Name: rs56310940
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.

rs56310940

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:24320742 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.170804 (45210/264690, TOPMED)
G=0.152784 (21339/139668, GnomAD)
G=0.45159 (12761/28258, 14KJPN) (+ 16 more)
G=0.12668 (2393/18890, ALFA)
G=0.45107 (7559/16758, 8.3KJPN)
G=0.2210 (1415/6404, 1000G_30x)
G=0.2214 (1109/5008, 1000G)
G=0.1163 (521/4480, Estonian)
G=0.0693 (267/3854, ALSPAC)
G=0.0747 (277/3708, TWINSUK)
G=0.3823 (1120/2930, KOREAN)
G=0.4039 (740/1832, Korea1K)
G=0.073 (73/998, GoNL)
G=0.097 (58/600, NorthernSweden)
C=0.383 (92/240, SGDP_PRJ)
G=0.093 (20/216, Qatari)
G=0.333 (70/210, Vietnamese)
G=0.05 (2/40, GENOME_DK)
C=0.44 (8/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC107986777 : 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	C=0.87332	G=0.12668
European	Sub	14286	C=0.91019	G=0.08981
African	Sub	2946	C=0.7549	G=0.2451
African Others	Sub	114	C=0.737	G=0.263
African American	Sub	2832	C=0.7556	G=0.2444
Asian	Sub	112	C=0.616	G=0.384
East Asian	Sub	86	C=0.63	G=0.37
Other Asian	Sub	26	C=0.58	G=0.42
Latin American 1	Sub	146	C=0.822	G=0.178
Latin American 2	Sub	610	C=0.698	G=0.302
South Asian	Sub	98	C=0.79	G=0.21
Other	Sub	692	C=0.835	G=0.165

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=0.829196	G=0.170804
gnomAD - Genomes	Global	Study-wide	139668	C=0.847216	G=0.152784
gnomAD - Genomes	European	Sub	75864	C=0.91777	G=0.08223
gnomAD - Genomes	African	Sub	41614	C=0.75871	G=0.24129
gnomAD - Genomes	American	Sub	13612	C=0.74640	G=0.25360
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.9171	G=0.0829
gnomAD - Genomes	East Asian	Sub	3118	C=0.6851	G=0.3149
gnomAD - Genomes	Other	Sub	2142	C=0.8361	G=0.1639
14KJPN	JAPANESE	Study-wide	28258	C=0.54841	G=0.45159
Allele Frequency Aggregator	Total	Global	18890	C=0.87332	G=0.12668
Allele Frequency Aggregator	European	Sub	14286	C=0.91019	G=0.08981
Allele Frequency Aggregator	African	Sub	2946	C=0.7549	G=0.2451
Allele Frequency Aggregator	Other	Sub	692	C=0.835	G=0.165
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.698	G=0.302
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.822	G=0.178
Allele Frequency Aggregator	Asian	Sub	112	C=0.616	G=0.384
Allele Frequency Aggregator	South Asian	Sub	98	C=0.79	G=0.21
8.3KJPN	JAPANESE	Study-wide	16758	C=0.54893	G=0.45107
1000Genomes_30x	Global	Study-wide	6404	C=0.7790	G=0.2210
1000Genomes_30x	African	Sub	1786	C=0.7721	G=0.2279
1000Genomes_30x	Europe	Sub	1266	C=0.9179	G=0.0821
1000Genomes_30x	South Asian	Sub	1202	C=0.7845	G=0.2155
1000Genomes_30x	East Asian	Sub	1170	C=0.6718	G=0.3282
1000Genomes_30x	American	Sub	980	C=0.734	G=0.266
1000Genomes	Global	Study-wide	5008	C=0.7786	G=0.2214
1000Genomes	African	Sub	1322	C=0.7716	G=0.2284
1000Genomes	East Asian	Sub	1008	C=0.6706	G=0.3294
1000Genomes	Europe	Sub	1006	C=0.9175	G=0.0825
1000Genomes	South Asian	Sub	978	C=0.785	G=0.215
1000Genomes	American	Sub	694	C=0.738	G=0.262
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8837	G=0.1163
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9307	G=0.0693
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9253	G=0.0747
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6177	G=0.3823
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5961	G=0.4039
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.927	G=0.073
Northern Sweden	ACPOP	Study-wide	600	C=0.903	G=0.097
SGDP_PRJ	Global	Study-wide	240	C=0.383	G=0.617
Qatari	Global	Study-wide	216	C=0.907	G=0.093
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.667	G=0.333
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	G=0.05
Siberian	Global	Study-wide	18	C=0.44	G=0.56

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 7	NC_000007.14:g.24320742C>G
GRCh37.p13 chr 7	NC_000007.13:g.24360361C>G

Gene: LOC107986777, uncharacterized LOC107986777 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107986777 transcript variant X3	XR_001745121.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X7	XR_001745122.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X8	XR_001745123.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X10	XR_001745124.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X11	XR_001745125.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X13	XR_001745127.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X9	XR_001745129.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X4	XR_001745130.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X14	XR_001745131.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X15	XR_001745132.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X1	XR_007060254.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X2	XR_007060255.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X5	XR_007060256.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X6	XR_007060257.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X12	XR_001745128.2:n.	N/A	Genic Upstream Transcript Variant
LOC107986777 transcript variant X16	XR_007060258.1:n.	N/A	Genic 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=	G
GRCh38.p14 chr 7	NC_000007.14:g.24320742=	NC_000007.14:g.24320742C>G
GRCh37.p13 chr 7	NC_000007.13:g.24360361=	NC_000007.13:g.24360361C>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#.

51 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss77272664	Dec 07, 2007 (129)
2	GMI	ss154522763	Dec 01, 2009 (131)
3	BUSHMAN	ss203084003	Jul 04, 2010 (132)
4	1000GENOMES	ss233892343	Jul 15, 2010 (132)
5	1000GENOMES	ss240864585	Jul 15, 2010 (132)
6	GMI	ss279227495	May 04, 2012 (137)
7	SSMP	ss654225904	Apr 25, 2013 (138)
8	EVA-GONL	ss984059020	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1074447537	Aug 21, 2014 (142)
10	1000GENOMES	ss1324328545	Aug 21, 2014 (142)
11	EVA_GENOME_DK	ss1582114560	Apr 01, 2015 (144)
12	EVA_DECODE	ss1593627843	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1617784476	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1660778509	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1804914923	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1927304327	Feb 12, 2016 (147)
17	GENOMED	ss1970650470	Jul 19, 2016 (147)
18	JJLAB	ss2024328860	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2152525058	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2292489379	Dec 20, 2016 (150)
21	SYSTEMSBIOZJU	ss2626653468	Nov 08, 2017 (151)
22	GRF	ss2708181955	Nov 08, 2017 (151)
23	GNOMAD	ss2850880013	Nov 08, 2017 (151)
24	SWEGEN	ss3000787092	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3025958694	Nov 08, 2017 (151)
26	CSHL	ss3347485939	Nov 08, 2017 (151)
27	EGCUT_WGS	ss3668715477	Jul 13, 2019 (153)
28	EVA_DECODE	ss3719295640	Jul 13, 2019 (153)
29	ACPOP	ss3734447741	Jul 13, 2019 (153)
30	EVA	ss3766311109	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3809478505	Jul 13, 2019 (153)
32	EVA	ss3830468035	Apr 26, 2020 (154)
33	EVA	ss3838721358	Apr 26, 2020 (154)
34	EVA	ss3844172575	Apr 26, 2020 (154)
35	SGDP_PRJ	ss3866843839	Apr 26, 2020 (154)
36	KRGDB	ss3913881678	Apr 26, 2020 (154)
37	KOGIC	ss3961069078	Apr 26, 2020 (154)
38	TOPMED	ss4739026912	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5182250167	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5272177057	Oct 14, 2022 (156)
41	EVA	ss5372279402	Oct 14, 2022 (156)
42	HUGCELL_USP	ss5469426752	Oct 14, 2022 (156)
43	EVA	ss5508883833	Oct 14, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5559995142	Oct 14, 2022 (156)
45	SANFORD_IMAGENETICS	ss5642547743	Oct 14, 2022 (156)
46	TOMMO_GENOMICS	ss5721827054	Oct 14, 2022 (156)
47	YY_MCH	ss5808423305	Oct 14, 2022 (156)
48	EVA	ss5822544720	Oct 14, 2022 (156)
49	EVA	ss5855807589	Oct 14, 2022 (156)
50	EVA	ss5858105560	Oct 14, 2022 (156)
51	EVA	ss5971747465	Oct 14, 2022 (156)
52	1000Genomes	NC_000007.13 - 24360361	Oct 12, 2018 (152)
53	1000Genomes_30x	NC_000007.14 - 24320742	Oct 14, 2022 (156)
54	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 24360361	Oct 12, 2018 (152)
55	Genetic variation in the Estonian population	NC_000007.13 - 24360361	Oct 12, 2018 (152)
56	The Danish reference pan genome	NC_000007.13 - 24360361	Apr 26, 2020 (154)
57	gnomAD - Genomes	NC_000007.14 - 24320742	Apr 26, 2021 (155)
58	Genome of the Netherlands Release 5	NC_000007.13 - 24360361	Apr 26, 2020 (154)
59	KOREAN population from KRGDB	NC_000007.13 - 24360361	Apr 26, 2020 (154)
60	Korean Genome Project	NC_000007.14 - 24320742	Apr 26, 2020 (154)
61	Northern Sweden	NC_000007.13 - 24360361	Jul 13, 2019 (153)
62	Qatari	NC_000007.13 - 24360361	Apr 26, 2020 (154)
63	SGDP_PRJ	NC_000007.13 - 24360361	Apr 26, 2020 (154)
64	Siberian	NC_000007.13 - 24360361	Apr 26, 2020 (154)
65	8.3KJPN	NC_000007.13 - 24360361	Apr 26, 2021 (155)
66	14KJPN	NC_000007.14 - 24320742	Oct 14, 2022 (156)
67	TopMed	NC_000007.14 - 24320742	Apr 26, 2021 (155)
68	UK 10K study - Twins	NC_000007.13 - 24360361	Oct 12, 2018 (152)
69	A Vietnamese Genetic Variation Database	NC_000007.13 - 24360361	Jul 13, 2019 (153)
70	ALFA	NC_000007.14 - 24320742	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77272664	NC_000007.11:24133600:C:G	NC_000007.14:24320741:C:G	(self)
ss203084003, ss279227495, ss1593627843	NC_000007.12:24326885:C:G	NC_000007.14:24320741:C:G	(self)
36269891, 20219442, 14453725, 8279499, 9014768, 21059072, 7732606, 9346257, 18860819, 5041412, 40219474, 20219442, 4505293, ss233892343, ss240864585, ss654225904, ss984059020, ss1074447537, ss1324328545, ss1582114560, ss1617784476, ss1660778509, ss1804914923, ss1927304327, ss1970650470, ss2024328860, ss2152525058, ss2626653468, ss2708181955, ss2850880013, ss3000787092, ss3347485939, ss3668715477, ss3734447741, ss3766311109, ss3830468035, ss3838721358, ss3866843839, ss3913881678, ss5182250167, ss5372279402, ss5508883833, ss5642547743, ss5822544720, ss5971747465	NC_000007.13:24360360:C:G	NC_000007.14:24320741:C:G	(self)
47521077, 255746211, 17447079, 55664158, 576404471, 7907373381, ss2292489379, ss3025958694, ss3719295640, ss3809478505, ss3844172575, ss3961069078, ss4739026912, ss5272177057, ss5469426752, ss5559995142, ss5721827054, ss5808423305, ss5855807589, ss5858105560	NC_000007.14:24320741:C:G	NC_000007.14:24320741:C:G	(self)
ss154522763	NT_007819.17:24350360:C:G	NC_000007.14:24320741:C: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 rs56310940

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

rs56310940