Name: rs2596527
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.

rs2596527

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:31416560 (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=0.051294 (13577/264690, TOPMED)
C=0.051316 (7012/136644, GnomAD)
C=0.05802 (3052/52600, ALFA) (+ 3 more)
C=0.19338 (5461/28240, 14KJPN)
C=0.0760 (487/6404, 1000G_30x)
C=0.23 (19/82, HapMap)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	14050	T=0.94726	C=0.05274
European	Sub	9690	T=0.9359	C=0.0641
African	Sub	2898	T=0.9914	C=0.0086
African Others	Sub	114	T=1.000	C=0.000
African American	Sub	2784	T=0.9910	C=0.0090
Asian	Sub	112	T=0.911	C=0.089
East Asian	Sub	86	T=0.88	C=0.12
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.911	C=0.089
Latin American 2	Sub	610	T=0.952	C=0.048
South Asian	Sub	98	T=0.85	C=0.15
Other	Sub	496	T=0.944	C=0.056

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=0.948706	C=0.051294
gnomAD - Genomes	Global	Study-wide	136644	T=0.948684	C=0.051316
gnomAD - Genomes	European	Sub	75280	T=0.93363	C=0.06637
gnomAD - Genomes	African	Sub	39878	T=0.98784	C=0.01216
gnomAD - Genomes	American	Sub	13036	T=0.93925	C=0.06075
gnomAD - Genomes	Ashkenazi Jewish	Sub	3258	T=0.8950	C=0.1050
gnomAD - Genomes	East Asian	Sub	3092	T=0.9234	C=0.0766
gnomAD - Genomes	Other	Sub	2100	T=0.9238	C=0.0762
Allele Frequency Aggregator	Total	Global	52600	T=0.94198	C=0.05802
Allele Frequency Aggregator	European	Sub	38750	T=0.93855	C=0.06145
Allele Frequency Aggregator	Latin American 2	Sub	4928	T=0.9456	C=0.0544
Allele Frequency Aggregator	Other	Sub	4284	T=0.9346	C=0.0654
Allele Frequency Aggregator	African	Sub	3784	T=0.9913	C=0.0087
Allele Frequency Aggregator	Asian	Sub	434	T=0.882	C=0.118
Allele Frequency Aggregator	Latin American 1	Sub	272	T=0.934	C=0.066
Allele Frequency Aggregator	South Asian	Sub	148	T=0.858	C=0.142
14KJPN	JAPANESE	Study-wide	28240	T=0.80662	C=0.19338
1000Genomes_30x	Global	Study-wide	6404	T=0.9240	C=0.0760
1000Genomes_30x	African	Sub	1786	T=0.9972	C=0.0028
1000Genomes_30x	Europe	Sub	1266	T=0.9163	C=0.0837
1000Genomes_30x	South Asian	Sub	1202	T=0.8220	C=0.1780
1000Genomes_30x	East Asian	Sub	1170	T=0.9128	C=0.0872
1000Genomes_30x	American	Sub	980	T=0.939	C=0.061
HapMap	Global	Study-wide	82	T=0.77	C=0.23
HapMap	Asian	Sub	82	T=0.77	C=0.23

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 6	NC_000006.12:g.31416560T>C
GRCh37.p13 chr 6	NC_000006.11:g.31384337T>C
MICA RefSeqGene	NG_034139.1:g.21877T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2896931T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2897037T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2672287T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2677883T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2718837T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2718135T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2725147T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2730767T>C

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 6	NC_000006.12:g.31416560=	NC_000006.12:g.31416560T>C
GRCh37.p13 chr 6	NC_000006.11:g.31384337=	NC_000006.11:g.31384337T>C
MICA RefSeqGene	NG_034139.1:g.21877=	NG_034139.1:g.21877T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2896931=	NT_113891.3:g.2896931T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2897037=	NT_113891.2:g.2897037T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2672287=	NT_167248.2:g.2672287T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2677883=	NT_167248.1:g.2677883T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2718837=	NT_167249.2:g.2718837T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2718135=	NT_167249.1:g.2718135T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2725147=	NT_167246.2:g.2725147T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2730767=	NT_167246.1:g.2730767T>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#.

11 SubSNP, 6 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HUMAN_LONGEVITY	ss2282939310	Dec 20, 2016 (150)
2	EVA_DECODE	ss3716905161	Jul 13, 2019 (153)
3	KHV_HUMAN_GENOMES	ss3807975720	Jul 13, 2019 (153)
4	TOPMED	ss4698363303	Apr 26, 2021 (155)
5	1000G_HIGH_COVERAGE	ss5267932797	Oct 13, 2022 (156)
6	HUGCELL_USP	ss5465667567	Oct 13, 2022 (156)
7	1000G_HIGH_COVERAGE	ss5553587960	Oct 13, 2022 (156)
8	TOMMO_GENOMICS	ss5714684461	Oct 13, 2022 (156)
9	YY_MCH	ss5807305393	Oct 13, 2022 (156)
10	EVA	ss5855282793	Oct 13, 2022 (156)
11	EVA	ss5883240141	Oct 13, 2022 (156)
12	1000Genomes_30x	NC_000006.12 - 31416560	Oct 13, 2022 (156)
13	gnomAD - Genomes	NC_000006.12 - 31416560	Apr 26, 2021 (155)
14	HapMap	NC_000006.12 - 31416560	Apr 26, 2020 (154)
15	14KJPN	NC_000006.12 - 31416560	Oct 13, 2022 (156)
16	TopMed	NC_000006.12 - 31416560	Apr 26, 2021 (155)
17	ALFA	NC_000006.12 - 31416560	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)
rs114291624	May 04, 2012 (137)
rs117345955	Aug 16, 2010 (132)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
41113895, 221191200, 3099629, 48521565, 535740861, 2502517908, ss2282939310, ss3716905161, ss3807975720, ss4698363303, ss5267932797, ss5465667567, ss5553587960, ss5714684461, ss5807305393, ss5855282793, ss5883240141	NC_000006.12:31416559:T:C	NC_000006.12:31416559:T:C	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss166425129, ss207576155, ss278725615, ss485227566, ss1592308077, ss2635155576	NC_000006.10:31492315:T:C	NC_000006.12:31416559:T:C	rs2113412530
31321252, 17464079, 12446587, 7770397, 7762879, 18202920, 6644593, 8058014, 16267510, 4323414, 34800614, 17464079, 3872442, ss233397884, ss240468815, ss481462897, ss483502981, ss537107407, ss653033748, ss778701126, ss780301822, ss782194885, ss834160087, ss835788560, ss982763914, ss1073504460, ss1319554054, ss1581605458, ss1615274904, ss1658268937, ss1926016084, ss1970356731, ss2023640842, ss2151807060, ss2451314023, ss2634429260, ss2634429261, ss2707400609, ss2837415990, ss2998792963, ss3629502374, ss3632347917, ss3632347918, ss3636777680, ss3642482314, ss3666708339, ss3733359728, ss3764820317, ss3829831448, ss3864250530, ss3911025526, ss5176831307	NC_000006.11:31384336:T:C	NC_000006.12:31416559:T:C	rs2113412540
ss3651285, ss156742883, ss160562151	NT_007592.15:31324336:T:C	NC_000006.12:31416559:T:C	rs2113412576
ss4025187662	NT_113891.3:2896930:T:C	NC_000006.12:31416559:T:C	rs2113412586
ss4025228751	NT_167246.2:2725146:T:C	NC_000006.12:31416559:T:C	rs2113412596
ss4025286645	NT_167249.2:2718836:T:C	NC_000006.12:31416559:T:C	rs2113412607

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

No publications for rs2596527

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

rs2596527