Name: rs11507987
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.

rs11507987

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:194894569 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.072526 (19197/264690, TOPMED)
T=0.069158 (9677/139926, GnomAD)
T=0.00004 (1/28256, 14KJPN) (+ 15 more)
T=0.04648 (878/18890, ALFA)
T=0.00000 (0/16760, 8.3KJPN)
T=0.0800 (512/6404, 1000G_30x)
T=0.0745 (373/5008, 1000G)
T=0.0100 (45/4480, Estonian)
T=0.0200 (77/3854, ALSPAC)
T=0.0208 (77/3708, TWINSUK)
T=0.0007 (2/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.019 (19/998, GoNL)
T=0.033 (20/600, NorthernSweden)
T=0.038 (21/554, SGDP_PRJ)
T=0.028 (6/216, Qatari)
T=0.00 (0/56, Siberian)
T=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105376755 : 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=0.04648	C=0.95352
European	Sub	14286	T=0.02023	C=0.97977
African	Sub	2946	T=0.1775	C=0.8225
African Others	Sub	114	T=0.228	C=0.772
African American	Sub	2832	T=0.1755	C=0.8245
Asian	Sub	112	T=0.009	C=0.991
East Asian	Sub	86	T=0.01	C=0.99
Other Asian	Sub	26	T=0.00	C=1.00
Latin American 1	Sub	146	T=0.068	C=0.932
Latin American 2	Sub	610	T=0.010	C=0.990
South Asian	Sub	98	T=0.04	C=0.96
Other	Sub	692	T=0.065	C=0.935

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=0.072526	C=0.927474
gnomAD - Genomes	Global	Study-wide	139926	T=0.069158	C=0.930842
gnomAD - Genomes	European	Sub	75826	T=0.01709	C=0.98291
gnomAD - Genomes	African	Sub	41896	T=0.18637	C=0.81363
gnomAD - Genomes	American	Sub	13604	T=0.02382	C=0.97618
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.0379	C=0.9621
gnomAD - Genomes	East Asian	Sub	3128	T=0.0016	C=0.9984
gnomAD - Genomes	Other	Sub	2150	T=0.0549	C=0.9451
14KJPN	JAPANESE	Study-wide	28256	T=0.00004	C=0.99996
Allele Frequency Aggregator	Total	Global	18890	T=0.04648	C=0.95352
Allele Frequency Aggregator	European	Sub	14286	T=0.02023	C=0.97977
Allele Frequency Aggregator	African	Sub	2946	T=0.1775	C=0.8225
Allele Frequency Aggregator	Other	Sub	692	T=0.065	C=0.935
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.010	C=0.990
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.068	C=0.932
Allele Frequency Aggregator	Asian	Sub	112	T=0.009	C=0.991
Allele Frequency Aggregator	South Asian	Sub	98	T=0.04	C=0.96
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00000	C=1.00000
1000Genomes_30x	Global	Study-wide	6404	T=0.0800	C=0.9200
1000Genomes_30x	African	Sub	1786	T=0.2391	C=0.7609
1000Genomes_30x	Europe	Sub	1266	T=0.0182	C=0.9818
1000Genomes_30x	South Asian	Sub	1202	T=0.0341	C=0.9659
1000Genomes_30x	East Asian	Sub	1170	T=0.0009	C=0.9991
1000Genomes_30x	American	Sub	980	T=0.020	C=0.980
1000Genomes	Global	Study-wide	5008	T=0.0745	C=0.9255
1000Genomes	African	Sub	1322	T=0.2322	C=0.7678
1000Genomes	East Asian	Sub	1008	T=0.0010	C=0.9990
1000Genomes	Europe	Sub	1006	T=0.0189	C=0.9811
1000Genomes	South Asian	Sub	978	T=0.034	C=0.966
1000Genomes	American	Sub	694	T=0.019	C=0.981
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.0100	C=0.9900
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0200	C=0.9800
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0208	C=0.9792
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0007	A=0.0003, C=0.9990, G=0.0000
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=0.019	C=0.981
Northern Sweden	ACPOP	Study-wide	600	T=0.033	C=0.967
SGDP_PRJ	Global	Study-wide	554	T=0.038	C=0.962
Qatari	Global	Study-wide	216	T=0.028	C=0.972
Siberian	Global	Study-wide	56	T=0.00	C=1.00
The Danish reference pan genome	Danish	Study-wide	40	T=0.00	C=1.00

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 2	NC_000002.12:g.194894569T>A
GRCh38.p14 chr 2	NC_000002.12:g.194894569T>C
GRCh38.p14 chr 2	NC_000002.12:g.194894569T>G
GRCh37.p13 chr 2	NC_000002.11:g.195759293T>A
GRCh37.p13 chr 2	NC_000002.11:g.195759293T>C
GRCh37.p13 chr 2	NC_000002.11:g.195759293T>G

Gene: LOC105376755, uncharacterized LOC105376755 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105376755 transcript variant X3	XR_007088699.1:n.	N/A	Intron Variant
LOC105376755 transcript variant X1	XR_001739834.1:n.	N/A	Genic Downstream Transcript Variant
LOC105376755 transcript variant X2	XR_001739835.1: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	G
GRCh38.p14 chr 2	NC_000002.12:g.194894569=	NC_000002.12:g.194894569T>A	NC_000002.12:g.194894569T>C	NC_000002.12:g.194894569T>G
GRCh37.p13 chr 2	NC_000002.11:g.195759293=	NC_000002.11:g.195759293T>A	NC_000002.11:g.195759293T>C	NC_000002.11:g.195759293T>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#.

75 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss15722249	Feb 28, 2004 (120)
2	SC_SNP	ss18067792	Feb 28, 2004 (126)
3	SSAHASNP	ss21685371	Apr 05, 2004 (126)
4	HGSV	ss77722166	Dec 07, 2007 (129)
5	BCMHGSC_JDW	ss91497125	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96461079	Feb 04, 2009 (130)
7	BGI	ss106151916	Feb 04, 2009 (130)
8	1000GENOMES	ss110523761	Jan 24, 2009 (130)
9	1000GENOMES	ss111469215	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss118028694	Dec 01, 2009 (131)
11	ENSEMBL	ss136014258	Dec 01, 2009 (131)
12	ENSEMBL	ss138605447	Dec 01, 2009 (131)
13	GMI	ss154522402	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss165193281	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss165789921	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss167514556	Jul 04, 2010 (132)
17	BUSHMAN	ss201560603	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss205714425	Jul 04, 2010 (132)
19	1000GENOMES	ss219735757	Jul 14, 2010 (132)
20	1000GENOMES	ss231531076	Jul 14, 2010 (132)
21	1000GENOMES	ss239005431	Jul 15, 2010 (132)
22	BL	ss253788156	May 09, 2011 (134)
23	GMI	ss276847648	May 04, 2012 (137)
24	GMI	ss284514775	Apr 25, 2013 (138)
25	PJP	ss292461382	May 09, 2011 (134)
26	TISHKOFF	ss556129866	Apr 25, 2013 (138)
27	SSMP	ss649794772	Apr 25, 2013 (138)
28	EVA-GONL	ss977808459	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1069828046	Aug 21, 2014 (142)
30	1000GENOMES	ss1301057174	Aug 21, 2014 (142)
31	DDI	ss1428867405	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1579263662	Apr 01, 2015 (144)
33	EVA_DECODE	ss1587256638	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1605480721	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1648474754	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1798139169	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1921056912	Feb 12, 2016 (147)
38	GENOMED	ss1968990140	Jul 19, 2016 (147)
39	JJLAB	ss2021069451	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2149134353	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2237908082	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2625038047	Nov 08, 2017 (151)
43	GRF	ss2703779612	Nov 08, 2017 (151)
44	GNOMAD	ss2784633148	Nov 08, 2017 (151)
45	SWEGEN	ss2991119731	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3024294922	Nov 08, 2017 (151)
47	CSHL	ss3344677303	Nov 08, 2017 (151)
48	URBANLAB	ss3647242431	Oct 11, 2018 (152)
49	EGCUT_WGS	ss3659004840	Jul 13, 2019 (153)
50	EVA_DECODE	ss3705733440	Jul 13, 2019 (153)
51	ACPOP	ss3729245293	Jul 13, 2019 (153)
52	EVA	ss3757910071	Jul 13, 2019 (153)
53	PACBIO	ss3784111302	Jul 13, 2019 (153)
54	PACBIO	ss3789656241	Jul 13, 2019 (153)
55	PACBIO	ss3794529390	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3802269432	Jul 13, 2019 (153)
57	EVA	ss3827431897	Apr 25, 2020 (154)
58	EVA	ss3837135750	Apr 25, 2020 (154)
59	EVA	ss3842556679	Apr 25, 2020 (154)
60	SGDP_PRJ	ss3854296413	Apr 25, 2020 (154)
61	KRGDB	ss3899971309	Apr 25, 2020 (154)
62	KOGIC	ss3949797085	Apr 25, 2020 (154)
63	TOPMED	ss4539384629	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5155827874	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5251517673	Oct 12, 2022 (156)
66	EVA	ss5335094481	Oct 12, 2022 (156)
67	HUGCELL_USP	ss5451184654	Oct 12, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5528599611	Oct 12, 2022 (156)
69	SANFORD_IMAGENETICS	ss5630665901	Oct 12, 2022 (156)
70	TOMMO_GENOMICS	ss5686513991	Oct 12, 2022 (156)
71	YY_MCH	ss5803101444	Oct 12, 2022 (156)
72	EVA	ss5821391962	Oct 12, 2022 (156)
73	EVA	ss5852895842	Oct 12, 2022 (156)
74	EVA	ss5934114393	Oct 12, 2022 (156)
75	EVA	ss5956907941	Oct 12, 2022 (156)
76	1000Genomes	NC_000002.11 - 195759293	Oct 11, 2018 (152)
77	1000Genomes_30x	NC_000002.12 - 194894569	Oct 12, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 195759293	Oct 11, 2018 (152)
79	Genetic variation in the Estonian population	NC_000002.11 - 195759293	Oct 11, 2018 (152)
80	The Danish reference pan genome	NC_000002.11 - 195759293	Apr 25, 2020 (154)
81	gnomAD - Genomes	NC_000002.12 - 194894569	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000002.11 - 195759293	Apr 25, 2020 (154)
83	KOREAN population from KRGDB	NC_000002.11 - 195759293	Apr 25, 2020 (154)
84	Korean Genome Project	NC_000002.12 - 194894569	Apr 25, 2020 (154)
85	Northern Sweden	NC_000002.11 - 195759293	Jul 13, 2019 (153)
86	Qatari	NC_000002.11 - 195759293	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000002.11 - 195759293	Apr 25, 2020 (154)
88	Siberian	NC_000002.11 - 195759293	Apr 25, 2020 (154)
89	8.3KJPN	NC_000002.11 - 195759293	Apr 26, 2021 (155)
90	14KJPN	NC_000002.12 - 194894569	Oct 12, 2022 (156)
91	TopMed	NC_000002.12 - 194894569	Apr 26, 2021 (155)
92	UK 10K study - Twins	NC_000002.11 - 195759293	Oct 11, 2018 (152)
93	ALFA	NC_000002.12 - 194894569	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)
rs12021305	Mar 10, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
7148703, ss3899971309	NC_000002.11:195759292:T:A	NC_000002.12:194894568:T:A	(self)
ss77722166	NC_000002.9:195584798:T:C	NC_000002.12:194894568:T:C	(self)
ss91497125, ss110523761, ss111469215, ss118028694, ss165193281, ss165789921, ss167514556, ss201560603, ss205714425, ss253788156, ss276847648, ss284514775, ss292461382, ss1587256638	NC_000002.10:195467537:T:C	NC_000002.12:194894568:T:C	(self)
12139732, 6706122, 4743088, 5428601, 2944707, 7148703, 2530158, 3098842, 6313393, 1650707, 13797181, 6706122, ss219735757, ss231531076, ss239005431, ss556129866, ss649794772, ss977808459, ss1069828046, ss1301057174, ss1428867405, ss1579263662, ss1605480721, ss1648474754, ss1798139169, ss1921056912, ss1968990140, ss2021069451, ss2149134353, ss2625038047, ss2703779612, ss2784633148, ss2991119731, ss3344677303, ss3659004840, ss3729245293, ss3757910071, ss3784111302, ss3789656241, ss3794529390, ss3827431897, ss3837135750, ss3854296413, ss3899971309, ss5155827874, ss5335094481, ss5630665901, ss5821391962, ss5956907941	NC_000002.11:195759292:T:C	NC_000002.12:194894568:T:C	(self)
16125546, 86544143, 6175086, 20351095, 343207508, 10488127177, ss2237908082, ss3024294922, ss3647242431, ss3705733440, ss3802269432, ss3842556679, ss3949797085, ss4539384629, ss5251517673, ss5451184654, ss5528599611, ss5686513991, ss5803101444, ss5852895842, ss5934114393	NC_000002.12:194894568:T:C	NC_000002.12:194894568:T:C	(self)
ss15722249, ss21685371	NT_005403.14:45968708:T:C	NC_000002.12:194894568:T:C	(self)
ss18067792, ss96461079, ss106151916, ss136014258, ss138605447, ss154522402	NT_005403.17:45968710:T:C	NC_000002.12:194894568:T:C	(self)
7148703, ss3899971309	NC_000002.11:195759292:T:G	NC_000002.12:194894568:T:G	(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 rs11507987

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

rs11507987