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dbSNP Short Genetic Variations

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.

rs1264813

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr6:29972123 (GRCh38.p12) 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=0.090819 (11404/125568, TOPMED)
T=0.10791 (3382/31340, GnomAD)
T=0.1254 (628/5008, 1000G) (+ 13 more)
T=0.1270 (569/4480, Estonian)
T=0.0981 (378/3854, ALSPAC)
T=0.0949 (352/3708, TWINSUK)
T=0.2266 (664/2930, KOREAN)
T=0.1074 (235/2188, ALFA Project)
T=0.121 (121/998, GoNL)
T=0.122 (73/600, NorthernSweden)
T=0.022 (12/534, MGP)
T=0.069 (15/216, Qatari)
C=0.391 (75/192, SGDP_PRJ)
T=0.07 (3/40, GENOME_DK)
C=0.50 (12/24, Siberian)
T=0.50 (12/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p12 chr 6 NC_000006.12:g.29972123C>T
GRCh37.p13 chr 6 NC_000006.11:g.29939900C>T
MICD pseudogene NG_015983.1:g.3723G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1227106C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1232702C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1451511C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1451617C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1227663C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1233248C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1269918C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1269216C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1232857C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1238477C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1316166C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1321751C>T
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

ALFA Allele Frequency (New)
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: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 2188 C=0.8926 T=0.1074
European Sub 2072 C=0.8885 T=0.1115
African Sub 82 C=0.98 T=0.02
African Others Sub 6 C=1.0 T=0.0
African American Sub 76 C=0.97 T=0.03
Asian Sub 4 C=1.0 T=0.0
East Asian Sub 2 C=1.0 T=0.0
Other Asian Sub 2 C=1.0 T=0.0
Latin American 1 Sub 0 C=0 T=0
Latin American 2 Sub 0 C=0 T=0
South Asian Sub 4 C=1.0 T=0.0
Other Sub 26 C=0.92 T=0.08


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
TopMed Global Study-wide 125568 C=0.909181 T=0.090819
gnomAD - Genomes Global Study-wide 31340 C=0.89209 T=0.10791
gnomAD - Genomes European Sub 18866 C=0.86531 T=0.13469
gnomAD - Genomes African Sub 8700 C=0.9710 T=0.0290
gnomAD - Genomes East Asian Sub 1550 C=0.8206 T=0.1794
gnomAD - Genomes Other Sub 1086 C=0.8471 T=0.1529
gnomAD - Genomes American Sub 848 C=0.863 T=0.137
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.900 T=0.100
1000Genomes Global Study-wide 5008 C=0.8746 T=0.1254
1000Genomes African Sub 1322 C=0.9902 T=0.0098
1000Genomes East Asian Sub 1008 C=0.7679 T=0.2321
1000Genomes Europe Sub 1006 C=0.8757 T=0.1243
1000Genomes South Asian Sub 978 C=0.836 T=0.164
1000Genomes American Sub 694 C=0.862 T=0.138
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8730 T=0.1270
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9019 T=0.0981
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9051 T=0.0949
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.7734 T=0.2266
ALFA Total Global 2188 C=0.8926 T=0.1074
ALFA European Sub 2072 C=0.8885 T=0.1115
ALFA African Sub 82 C=0.98 T=0.02
ALFA Other Sub 26 C=0.92 T=0.08
ALFA South Asian Sub 4 C=1.0 T=0.0
ALFA Asian Sub 4 C=1.0 T=0.0
ALFA Latin American 1 Sub 0 C=0 T=0
ALFA Latin American 2 Sub 0 C=0 T=0
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.879 T=0.121
Northern Sweden ACPOP Study-wide 600 C=0.878 T=0.122
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.978 T=0.022
Qatari Global Study-wide 216 C=0.931 T=0.069
SGDP_PRJ Global Study-wide 192 C=0.391 T=0.609
The Danish reference pan genome Danish Study-wide 40 C=0.93 T=0.07
Siberian Global Study-wide 24 C=0.50 T=0.50
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= T
GRCh38.p12 chr 6 NC_000006.12:g.29972123= NC_000006.12:g.29972123C>T
GRCh37.p13 chr 6 NC_000006.11:g.29939900= NC_000006.11:g.29939900C>T
MICD pseudogene NG_015983.1:g.3723= NG_015983.1:g.3723G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1227106= NT_167248.2:g.1227106C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1232702= NT_167248.1:g.1232702C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1451511= NT_113891.3:g.1451511C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1451617= NT_113891.2:g.1451617C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1227663= NT_167245.2:g.1227663C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1233248= NT_167245.1:g.1233248C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1269918= NT_167249.2:g.1269918C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1269216= NT_167249.1:g.1269216C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1232857= NT_167246.2:g.1232857C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1238477= NT_167246.1:g.1238477C>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1316166= NT_167247.2:g.1316166C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1321751= NT_167247.1:g.1321751C>T
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#.

49 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1950432 Oct 18, 2000 (87)
2 SC_JCM ss2432709 Nov 09, 2000 (92)
3 BCM_SSAHASNP ss10285743 Jul 11, 2003 (117)
4 SC_SNP ss12813356 Dec 05, 2003 (119)
5 SSAHASNP ss22397803 Apr 05, 2004 (121)
6 FHCRC ss23135603 Sep 20, 2004 (126)
7 ABI ss42852446 Mar 10, 2006 (126)
8 1000GENOMES ss109878223 Feb 13, 2009 (137)
9 GMI ss156705506 Dec 01, 2009 (131)
10 1000GENOMES ss233385593 Jul 14, 2010 (137)
11 1000GENOMES ss240457226 Jul 15, 2010 (137)
12 GMI ss278712698 May 04, 2012 (137)
13 GMI ss285368494 Apr 25, 2013 (138)
14 TISHKOFF ss559100091 Apr 25, 2013 (138)
15 SSMP ss653016423 Apr 25, 2013 (138)
16 EVA-GONL ss982741675 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1073490933 Aug 21, 2014 (142)
18 1000GENOMES ss1319506211 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1581594638 Apr 01, 2015 (144)
20 EVA_DECODE ss1592289273 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1615247028 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1658241061 Apr 01, 2015 (144)
23 EVA_MGP ss1711118503 Apr 01, 2015 (144)
24 WEILL_CORNELL_DGM ss1925993856 Feb 12, 2016 (147)
25 ILLUMINA ss1958879798 Feb 12, 2016 (147)
26 GENOMED ss1970349470 Jul 19, 2016 (147)
27 JJLAB ss2023624358 Sep 14, 2016 (149)
28 ILLUMINA ss2094950288 Dec 20, 2016 (150)
29 ILLUMINA ss2095173441 Dec 20, 2016 (150)
30 USC_VALOUEV ss2151789641 Nov 08, 2017 (151)
31 HUMAN_LONGEVITY ss2282863050 Dec 20, 2016 (150)
32 TOPMED ss2451232023 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2626298391 Nov 08, 2017 (151)
34 GRF ss2707381829 Nov 08, 2017 (151)
35 GNOMAD ss2837297214 Nov 08, 2017 (151)
36 SWEGEN ss2998760666 Nov 08, 2017 (151)
37 ILLUMINA ss3022591670 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3025597405 Nov 08, 2017 (151)
39 TOPMED ss3493566901 Nov 08, 2017 (151)
40 ILLUMINA ss3653102070 Oct 12, 2018 (152)
41 EGCUT_WGS ss3666683536 Jul 13, 2019 (153)
42 EVA_DECODE ss3716870957 Jul 13, 2019 (153)
43 ILLUMINA ss3726324676 Jul 13, 2019 (153)
44 ACPOP ss3733337117 Jul 13, 2019 (153)
45 EVA ss3764796019 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3807952008 Jul 13, 2019 (153)
47 EVA ss3829815153 Apr 26, 2020 (154)
48 SGDP_PRJ ss3864214615 Apr 26, 2020 (154)
49 KRGDB ss3910989659 Apr 26, 2020 (154)
50 1000Genomes NC_000006.11 - 29939900 Oct 12, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 29939900 Oct 12, 2018 (152)
52 Genetic variation in the Estonian population NC_000006.11 - 29939900 Oct 12, 2018 (152)
53 The Danish reference pan genome NC_000006.11 - 29939900 Apr 26, 2020 (154)
54 gnomAD - Genomes NC_000006.11 - 29939900 Jul 13, 2019 (153)
55 Genome of the Netherlands Release 5 NC_000006.11 - 29939900 Apr 26, 2020 (154)
56 KOREAN population from KRGDB NC_000006.11 - 29939900 Apr 26, 2020 (154)
57 Medical Genome Project healthy controls from Spanish population NC_000006.11 - 29939900 Apr 26, 2020 (154)
58 Northern Sweden NC_000006.11 - 29939900 Jul 13, 2019 (153)
59 Qatari NC_000006.11 - 29939900 Apr 26, 2020 (154)
60 SGDP_PRJ NC_000006.11 - 29939900 Apr 26, 2020 (154)
61 Siberian NC_000006.11 - 29939900 Apr 26, 2020 (154)
62 TopMed NC_000006.12 - 29972123 Oct 12, 2018 (152)
63 UK 10K study - Twins NC_000006.11 - 29939900 Oct 12, 2018 (152)
64 dbGaP Population Frequency Project NC_000006.12 - 29972123 Apr 26, 2020 (154)
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)
rs1617382 Jan 18, 2001 (92)
rs6908134 Aug 27, 2003 (117)
rs17180290 Mar 10, 2006 (126)
rs114660809 May 04, 2012 (137)
rs117616858 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss109878223, ss278712698, ss285368494, ss1592289273, ss2094950288 NC_000006.10:30047878:C:T NC_000006.12:29972122:C:T (self)
31271378, 17433040, 12421784, 7759577, 85547164, 7741799, 18167053, 234263, 6621982, 8035786, 16231595, 4305995, 17433040, ss233385593, ss240457226, ss559100091, ss653016423, ss982741675, ss1073490933, ss1319506211, ss1581594638, ss1615247028, ss1658241061, ss1711118503, ss1925993856, ss1958879798, ss1970349470, ss2023624358, ss2095173441, ss2151789641, ss2451232023, ss2626298391, ss2707381829, ss2837297214, ss2998760666, ss3022591670, ss3653102070, ss3666683536, ss3733337117, ss3764796019, ss3829815153, ss3864214615, ss3910989659 NC_000006.11:29939899:C:T NC_000006.12:29972122:C:T (self)
334838488, 257100005, ss2282863050, ss3025597405, ss3493566901, ss3716870957, ss3726324676, ss3807952008 NC_000006.12:29972122:C:T NC_000006.12:29972122:C:T (self)
ss10285743, ss12813356, ss22397803 NT_007592.13:20796008:T:T NC_000006.12:29972122:C:T (self)
ss1950432, ss2432709, ss23135603, ss42852446, ss156705506 NT_007592.15:29879899:C:T NC_000006.12:29972122: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 rs1264813
PMID Title Author Year Journal
30083439 Single nucleotide polymorphisms within HLA region are associated with disease relapse for patients with unrelated cord blood transplantation. Chen DP et al. 2018 PeerJ
Help

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.

Software version is: 2.0.1.post536+f5d31d6