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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1136754

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:29944144 (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 / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.002818 (331/117460, ExAC)
T=0.06897 (3092/44834, ALFA)
T=0.03632 (970/26708, 14KJPN) (+ 6 more)
T=0.42469 (7105/16730, 8.3KJPN)
T=0.0084 (54/6404, 1000G_30x)
T=0.4329 (1264/2920, KOREAN)
C=0.490 (196/400, SGDP_PRJ)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HLA-A : Synonymous Variant
LOC124901298 : Intron Variant
Publications
1 citation
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 44834 C=0.93103 G=0.00000, T=0.06897
European Sub 33766 C=0.92102 G=0.00000, T=0.07898
African Sub 3108 C=0.9817 G=0.0000, T=0.0183
African Others Sub 100 C=0.99 G=0.00, T=0.01
African American Sub 3008 C=0.9814 G=0.0000, T=0.0186
Asian Sub 150 C=0.920 G=0.000, T=0.080
East Asian Sub 100 C=0.93 G=0.00, T=0.07
Other Asian Sub 50 C=0.90 G=0.00, T=0.10
Latin American 1 Sub 470 C=0.994 G=0.000, T=0.006
Latin American 2 Sub 570 C=1.000 G=0.000, T=0.000
South Asian Sub 84 C=1.00 G=0.00, T=0.00
Other Sub 6686 C=0.9472 G=0.0000, T=0.0528


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
ExAC Global Study-wide 117460 C=0.997182 T=0.002818
ExAC Europe Sub 71250 C=0.99771 T=0.00229
ExAC Asian Sub 24536 C=0.99605 T=0.00395
ExAC American Sub 11440 C=0.99825 T=0.00175
ExAC African Sub 9352 C=0.9948 T=0.0052
ExAC Other Sub 882 C=0.998 T=0.002
Allele Frequency Aggregator Total Global 44834 C=0.93103 G=0.00000, T=0.06897
Allele Frequency Aggregator European Sub 33766 C=0.92102 G=0.00000, T=0.07898
Allele Frequency Aggregator Other Sub 6686 C=0.9472 G=0.0000, T=0.0528
Allele Frequency Aggregator African Sub 3108 C=0.9817 G=0.0000, T=0.0183
Allele Frequency Aggregator Latin American 2 Sub 570 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 470 C=0.994 G=0.000, T=0.006
Allele Frequency Aggregator Asian Sub 150 C=0.920 G=0.000, T=0.080
Allele Frequency Aggregator South Asian Sub 84 C=1.00 G=0.00, T=0.00
14KJPN JAPANESE Study-wide 26708 C=0.96368 T=0.03632
8.3KJPN JAPANESE Study-wide 16730 C=0.57531 T=0.42469
1000Genomes_30x Global Study-wide 6404 C=0.9916 T=0.0084
1000Genomes_30x African Sub 1786 C=0.9922 T=0.0078
1000Genomes_30x Europe Sub 1266 C=0.9961 T=0.0039
1000Genomes_30x South Asian Sub 1202 C=0.9875 T=0.0125
1000Genomes_30x East Asian Sub 1170 C=0.9897 T=0.0103
1000Genomes_30x American Sub 980 C=0.992 T=0.008
KOREAN population from KRGDB KOREAN Study-wide 2920 C=0.5671 T=0.4329
SGDP_PRJ Global Study-wide 400 C=0.490 T=0.510
Siberian Global Study-wide 6 C=0.5 T=0.5
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.p14 chr 6 NC_000006.12:g.29944144C>G
GRCh38.p14 chr 6 NC_000006.12:g.29944144C>T
GRCh37.p13 chr 6 NC_000006.11:g.29911921C>G
GRCh37.p13 chr 6 NC_000006.11:g.29911921C>T
HLA-A RefSeqGene NG_029217.2:g.6680C>G
HLA-A RefSeqGene NG_029217.2:g.6680C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1423567C>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1423567C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1423673C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1423673C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1201892C>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1201892C>T
GRCh37.p13 chr 6 fix patch HG1322_PATCH NW_003871063.1:g.178069C>G
GRCh37.p13 chr 6 fix patch HG1322_PATCH NW_003871063.1:g.178069C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1199125T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1199125T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1204721T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1204721T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1199719T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1199719T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1205304T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1205304T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1241979T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1241979T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1241277T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1241277T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1198707T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1198707T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1204327T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1204327T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1288246T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1288246T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1293831T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1293831T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1151808C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1151808C>T
Gene: HLA-A, major histocompatibility complex, class I, A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
HLA-A transcript variant 1 (A*03:01:01:01) NM_002116.8:c.642C>G T [ACC] > T [ACG] Coding Sequence Variant
HLA class I histocompatibility antigen, A alpha chain isoform A*03:01:01:01 precursor NP_002107.3:p.Thr214= T (Thr) > T (Thr) Synonymous Variant
HLA-A transcript variant 1 (A*03:01:01:01) NM_002116.8:c.642C>T T [ACC] > T [ACT] Coding Sequence Variant
HLA class I histocompatibility antigen, A alpha chain isoform A*03:01:01:01 precursor NP_002107.3:p.Thr214= T (Thr) > T (Thr) Synonymous Variant
Gene: LOC124901298, uncharacterized LOC124901298 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124901298 transcript variant X1 XR_007059541.1:n. N/A Intron 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

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 T
GRCh38.p14 chr 6 NC_000006.12:g.29944144= NC_000006.12:g.29944144C>G NC_000006.12:g.29944144C>T
GRCh37.p13 chr 6 NC_000006.11:g.29911921= NC_000006.11:g.29911921C>G NC_000006.11:g.29911921C>T
HLA-A RefSeqGene NG_029217.2:g.6680= NG_029217.2:g.6680C>G NG_029217.2:g.6680C>T
HLA-A transcript variant 1 (A*03:01:01:01) NM_002116.8:c.642= NM_002116.8:c.642C>G NM_002116.8:c.642C>T
HLA-A transcript variant 1 (A*03:01:0:01) NM_002116.7:c.642= NM_002116.7:c.642C>G NM_002116.7:c.642C>T
HLA-A transcript variant 2 (A*01:01:01:01) NM_001242758.1:c.709-91T>C NM_001242758.1:c.709-91T>G NM_001242758.1:c.709-91=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1423567= NT_113891.3:g.1423567C>G NT_113891.3:g.1423567C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1423673= NT_113891.2:g.1423673C>G NT_113891.2:g.1423673C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1201892= NT_167244.2:g.1201892C>G NT_167244.2:g.1201892C>T
GRCh37.p13 chr 6 fix patch HG1322_PATCH NW_003871063.1:g.178069= NW_003871063.1:g.178069C>G NW_003871063.1:g.178069C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1199125T>C NT_167248.2:g.1199125T>G NT_167248.2:g.1199125=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1204721T>C NT_167248.1:g.1204721T>G NT_167248.1:g.1204721=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1199719T>C NT_167245.2:g.1199719T>G NT_167245.2:g.1199719=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1205304T>C NT_167245.1:g.1205304T>G NT_167245.1:g.1205304=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1241979T>C NT_167249.2:g.1241979T>G NT_167249.2:g.1241979=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1241277T>C NT_167249.1:g.1241277T>G NT_167249.1:g.1241277=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1198707T>C NT_167246.2:g.1198707T>G NT_167246.2:g.1198707=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1204327T>C NT_167246.1:g.1204327T>G NT_167246.1:g.1204327=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1288246T>C NT_167247.2:g.1288246T>G NT_167247.2:g.1288246=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1293831T>C NT_167247.1:g.1293831T>G NT_167247.1:g.1293831=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1151808= NT_167244.1:g.1151808C>G NT_167244.1:g.1151808C>T
HLA-A29.1 transcript NM_001080840.1:c.642T>C NM_001080840.1:c.642T>G NM_001080840.1:c.642=
HLA-A transcript variant X1 XM_041680768.2:c.633T>C XM_041680768.2:c.633T>G XM_041680768.2:c.633=
HLA-A transcript variant X2 XM_041680768.1:c.633T>C XM_041680768.1:c.633T>G XM_041680768.1:c.633=
HLA-A transcript variant X2 XM_041680767.1:c.633T>C XM_041680767.1:c.633T>G XM_041680767.1:c.633=
HLA class I histocompatibility antigen, A alpha chain isoform A*03:01:01:01 precursor NP_002107.3:p.Thr214= NP_002107.3:p.Thr214= NP_002107.3:p.Thr214=
HLA class I histocompatibility antigen, A alpha chain isoform A*01:01:01:01 precursor NP_001229687.1:p.Thr214= NP_001229687.1:p.Thr214= NP_001229687.1:p.Thr214=
HLA class I histocompatibility antigen, A alpha chain isoform X1 XP_041536701.1:p.Thr211= XP_041536701.1:p.Thr211= XP_041536701.1:p.Thr211=
HLA class I histocompatibility antigen, A alpha chain isoform X2 XP_041536702.1:p.Thr211= XP_041536702.1:p.Thr211= XP_041536702.1:p.Thr211=
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#.

37 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 LEE ss1542180 Oct 13, 2000 (86)
2 LEE ss4399147 May 29, 2002 (147)
3 LEE ss4428815 May 29, 2002 (108)
4 SI_MHC_SNP ss12681218 Oct 31, 2003 (126)
5 MGC_GENOME_DIFF ss28504658 Sep 24, 2004 (147)
6 MGC_GENOME_DIFF ss28506024 Sep 24, 2004 (147)
7 CLINSEQ_SNP ss491883603 May 04, 2012 (137)
8 DBMHC ss539215346 Oct 04, 2012 (137)
9 EVA_EXAC ss1688212210 Apr 01, 2015 (144)
10 HAMMER_LAB ss1804345669 Sep 08, 2015 (146)
11 USC_VALOUEV ss2151788480 Nov 08, 2017 (151)
12 SYSTEMSBIOZJU ss2626297804 Nov 08, 2017 (151)
13 GRF ss2707380626 Nov 08, 2017 (151)
14 GNOMAD ss2735619515 Nov 08, 2017 (151)
15 GNOMAD ss2747572113 Nov 08, 2017 (151)
16 SWEGEN ss2998758332 Nov 08, 2017 (151)
17 URBANLAB ss3648303462 Oct 12, 2018 (152)
18 PACBIO ss3785415455 Jul 13, 2019 (153)
19 PACBIO ss3790775381 Jul 13, 2019 (153)
20 PACBIO ss3795652746 Jul 13, 2019 (153)
21 EVA ss3843826123 Apr 26, 2020 (154)
22 SGDP_PRJ ss3864212186 Apr 26, 2020 (154)
23 KRGDB ss3910987197 Apr 26, 2020 (154)
24 EVA ss3986034119 Apr 26, 2021 (155)
25 TOMMO_GENOMICS ss5176771082 Apr 26, 2021 (155)
26 EVA ss5237189899 Apr 26, 2021 (155)
27 1000G_HIGH_COVERAGE ss5267883931 Oct 13, 2022 (156)
28 EVA ss5364648963 Oct 13, 2022 (156)
29 1000G_HIGH_COVERAGE ss5553525735 Oct 13, 2022 (156)
30 EVA ss5623935175 Oct 13, 2022 (156)
31 SANFORD_IMAGENETICS ss5640050643 Oct 13, 2022 (156)
32 TOMMO_GENOMICS ss5714608489 Oct 13, 2022 (156)
33 EVA ss5799402381 Oct 13, 2022 (156)
34 EVA ss5800128225 Oct 13, 2022 (156)
35 YY_MCH ss5807281822 Oct 13, 2022 (156)
36 EVA ss5936530187 Oct 13, 2022 (156)
37 EVA ss5980353244 Oct 13, 2022 (156)
38 1000Genomes_30x NC_000006.12 - 29944144 Oct 13, 2022 (156)
39 ExAC NC_000006.11 - 29911921 Oct 12, 2018 (152)
40 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 220908080 (NC_000006.12:29944143:C:G 1/87704)
Row 220908081 (NC_000006.12:29944143:C:T 633/85546)

- Apr 26, 2021 (155)
41 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 220908080 (NC_000006.12:29944143:C:G 1/87704)
Row 220908081 (NC_000006.12:29944143:C:T 633/85546)

- Apr 26, 2021 (155)
42 KOREAN population from KRGDB NC_000006.11 - 29911921 Apr 26, 2020 (154)
43 SGDP_PRJ NC_000006.11 - 29911921 Apr 26, 2020 (154)
44 Siberian NC_000006.11 - 29911921 Apr 26, 2020 (154)
45 8.3KJPN NC_000006.11 - 29911921 Apr 26, 2021 (155)
46 14KJPN NC_000006.12 - 29944144 Oct 13, 2022 (156)
47 ALFA NC_000006.12 - 29944144 Apr 26, 2021 (155)
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)
rs2231075 Jul 19, 2016 (147)
rs3179212 May 24, 2008 (130)
rs3200282 Oct 09, 2002 (108)
rs9260176 Mar 10, 2006 (126)
rs17850356 May 23, 2006 (127)
rs17851722 Mar 11, 2006 (126)
rs41557812 Sep 21, 2007 (128)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
11525372496 NC_000006.12:29944143:C:G NC_000006.12:29944143:C:G (self)
ss1542180, ss4428815, ss491883603 NC_000006.10:30019899:C:T NC_000006.12:29944143:C:T (self)
8235762, 18164591, 16229166, 4304834, 34740389, ss1688212210, ss1804345669, ss2151788480, ss2626297804, ss2707380626, ss2735619515, ss2747572113, ss2998758332, ss3785415455, ss3790775381, ss3795652746, ss3864212186, ss3910987197, ss3986034119, ss5176771082, ss5364648963, ss5623935175, ss5640050643, ss5799402381, ss5800128225, ss5936530187, ss5980353244 NC_000006.11:29911920:C:T NC_000006.12:29944143:C:T (self)
41051670, 48445593, 11525372496, ss539215346, ss3648303462, ss3843826123, ss5237189899, ss5267883931, ss5553525735, ss5714608489, ss5807281822 NC_000006.12:29944143:C:T NC_000006.12:29944143:C:T (self)
ss4399147, ss12681218, ss28504658, ss28506024 NT_007592.15:29851920:C:T NC_000006.12:29944143: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 rs1136754
PMID Title Author Year Journal
32964195 SNPs in IL4 and IFNG show no protective associations with human African trypanosomiasis in the Democratic Republic of the Congo: a case-control study. Fataki Asina O et al. 2020 AAS open research
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.post761+d5e8e07