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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs2596494

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr6:31356061 (GRCh38.p7) 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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.15467 (22930/148252, GnomAD)
C=0.1745 (5828/33394, ExAC)
C=0.1684 (5195/30842, GnomAD) (+ 3 more)
C=0.127 (638/5008, 1000G)
C=0.202 (780/3854, ALSPAC)
C=0.208 (771/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HLA-B : Non Coding Transcript Variant
MIR6891 : 2KB Upstream Variant
Publications
1 citation
Genomic View
See rs on genome
Help

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.p7 chr 6 NC_000006.12:g.31356061C>A
GRCh38.p7 chr 6 NC_000006.12:g.31356061C>G
GRCh38.p7 chr 6 NC_000006.12:g.31356061C>T
GRCh37.p13 chr 6 NC_000006.11:g.31323838C>A
GRCh37.p13 chr 6 NC_000006.11:g.31323838C>G
GRCh37.p13 chr 6 NC_000006.11:g.31323838C>T
HLA-B RefSeqGene NG_023187.1:g.6152G>T
HLA-B RefSeqGene NG_023187.1:g.6152G>C
HLA-B RefSeqGene NG_023187.1:g.6152G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2836419G>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2836419G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2836419G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2836525G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2836525G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2836525G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2611757G>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2611757G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2611757G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2617353G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2617353G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2617353G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2658300G>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2658300G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2658300G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2657598G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2657598G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2657598G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2664674G>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2664674G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2664674G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2670294G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2670294G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2670294G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2698045G>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2698045G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2698045G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2703630G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2703630G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2703630G>T
Gene: HLA-B, major histocompatibility complex, class I, B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HLA-B transcript NM_005514.7:c. N/A Intron Variant
HLA-B transcript variant X1 XM_011514557.1:c. N/A Intron Variant
HLA-B transcript variant X2 XR_926175.1:n.735G>T N/A Non Coding Transcript Variant
HLA-B transcript variant X2 XR_926175.1:n.735G>C N/A Non Coding Transcript Variant
HLA-B transcript variant X2 XR_926175.1:n.735G>A N/A Non Coding Transcript Variant
Gene: MIR6891, microRNA 6891 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR6891 transcript NR_106951.1:n. N/A Upstream Transcript Variant
Help

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
Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 148252 C=0.15467 G=0.84533
The Genome Aggregation Database European Sub 73848 C=0.2065 G=0.7935
The Genome Aggregation Database Asian Sub 33452 C=0.1147 G=0.8853
The Genome Aggregation Database American Sub 22442 C=0.0933 G=0.9067
The Genome Aggregation Database African Sub 7932 C=0.122 G=0.878
The Genome Aggregation Database Ashkenazi Jewish Sub 6794 C=0.051 G=0.949
The Genome Aggregation Database Other Sub 3784 C=0.116 G=0.884
The Genome Aggregation Database Global Study-wide 30842 C=0.1684 G=0.8316
The Genome Aggregation Database European Sub 18420 C=0.1972 G=0.8028
The Genome Aggregation Database African Sub 8692 C=0.113 G=0.887
The Genome Aggregation Database East Asian Sub 1616 C=0.203 G=0.797
The Genome Aggregation Database Other Sub 976 C=0.15 G=0.85
The Genome Aggregation Database American Sub 838 C=0.10 G=0.90
The Genome Aggregation Database Ashkenazi Jewish Sub 300 C=0.08 G=0.92
1000Genomes Global Study-wide 5008 C=0.127 G=0.873
1000Genomes African Sub 1322 C=0.092 G=0.908
1000Genomes East Asian Sub 1008 C=0.182 G=0.818
1000Genomes Europe Sub 1006 C=0.169 G=0.831
1000Genomes South Asian Sub 978 C=0.09 G=0.91
1000Genomes American Sub 694 C=0.11 G=0.89
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.202 G=0.798
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.208 G=0.792
Help

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= A G T Note
GRCh38.p7 chr 6 NC_000006.12:...

NC_000006.12:g.31356061C=

NC_000006.12:...

NC_000006.12:g.31356061C>A

NC_000006.12:...

NC_000006.12:g.31356061C>G

NC_000006.12:...

NC_000006.12:g.31356061C>T

GRCh37.p13 chr 6 NC_000006.11:...

NC_000006.11:g.31323838C=

NC_000006.11:...

NC_000006.11:g.31323838C>A

NC_000006.11:...

NC_000006.11:g.31323838C>G

NC_000006.11:...

NC_000006.11:g.31323838C>T

HLA-B RefSeqGene NG_023187.1:g...

NG_023187.1:g.6152G=

NG_023187.1:g...

NG_023187.1:g.6152G>T

NG_023187.1:g...

NG_023187.1:g.6152G>C

NG_023187.1:g...

NG_023187.1:g.6152G>A

GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g...

NT_113891.3:g.2836419G>C

NT_113891.3:g...

NT_113891.3:g.2836419G>A

NT_113891.3:g...

NT_113891.3:g.2836419G=

NT_113891.3:g...

NT_113891.3:g.2836419G>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g...

NT_113891.2:g.2836525G>C

NT_113891.2:g...

NT_113891.2:g.2836525G>A

NT_113891.2:g...

NT_113891.2:g.2836525G=

NT_113891.2:g...

NT_113891.2:g.2836525G>T

GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g...

NT_167248.2:g.2611757G>C

NT_167248.2:g...

NT_167248.2:g.2611757G>A

NT_167248.2:g...

NT_167248.2:g.2611757G=

NT_167248.2:g...

NT_167248.2:g.2611757G>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g...

NT_167248.1:g.2617353G>C

NT_167248.1:g...

NT_167248.1:g.2617353G>A

NT_167248.1:g...

NT_167248.1:g.2617353G=

NT_167248.1:g...

NT_167248.1:g.2617353G>T

GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g...

NT_167249.2:g.2658300G>C

NT_167249.2:g...

NT_167249.2:g.2658300G>A

NT_167249.2:g...

NT_167249.2:g.2658300G=

NT_167249.2:g...

NT_167249.2:g.2658300G>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g...

NT_167249.1:g.2657598G>C

NT_167249.1:g...

NT_167249.1:g.2657598G>A

NT_167249.1:g...

NT_167249.1:g.2657598G=

NT_167249.1:g...

NT_167249.1:g.2657598G>T

GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g...

NT_167246.2:g.2664674G>C

NT_167246.2:g...

NT_167246.2:g.2664674G>A

NT_167246.2:g...

NT_167246.2:g.2664674G=

NT_167246.2:g...

NT_167246.2:g.2664674G>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g...

NT_167246.1:g.2670294G>C

NT_167246.1:g...

NT_167246.1:g.2670294G>A

NT_167246.1:g...

NT_167246.1:g.2670294G=

NT_167246.1:g...

NT_167246.1:g.2670294G>T

GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g...

NT_167247.2:g.2698045G>C

NT_167247.2:g...

NT_167247.2:g.2698045G>A

NT_167247.2:g...

NT_167247.2:g.2698045G=

NT_167247.2:g...

NT_167247.2:g.2698045G>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g...

NT_167247.1:g.2703630G>C

NT_167247.1:g...

NT_167247.1:g.2703630G>A

NT_167247.1:g...

NT_167247.1:g.2703630G=

NT_167247.1:g...

NT_167247.1:g.2703630G>T

HLA-B transcript variant X2 XR_926175.1:n...

XR_926175.1:n.735G=

XR_926175.1:n...

XR_926175.1:n.735G>T

XR_926175.1:n...

XR_926175.1:n.735G>C

XR_926175.1:n...

XR_926175.1:n.735G>A

Help

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#.

54 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3651250 Sep 28, 2001 (100)
2 SI_MHC_SNP ss12689641 Oct 31, 2003 (119)
3 ABI ss42672803 Mar 11, 2006 (126)
4 HUMANGENOME_JCVI ss98379600 Feb 04, 2009 (130)
5 BGI ss105990493 Feb 04, 2009 (130)
6 1000GENOMES ss109896806 Feb 13, 2009 (130)
7 ILLUMINA-UK ss116392642 Feb 14, 2009 (130)
8 ENSEMBL ss139855504 Dec 01, 2009 (131)
9 GMI ss156738231 Dec 01, 2009 (131)
10 ILLUMINA ss160562141 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss162194295 Jul 04, 2010 (132)
12 ILLUMINA ss168909536 Jul 04, 2010 (132)
13 BUSHMAN ss201619619 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss207670545 Jul 04, 2010 (132)
15 1000GENOMES ss222301695 Jul 14, 2010 (132)
16 1000GENOMES ss233396543 Jul 14, 2010 (132)
17 1000GENOMES ss240467622 Jul 15, 2010 (132)
18 ILLUMINA ss244291219 Jul 04, 2010 (132)
19 BL ss254182447 May 09, 2011 (136)
20 GMI ss278724301 May 04, 2012 (137)
21 GMI ss285373196 Apr 25, 2013 (138)
22 PJP ss293824736 May 09, 2011 (136)
23 ILLUMINA ss481462857 Sep 08, 2015 (146)
24 ILLUMINA ss532732397 Sep 08, 2015 (146)
25 DBMHC ss539212509 Oct 03, 2012 (137)
26 TISHKOFF ss559111898 Apr 25, 2013 (138)
27 SSMP ss653032118 Apr 25, 2013 (138)
28 EVA-GONL ss982762111 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1073503362 Aug 21, 2014 (142)
30 1000GENOMES ss1319550919 Aug 21, 2014 (142)
31 EVA_UK10K_ALSPAC ss1615273383 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1658267416 Apr 01, 2015 (144)
33 EVA_EXAC ss1688228557 Apr 01, 2015 (144)
34 EVA_MGP ss1711120636 Apr 01, 2015 (144)
35 HAMMER_LAB ss1804356132 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1926014006 Feb 12, 2016 (147)
37 GENOMED ss1970355912 Jul 19, 2016 (147)
38 JJLAB ss2023639339 Sep 14, 2016 (149)
39 USC_VALOUEV ss2151805336 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2282937676 Dec 20, 2016 (150)
41 TOPMED ss2451310274 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2626306469 Nov 08, 2017 (151)
43 GRF ss2707398709 Nov 08, 2017 (151)
44 GNOMAD ss2735645501 Nov 08, 2017 (151)
45 GNOMAD ss2747580671 Nov 08, 2017 (151)
46 GNOMAD ss2837409779 Nov 08, 2017 (151)
47 AFFY ss2985360833 Nov 08, 2017 (151)
48 SWEGEN ss2998790534 Nov 08, 2017 (151)
49 TOPMED ss3493805891 Nov 08, 2017 (151)
50 TOPMED ss3493805892 Nov 08, 2017 (151)
51 TOPMED ss3493805893 Nov 08, 2017 (151)
52 ILLUMINA ss3629501510 Jul 20, 2018 (151)
53 ILLUMINA ss3636777262 Jul 20, 2018 (151)
54 ILLUMINA ss3638619348 Jul 20, 2018 (151)
55 1000Genomes NC_000006.11 - 31323838 Jul 20, 2018 (151)
56 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 31323838 Jul 20, 2018 (151)
57 The Exome Aggregation Consortium NC_000006.11 - 31323838 Jul 20, 2018 (151)
58 The Genome Aggregation Database NC_000006.11 - 31323838 Jul 20, 2018 (151)
59 The Genome Aggregation Database NC_000006.11 - 31323838 Jul 20, 2018 (151)
60 UK 10K study - Twins NC_000006.11 - 31323838 Jul 20, 2018 (151)
Help

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)
rs9266130 Dec 04, 2003 (119)
rs17884228 Mar 11, 2006 (126)
rs111449582 Oct 26, 2010 (133)
rs147220191 Mar 28, 2012 (136)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss109896806, ss116392642, ss162194295, ss201619619, ss207670545, ss254182447, ss278724301, ss285373196, ss293824736 NC_000006.10:31431816:C= NC_000006.12:31356060:C= (self)
31318001, 17462389, 8253612, 178037536, 4660236, 17462389, ss222301695, ss233396543, ss240467622, ss481462857, ss532732397, ss559111898, ss653032118, ss982762111, ss1073503362, ss1319550919, ss1615273383, ss1658267416, ss1688228557, ss1711120636, ss1804356132, ss1926014006, ss1970355912, ss2023639339, ss2151805336, ss2451310274, ss2626306469, ss2707398709, ss2735645501, ss2747580671, ss2837409779, ss2985360833, ss2998790534, ss3629501510, ss3636777262, ss3638619348 NC_000006.11:31323837:C= NC_000006.12:31356060:C= (self)
ss539212509, ss2282937676, ss3493805891, ss3493805892, ss3493805893 NC_000006.12:31356060:C= NC_000006.12:31356060:C= (self)
ss3651250, ss12689641, ss42672803, ss98379600, ss105990493, ss139855504, ss156738231, ss160562141, ss168909536, ss244291219 NT_007592.15:31263837:C= NC_000006.12:31356060:C= (self)
ss3493805891 NC_000006.12:31356060:C>A NC_000006.12:31356060:C>A (self)
ss109896806, ss116392642, ss162194295, ss201619619, ss207670545, ss254182447, ss278724301, ss285373196, ss293824736 NC_000006.10:31431816:C>G NC_000006.12:31356060:C>G (self)
31318001, 17462389, 8253612, 178037536, 4660236, 17462389, ss222301695, ss233396543, ss240467622, ss481462857, ss532732397, ss559111898, ss653032118, ss982762111, ss1073503362, ss1319550919, ss1615273383, ss1658267416, ss1688228557, ss1711120636, ss1804356132, ss1926014006, ss1970355912, ss2023639339, ss2151805336, ss2451310274, ss2626306469, ss2707398709, ss2735645501, ss2747580671, ss2837409779, ss2985360833, ss2998790534, ss3629501510, ss3636777262, ss3638619348 NC_000006.11:31323837:C>G NC_000006.12:31356060:C>G (self)
ss539212509, ss2282937676, ss3493805892 NC_000006.12:31356060:C>G NC_000006.12:31356060:C>G (self)
ss3651250, ss12689641, ss42672803, ss98379600, ss105990493, ss139855504, ss156738231, ss160562141, ss168909536, ss244291219 NT_007592.15:31263837:C>G NC_000006.12:31356060:C>G (self)
ss3493805893 NC_000006.12:31356060:C>T NC_000006.12:31356060:C>T (self)
Help

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

1 citation for rs2596494
PMID Title Author Year Journal
21194676 Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Lanktree MB et al. 2011 American journal of human genetics

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.

Software version is: 0.1.4.post833+d3ba21e