T	(self)
ss24703436, ss66230356, ss67193633, ss67578259, ss68186731, ss69198738, ss70671808, ss71234338, ss75713644, ss76376356, ss85403556, ss153717917, ss159326132, ss172892367, ss173418076	NT_010783.15:19885442:C:T	NC_000017.11:56533929:C:T	(self)

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

1 citation for rs17760268

PMID	Title	Author	Year	Journal
23936387	A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease.	Östensson M et al.	2013	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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs17760268