Name: rs7959787
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.

rs7959787

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:40157271 (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=0.068522 (18137/264690, TOPMED)
T=0.070522 (9882/140126, GnomAD)
T=0.080432 (8521/105940, ALFA) (+ 16 more)
T=0.0668 (428/6404, 1000G_30x)
T=0.0649 (325/5008, 1000G)
T=0.0667 (299/4480, Estonian)
T=0.0804 (310/3854, ALSPAC)
T=0.0793 (294/3708, TWINSUK)
T=0.0629 (131/2084, HGDP_Stanford)
T=0.0552 (100/1810, HapMap)
T=0.093 (93/998, GoNL)
T=0.053 (32/600, NorthernSweden)
T=0.079 (17/216, Qatari)
T=0.019 (4/214, Vietnamese)
C=0.45 (28/62, SGDP_PRJ)
T=0.07 (3/40, GENOME_DK)
T=0.07 (2/28, Ancient Sardinia)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC02471 : Intron Variant
LINC02555 : 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	105940	C=0.919568	T=0.080432
European	Sub	80432	C=0.91864	T=0.08136
African	Sub	7448	C=0.9286	T=0.0714
African Others	Sub	254	C=0.902	T=0.098
African American	Sub	7194	C=0.9295	T=0.0705
Asian	Sub	212	C=0.995	T=0.005
East Asian	Sub	166	C=0.994	T=0.006
Other Asian	Sub	46	C=1.00	T=0.00
Latin American 1	Sub	330	C=0.952	T=0.048
Latin American 2	Sub	5330	C=0.9563	T=0.0437
South Asian	Sub	4972	C=0.8842	T=0.1158
Other	Sub	7216	C=0.9142	T=0.0858

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=0.931478	T=0.068522
gnomAD - Genomes	Global	Study-wide	140126	C=0.929478	T=0.070522
gnomAD - Genomes	European	Sub	75898	C=0.92460	T=0.07540
gnomAD - Genomes	African	Sub	41984	C=0.92828	T=0.07172
gnomAD - Genomes	American	Sub	13646	C=0.94343	T=0.05657
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9313	T=0.0687
gnomAD - Genomes	East Asian	Sub	3126	C=0.9968	T=0.0032
gnomAD - Genomes	Other	Sub	2152	C=0.9359	T=0.0641
Allele Frequency Aggregator	Total	Global	105940	C=0.919568	T=0.080432
Allele Frequency Aggregator	European	Sub	80432	C=0.91864	T=0.08136
Allele Frequency Aggregator	African	Sub	7448	C=0.9286	T=0.0714
Allele Frequency Aggregator	Other	Sub	7216	C=0.9142	T=0.0858
Allele Frequency Aggregator	Latin American 2	Sub	5330	C=0.9563	T=0.0437
Allele Frequency Aggregator	South Asian	Sub	4972	C=0.8842	T=0.1158
Allele Frequency Aggregator	Latin American 1	Sub	330	C=0.952	T=0.048
Allele Frequency Aggregator	Asian	Sub	212	C=0.995	T=0.005
1000Genomes_30x	Global	Study-wide	6404	C=0.9332	T=0.0668
1000Genomes_30x	African	Sub	1786	C=0.9194	T=0.0806
1000Genomes_30x	Europe	Sub	1266	C=0.9179	T=0.0821
1000Genomes_30x	South Asian	Sub	1202	C=0.8985	T=0.1015
1000Genomes_30x	East Asian	Sub	1170	C=0.9923	T=0.0077
1000Genomes_30x	American	Sub	980	C=0.950	T=0.050
1000Genomes	Global	Study-wide	5008	C=0.9351	T=0.0649
1000Genomes	African	Sub	1322	C=0.9206	T=0.0794
1000Genomes	East Asian	Sub	1008	C=0.9921	T=0.0079
1000Genomes	Europe	Sub	1006	C=0.9215	T=0.0785
1000Genomes	South Asian	Sub	978	C=0.897	T=0.103
1000Genomes	American	Sub	694	C=0.954	T=0.046
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9333	T=0.0667
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9196	T=0.0804
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9207	T=0.0793
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	C=0.9371	T=0.0629
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	C=0.994	T=0.006
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	C=0.855	T=0.145
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	C=0.949	T=0.051
HGDP-CEPH-db Supplement 1	Europe	Sub	320	C=0.891	T=0.109
HGDP-CEPH-db Supplement 1	Africa	Sub	242	C=0.946	T=0.054
HGDP-CEPH-db Supplement 1	America	Sub	216	C=1.000	T=0.000
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	C=0.97	T=0.03
HapMap	Global	Study-wide	1810	C=0.9448	T=0.0552
HapMap	American	Sub	770	C=0.936	T=0.064
HapMap	African	Sub	692	C=0.944	T=0.056
HapMap	Europe	Sub	176	C=0.932	T=0.068
HapMap	Asian	Sub	172	C=1.000	T=0.000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.907	T=0.093
Northern Sweden	ACPOP	Study-wide	600	C=0.947	T=0.053
Qatari	Global	Study-wide	216	C=0.921	T=0.079
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.981	T=0.019
SGDP_PRJ	Global	Study-wide	62	C=0.45	T=0.55
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	T=0.07
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	28	C=0.93	T=0.07
Siberian	Global	Study-wide	6	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 12	NC_000012.12:g.40157271C>T
GRCh37.p13 chr 12	NC_000012.11:g.40551073C>T

Gene: LINC02471, long intergenic non-protein coding RNA 2471 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02471 transcript	NR_146526.1:n.	N/A	Intron Variant

Gene: LINC02555, uncharacterized LINC02555 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02555 transcript variant X1	XR_001749085.2:n.	N/A	Intron Variant
LINC02555 transcript variant X3	XR_429125.4:n.	N/A	Intron Variant
LINC02555 transcript variant X2	XR_944864.3: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 12	NC_000012.12:g.40157271=	NC_000012.12:g.40157271C>T
GRCh37.p13 chr 12	NC_000012.11:g.40551073=	NC_000012.11:g.40551073C>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, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss12188044	Jul 11, 2003 (116)
2	BCM-HGSC	ss28465027	Sep 20, 2004 (126)
3	BCM-HGSC	ss28473061	Sep 20, 2004 (126)
4	ILLUMINA	ss66693047	Nov 30, 2006 (127)
5	ILLUMINA	ss67852990	Nov 30, 2006 (127)
6	ILLUMINA	ss68004996	Nov 30, 2006 (127)
7	ILLUMINA	ss70961052	May 26, 2008 (130)
8	ILLUMINA	ss71569570	May 17, 2007 (127)
9	ILLUMINA	ss75572866	Dec 06, 2007 (129)
10	ILLUMINA	ss79276203	Dec 16, 2007 (130)
11	KRIBB_YJKIM	ss84758434	Dec 16, 2007 (130)
12	ILLUMINA	ss122871331	Dec 01, 2009 (131)
13	ILLUMINA	ss154459106	Dec 01, 2009 (131)
14	ILLUMINA	ss159633720	Dec 01, 2009 (131)
15	ILLUMINA	ss161046307	Dec 01, 2009 (131)
16	ILLUMINA	ss172375076	Jul 04, 2010 (132)
17	ILLUMINA	ss174640071	Jul 04, 2010 (132)
18	1000GENOMES	ss225712114	Jul 14, 2010 (132)
19	1000GENOMES	ss235905217	Jul 15, 2010 (132)
20	PJP	ss291425219	May 09, 2011 (134)
21	ILLUMINA	ss479187074	Sep 08, 2015 (146)
22	ILLUMINA	ss537536319	Sep 08, 2015 (146)
23	TISHKOFF	ss563119476	Apr 25, 2013 (138)
24	SSMP	ss658664741	Apr 25, 2013 (138)
25	ILLUMINA	ss825606721	Jul 19, 2016 (147)
26	ILLUMINA	ss833144596	Jul 13, 2019 (153)
27	EVA-GONL	ss989450729	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1078401642	Aug 21, 2014 (142)
29	1000GENOMES	ss1344696797	Aug 21, 2014 (142)
30	DDI	ss1426909649	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1576234212	Apr 01, 2015 (144)
32	EVA_DECODE	ss1599118012	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1628426021	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1671420054	Apr 01, 2015 (144)
35	EVA_SVP	ss1713321657	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1807209831	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1932814652	Feb 12, 2016 (147)
38	JJLAB	ss2027157697	Sep 14, 2016 (149)
39	ILLUMINA	ss2094872528	Dec 20, 2016 (150)
40	ILLUMINA	ss2095033458	Dec 20, 2016 (150)
41	USC_VALOUEV	ss2155490756	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2189129119	Dec 20, 2016 (150)
43	ILLUMINA	ss2635035953	Nov 08, 2017 (151)
44	GNOMAD	ss2909587760	Nov 08, 2017 (151)
45	SWEGEN	ss3009553098	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3027386913	Nov 08, 2017 (151)
47	CSHL	ss3350027014	Nov 08, 2017 (151)
48	ILLUMINA	ss3626859176	Oct 12, 2018 (152)
49	ILLUMINA	ss3636185539	Oct 12, 2018 (152)
50	ILLUMINA	ss3637958263	Oct 12, 2018 (152)
51	ILLUMINA	ss3638993226	Oct 12, 2018 (152)
52	ILLUMINA	ss3639498605	Oct 12, 2018 (152)
53	ILLUMINA	ss3642952279	Oct 12, 2018 (152)
54	ILLUMINA	ss3651798394	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3676828643	Jul 13, 2019 (153)
56	EVA_DECODE	ss3693514241	Jul 13, 2019 (153)
57	ACPOP	ss3738950222	Jul 13, 2019 (153)
58	ILLUMINA	ss3744393895	Jul 13, 2019 (153)
59	EVA	ss3750381686	Jul 13, 2019 (153)
60	KHV_HUMAN_GENOMES	ss3815710749	Jul 13, 2019 (153)
61	EVA	ss3833081739	Apr 27, 2020 (154)
62	HGDP	ss3847448278	Apr 27, 2020 (154)
63	SGDP_PRJ	ss3878108375	Apr 27, 2020 (154)
64	EVA	ss3985586386	Apr 26, 2021 (155)
65	EVA	ss4017584493	Apr 26, 2021 (155)
66	TOPMED	ss4915488389	Apr 26, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5290526820	Oct 16, 2022 (156)
68	EVA	ss5405133752	Oct 16, 2022 (156)
69	HUGCELL_USP	ss5485315235	Oct 16, 2022 (156)
70	EVA	ss5510670597	Oct 16, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5587875719	Oct 16, 2022 (156)
72	SANFORD_IMAGENETICS	ss5652994077	Oct 16, 2022 (156)
73	EVA	ss5837860054	Oct 16, 2022 (156)
74	EVA	ss5904072993	Oct 16, 2022 (156)
75	EVA	ss5944351417	Oct 16, 2022 (156)
76	1000Genomes	NC_000012.11 - 40551073	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000012.12 - 40157271	Oct 16, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 40551073	Oct 12, 2018 (152)
79	Genetic variation in the Estonian population	NC_000012.11 - 40551073	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000012.11 - 40551073	Apr 27, 2020 (154)
81	gnomAD - Genomes	NC_000012.12 - 40157271	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000012.11 - 40551073	Apr 27, 2020 (154)
83	HGDP-CEPH-db Supplement 1	NC_000012.10 - 38837340	Apr 27, 2020 (154)
84	HapMap	NC_000012.12 - 40157271	Apr 27, 2020 (154)
85	Northern Sweden	NC_000012.11 - 40551073	Jul 13, 2019 (153)
86	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000012.11 - 40551073	Apr 26, 2021 (155)
87	Qatari	NC_000012.11 - 40551073	Apr 27, 2020 (154)
88	SGDP_PRJ	NC_000012.11 - 40551073	Apr 27, 2020 (154)
89	Siberian	NC_000012.11 - 40551073	Apr 27, 2020 (154)
90	TopMed	NC_000012.12 - 40157271	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000012.11 - 40551073	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000012.11 - 40551073	Jul 13, 2019 (153)
93	ALFA	NC_000012.12 - 40157271	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)
rs17458905	Mar 10, 2006 (126)
rs17490097	Mar 10, 2006 (126)
rs61364067	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3638993226, ss3639498605	NC_000012.9:38837339:C:T	NC_000012.12:40157270:C:T	(self)
126170, ss291425219, ss825606721, ss1599118012, ss1713321657, ss2094872528, ss2635035953, ss3642952279, ss3847448278	NC_000012.10:38837339:C:T	NC_000012.12:40157270:C:T	(self)
57433685, 31893035, 22566891, 2931296, 14233507, 12235087, 812313, 14856582, 30125355, 8007110, 31893035, 7077668, ss225712114, ss235905217, ss479187074, ss537536319, ss563119476, ss658664741, ss833144596, ss989450729, ss1078401642, ss1344696797, ss1426909649, ss1576234212, ss1628426021, ss1671420054, ss1807209831, ss1932814652, ss2027157697, ss2095033458, ss2155490756, ss2909587760, ss3009553098, ss3350027014, ss3626859176, ss3636185539, ss3637958263, ss3651798394, ss3676828643, ss3738950222, ss3744393895, ss3750381686, ss3833081739, ss3878108375, ss3985586386, ss4017584493, ss5405133752, ss5510670597, ss5652994077, ss5837860054, ss5944351417	NC_000012.11:40551072:C:T	NC_000012.12:40157270:C:T	(self)
75401654, 405005230, 798027, 131034046, 1438772894, ss2189129119, ss3027386913, ss3693514241, ss3815710749, ss4915488389, ss5290526820, ss5485315235, ss5587875719, ss5904072993	NC_000012.12:40157270:C:T	NC_000012.12:40157270:C:T	(self)
ss12188044	NT_029419.10:2694378:C:T	NC_000012.12:40157270:C:T	(self)
ss28465027, ss28473061, ss66693047, ss67852990, ss68004996, ss70961052, ss71569570, ss75572866, ss79276203, ss84758434, ss122871331, ss154459106, ss159633720, ss161046307, ss172375076, ss174640071	NT_029419.12:2694378:C:T	NC_000012.12:40157270: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 rs7959787

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

rs7959787