Name: rs11040825
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.

rs11040825

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:6265799 (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: C=0.168457 (44589/264690, TOPMED)
C=0.178362 (24995/140136, GnomAD)
C=0.20586 (19392/94202, ALFA) (+ 20 more)
C=0.09647 (2726/28258, 14KJPN)
C=0.09619 (1612/16758, 8.3KJPN)
C=0.1318 (844/6404, 1000G_30x)
C=0.1334 (668/5008, 1000G)
C=0.2268 (1016/4480, Estonian)
C=0.2008 (774/3854, ALSPAC)
C=0.2050 (760/3708, TWINSUK)
C=0.0715 (209/2922, KOREAN)
C=0.1763 (367/2082, HGDP_Stanford)
C=0.1527 (288/1886, HapMap)
C=0.0852 (156/1832, Korea1K)
C=0.200 (200/998, GoNL)
C=0.228 (137/600, NorthernSweden)
C=0.310 (67/216, Qatari)
C=0.160 (34/212, Vietnamese)
T=0.434 (72/166, SGDP_PRJ)
C=0.32 (24/74, Ancient Sardinia)
C=0.25 (10/40, GENOME_DK)
T=0.50 (6/12, Siberian)
C=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CCKBR : 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	94202	T=0.79414	C=0.20586
European	Sub	78266	T=0.78724	C=0.21276
African	Sub	4524	T=0.8630	C=0.1370
African Others	Sub	170	T=0.900	C=0.100
African American	Sub	4354	T=0.8615	C=0.1385
Asian	Sub	190	T=0.884	C=0.116
East Asian	Sub	148	T=0.926	C=0.074
Other Asian	Sub	42	T=0.74	C=0.26
Latin American 1	Sub	254	T=0.780	C=0.220
Latin American 2	Sub	1232	T=0.8604	C=0.1396
South Asian	Sub	4956	T=0.8309	C=0.1691
Other	Sub	4780	T=0.7841	C=0.2159

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=0.831543	C=0.168457
gnomAD - Genomes	Global	Study-wide	140136	T=0.821638	C=0.178362
gnomAD - Genomes	European	Sub	75882	T=0.79371	C=0.20629
gnomAD - Genomes	African	Sub	41992	T=0.86578	C=0.13422
gnomAD - Genomes	American	Sub	13656	T=0.85391	C=0.14609
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.7339	C=0.2661
gnomAD - Genomes	East Asian	Sub	3130	T=0.8658	C=0.1342
gnomAD - Genomes	Other	Sub	2154	T=0.8115	C=0.1885
Allele Frequency Aggregator	Total	Global	94202	T=0.79414	C=0.20586
Allele Frequency Aggregator	European	Sub	78266	T=0.78724	C=0.21276
Allele Frequency Aggregator	South Asian	Sub	4956	T=0.8309	C=0.1691
Allele Frequency Aggregator	Other	Sub	4780	T=0.7841	C=0.2159
Allele Frequency Aggregator	African	Sub	4524	T=0.8630	C=0.1370
Allele Frequency Aggregator	Latin American 2	Sub	1232	T=0.8604	C=0.1396
Allele Frequency Aggregator	Latin American 1	Sub	254	T=0.780	C=0.220
Allele Frequency Aggregator	Asian	Sub	190	T=0.884	C=0.116
14KJPN	JAPANESE	Study-wide	28258	T=0.90353	C=0.09647
8.3KJPN	JAPANESE	Study-wide	16758	T=0.90381	C=0.09619
1000Genomes_30x	Global	Study-wide	6404	T=0.8682	C=0.1318
1000Genomes_30x	African	Sub	1786	T=0.8992	C=0.1008
1000Genomes_30x	Europe	Sub	1266	T=0.8246	C=0.1754
1000Genomes_30x	South Asian	Sub	1202	T=0.8702	C=0.1298
1000Genomes_30x	East Asian	Sub	1170	T=0.8667	C=0.1333
1000Genomes_30x	American	Sub	980	T=0.867	C=0.133
1000Genomes	Global	Study-wide	5008	T=0.8666	C=0.1334
1000Genomes	African	Sub	1322	T=0.9047	C=0.0953
1000Genomes	East Asian	Sub	1008	T=0.8681	C=0.1319
1000Genomes	Europe	Sub	1006	T=0.8211	C=0.1789
1000Genomes	South Asian	Sub	978	T=0.864	C=0.136
1000Genomes	American	Sub	694	T=0.862	C=0.138
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7732	C=0.2268
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7992	C=0.2008
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7950	C=0.2050
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9285	C=0.0715
HGDP-CEPH-db Supplement 1	Global	Study-wide	2082	T=0.8237	C=0.1763
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	T=0.902	C=0.098
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.797	C=0.203
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.663	C=0.337
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.762	C=0.237
HGDP-CEPH-db Supplement 1	Africa	Sub	240	T=0.846	C=0.154
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.991	C=0.009
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=0.94	C=0.06
HapMap	Global	Study-wide	1886	T=0.8473	C=0.1527
HapMap	American	Sub	766	T=0.849	C=0.151
HapMap	African	Sub	690	T=0.845	C=0.155
HapMap	Asian	Sub	254	T=0.894	C=0.106
HapMap	Europe	Sub	176	T=0.784	C=0.216
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9148	C=0.0852
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.800	C=0.200
Northern Sweden	ACPOP	Study-wide	600	T=0.772	C=0.228
Qatari	Global	Study-wide	216	T=0.690	C=0.310
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.840	C=0.160
SGDP_PRJ	Global	Study-wide	166	T=0.434	C=0.566
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	74	T=0.68	C=0.32
The Danish reference pan genome	Danish	Study-wide	40	T=0.75	C=0.25
Siberian	Global	Study-wide	12	T=0.50	C=0.50

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.6265799T>C
GRCh37.p13 chr 11	NC_000011.9:g.6287029T>C
CCKBR RefSeqGene	NG_030591.1:g.11126T>C

Gene: CCKBR, cholecystokinin B receptor (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CCKBR transcript variant 2	NM_001318029.2:c.152-4289… NM_001318029.2:c.152-4289T>C	N/A	Intron Variant
CCKBR transcript variant 3	NM_001363552.2:c.152-3870… NM_001363552.2:c.152-3870T>C	N/A	Intron Variant
CCKBR transcript variant 1	NM_176875.4:c.152-3870T>C	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.6265799=	NC_000011.10:g.6265799T>C
GRCh37.p13 chr 11	NC_000011.9:g.6287029=	NC_000011.9:g.6287029T>C
CCKBR RefSeqGene	NG_030591.1:g.11126=	NG_030591.1:g.11126T>C
CCKBR transcript variant 2	NM_001318029.2:c.152-4289=	NM_001318029.2:c.152-4289T>C
CCKBR transcript variant 3	NM_001363552.2:c.152-3870=	NM_001363552.2:c.152-3870T>C
CCKBR transcript variant 1	NM_176875.3:c.152-3870=	NM_176875.3:c.152-3870T>C
CCKBR transcript variant 1	NM_176875.4:c.152-3870=	NM_176875.4:c.152-3870T>C
CCKBR transcript variant X1	XM_005253210.1:c.152-3870=	XM_005253210.1:c.152-3870T>C
CCKBR transcript variant X2	XM_005253211.1:c.152-3870=	XM_005253211.1:c.152-3870T>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#.

84 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss16118282	Feb 27, 2004 (120)
2	SC_SNP	ss18461583	Feb 27, 2004 (120)
3	ABI	ss38724681	Mar 15, 2006 (126)
4	ILLUMINA	ss66916803	Dec 01, 2006 (127)
5	ILLUMINA	ss67056501	Dec 01, 2006 (127)
6	ILLUMINA	ss68098381	Dec 12, 2006 (127)
7	ILLUMINA	ss70514561	May 25, 2008 (130)
8	ILLUMINA	ss71042589	May 18, 2007 (127)
9	ILLUMINA	ss75877202	Dec 06, 2007 (129)
10	KRIBB_YJKIM	ss85055752	Dec 15, 2007 (130)
11	BCMHGSC_JDW	ss88448569	Mar 23, 2008 (129)
12	1000GENOMES	ss109941450	Jan 24, 2009 (130)
13	1000GENOMES	ss114149927	Jan 25, 2009 (130)
14	ILLUMINA-UK	ss118480469	Feb 14, 2009 (130)
15	ENSEMBL	ss132018825	Dec 01, 2009 (131)
16	ILLUMINA	ss152911174	Dec 01, 2009 (131)
17	ILLUMINA	ss159160082	Dec 01, 2009 (131)
18	COMPLETE_GENOMICS	ss167733883	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss168970584	Jul 04, 2010 (132)
20	ILLUMINA	ss170951344	Jul 04, 2010 (132)
21	1000GENOMES	ss225070875	Jul 14, 2010 (132)
22	1000GENOMES	ss235430848	Jul 15, 2010 (132)
23	1000GENOMES	ss242087909	Jul 15, 2010 (132)
24	GMI	ss280869944	May 04, 2012 (137)
25	ILLUMINA	ss536666621	Sep 08, 2015 (146)
26	TISHKOFF	ss562360656	Apr 25, 2013 (138)
27	SSMP	ss657719644	Apr 25, 2013 (138)
28	ILLUMINA	ss832672665	Jul 13, 2019 (153)
29	EVA-GONL	ss988169598	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1077472730	Aug 21, 2014 (142)
31	1000GENOMES	ss1339974543	Aug 21, 2014 (142)
32	DDI	ss1426523561	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1575498470	Apr 01, 2015 (144)
34	EVA_DECODE	ss1597845571	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1625913608	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1668907641	Apr 01, 2015 (144)
37	EVA_SVP	ss1713230329	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1806676464	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1931533662	Feb 12, 2016 (147)
40	JJLAB	ss2026507798	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2154794689	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2179896031	Dec 20, 2016 (150)
43	GRF	ss2699065026	Nov 08, 2017 (151)
44	GNOMAD	ss2895934811	Nov 08, 2017 (151)
45	SWEGEN	ss3007538556	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3027047137	Nov 08, 2017 (151)
47	CSHL	ss3349435621	Nov 08, 2017 (151)
48	ILLUMINA	ss3626590875	Oct 12, 2018 (152)
49	ILLUMINA	ss3637888640	Oct 12, 2018 (152)
50	ILLUMINA	ss3638959477	Oct 12, 2018 (152)
51	ILLUMINA	ss3639790946	Oct 12, 2018 (152)
52	ILLUMINA	ss3642888564	Oct 12, 2018 (152)
53	ILLUMINA	ss3643843292	Oct 12, 2018 (152)
54	URBANLAB	ss3649524557	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3674934599	Jul 13, 2019 (153)
56	EVA_DECODE	ss3691144269	Jul 13, 2019 (153)
57	ACPOP	ss3737888004	Jul 13, 2019 (153)
58	ILLUMINA	ss3744376180	Jul 13, 2019 (153)
59	EVA	ss3748898324	Jul 13, 2019 (153)
60	PACBIO	ss3786855572	Jul 13, 2019 (153)
61	PACBIO	ss3792010577	Jul 13, 2019 (153)
62	PACBIO	ss3796892602	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3814247575	Jul 13, 2019 (153)
64	EVA	ss3832458232	Apr 26, 2020 (154)
65	HGDP	ss3847408000	Apr 26, 2020 (154)
66	SGDP_PRJ	ss3875572616	Apr 26, 2020 (154)
67	KRGDB	ss3923796114	Apr 26, 2020 (154)
68	KOGIC	ss3969136578	Apr 26, 2020 (154)
69	EVA	ss3985515543	Apr 26, 2021 (155)
70	EVA	ss4017521123	Apr 26, 2021 (155)
71	TOPMED	ss4873974854	Apr 26, 2021 (155)
72	TOMMO_GENOMICS	ss5200527806	Apr 26, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5286281088	Oct 16, 2022 (156)
74	EVA	ss5397515752	Oct 16, 2022 (156)
75	HUGCELL_USP	ss5481596519	Oct 16, 2022 (156)
76	EVA	ss5510239181	Oct 16, 2022 (156)
77	1000G_HIGH_COVERAGE	ss5581340752	Oct 16, 2022 (156)
78	SANFORD_IMAGENETICS	ss5650566579	Oct 16, 2022 (156)
79	TOMMO_GENOMICS	ss5747237690	Oct 16, 2022 (156)
80	YY_MCH	ss5812098199	Oct 16, 2022 (156)
81	EVA	ss5836213559	Oct 16, 2022 (156)
82	EVA	ss5849842977	Oct 16, 2022 (156)
83	EVA	ss5918686469	Oct 16, 2022 (156)
84	EVA	ss5941869002	Oct 16, 2022 (156)
85	1000Genomes	NC_000011.9 - 6287029	Oct 12, 2018 (152)
86	1000Genomes_30x	NC_000011.10 - 6265799	Oct 16, 2022 (156)
87	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 6287029	Oct 12, 2018 (152)
88	Genetic variation in the Estonian population	NC_000011.9 - 6287029	Oct 12, 2018 (152)
89	The Danish reference pan genome	NC_000011.9 - 6287029	Apr 26, 2020 (154)
90	gnomAD - Genomes	NC_000011.10 - 6265799	Apr 26, 2021 (155)
91	Genome of the Netherlands Release 5	NC_000011.9 - 6287029	Apr 26, 2020 (154)
92	HGDP-CEPH-db Supplement 1	NC_000011.8 - 6243605	Apr 26, 2020 (154)
93	HapMap	NC_000011.10 - 6265799	Apr 26, 2020 (154)
94	KOREAN population from KRGDB	NC_000011.9 - 6287029	Apr 26, 2020 (154)
95	Korean Genome Project	NC_000011.10 - 6265799	Apr 26, 2020 (154)
96	Northern Sweden	NC_000011.9 - 6287029	Jul 13, 2019 (153)
97	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000011.9 - 6287029	Apr 26, 2021 (155)
98	Qatari	NC_000011.9 - 6287029	Apr 26, 2020 (154)
99	SGDP_PRJ	NC_000011.9 - 6287029	Apr 26, 2020 (154)
100	Siberian	NC_000011.9 - 6287029	Apr 26, 2020 (154)
101	8.3KJPN	NC_000011.9 - 6287029	Apr 26, 2021 (155)
102	14KJPN	NC_000011.10 - 6265799	Oct 16, 2022 (156)
103	TopMed	NC_000011.10 - 6265799	Apr 26, 2021 (155)
104	UK 10K study - Twins	NC_000011.9 - 6287029	Oct 12, 2018 (152)
105	A Vietnamese Genetic Variation Database	NC_000011.9 - 6287029	Jul 13, 2019 (153)
106	ALFA	NC_000011.10 - 6265799	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)
rs59859656	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
85892, ss88448569, ss109941450, ss114149927, ss118480469, ss167733883, ss168970584, ss280869944, ss1597845571, ss1713230329, ss3638959477, ss3639790946, ss3642888564, ss3643843292, ss3847408000	NC_000011.8:6243604:T:C	NC_000011.10:6265798:T:C	(self)
52452332, 29132825, 20672847, 2426601, 12989457, 30973508, 11172869, 741470, 13575592, 27589596, 7311043, 58497113, 29132825, 6466679, ss225070875, ss235430848, ss242087909, ss536666621, ss562360656, ss657719644, ss832672665, ss988169598, ss1077472730, ss1339974543, ss1426523561, ss1575498470, ss1625913608, ss1668907641, ss1806676464, ss1931533662, ss2026507798, ss2154794689, ss2699065026, ss2895934811, ss3007538556, ss3349435621, ss3626590875, ss3637888640, ss3674934599, ss3737888004, ss3744376180, ss3748898324, ss3786855572, ss3792010577, ss3796892602, ss3832458232, ss3875572616, ss3923796114, ss3985515543, ss4017521123, ss5200527806, ss5397515752, ss5510239181, ss5650566579, ss5836213559, ss5941869002	NC_000011.9:6287028:T:C	NC_000011.10:6265798:T:C	(self)
68866687, 370348688, 540928, 25514579, 81074794, 89520510, 14258130930, ss2179896031, ss3027047137, ss3649524557, ss3691144269, ss3814247575, ss3969136578, ss4873974854, ss5286281088, ss5481596519, ss5581340752, ss5747237690, ss5812098199, ss5849842977, ss5918686469	NC_000011.10:6265798:T:C	NC_000011.10:6265798:T:C	(self)
ss16118282, ss18461583	NT_009237.16:5050968:T:C	NC_000011.10:6265798:T:C	(self)
ss38724681, ss66916803, ss67056501, ss68098381, ss70514561, ss71042589, ss75877202, ss85055752, ss132018825, ss152911174, ss159160082, ss170951344	NT_009237.18:6227028:T:C	NC_000011.10:6265798: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 rs11040825

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

rs11040825