Name: rs1137110
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.

rs1137110

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:29944596 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.035494 (4090/115230, ExAC)
G=0.00154 (117/75738, GnomAD)
G=0.01615 (736/45586, ALFA) (+ 8 more)
G=0.01249 (296/23694, 14KJPN)
G=0.14350 (2405/16760, 8.3KJPN)
G=0.0031 (20/6404, 1000G_30x)
G=0.1949 (571/2930, KOREAN)
G=0.099 (99/998, GoNL)
G=0.082 (49/600, NorthernSweden)
G=0.097 (21/216, Qatari)
T=0.485 (65/134, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HLA-A : Missense 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	45586	T=0.98385	G=0.01615
European	Sub	34174	T=0.98423	G=0.01577
African	Sub	3442	T=0.9567	G=0.0433
African Others	Sub	116	T=0.966	G=0.034
African American	Sub	3326	T=0.9564	G=0.0436
Asian	Sub	164	T=0.982	G=0.018
East Asian	Sub	110	T=0.973	G=0.027
Other Asian	Sub	54	T=1.00	G=0.00
Latin American 1	Sub	476	T=0.987	G=0.013
Latin American 2	Sub	628	T=0.978	G=0.022
South Asian	Sub	94	T=0.99	G=0.01
Other	Sub	6608	T=0.9964	G=0.0036

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
ExAC	Global	Study-wide	115230	T=0.964506	G=0.035494
ExAC	Europe	Sub	69580	T=0.96128	G=0.03872
ExAC	Asian	Sub	24510	T=0.97976	G=0.02024
ExAC	American	Sub	11138	T=0.96256	G=0.03744
ExAC	African	Sub	9126	T=0.9522	G=0.0478
ExAC	Other	Sub	876	T=0.946	G=0.054
gnomAD - Genomes	Global	Study-wide	75738	T=0.99846	G=0.00154
gnomAD - Genomes	European	Sub	45066	T=0.99882	G=0.00118
gnomAD - Genomes	African	Sub	20564	T=0.99830	G=0.00170
gnomAD - Genomes	American	Sub	5604	T=0.9973	G=0.0027
gnomAD - Genomes	East Asian	Sub	1752	T=0.9960	G=0.0040
gnomAD - Genomes	Ashkenazi Jewish	Sub	1698	T=0.9971	G=0.0029
gnomAD - Genomes	Other	Sub	1054	T=0.9981	G=0.0019
Allele Frequency Aggregator	Total	Global	45586	T=0.98385	G=0.01615
Allele Frequency Aggregator	European	Sub	34174	T=0.98423	G=0.01577
Allele Frequency Aggregator	Other	Sub	6608	T=0.9964	G=0.0036
Allele Frequency Aggregator	African	Sub	3442	T=0.9567	G=0.0433
Allele Frequency Aggregator	Latin American 2	Sub	628	T=0.978	G=0.022
Allele Frequency Aggregator	Latin American 1	Sub	476	T=0.987	G=0.013
Allele Frequency Aggregator	Asian	Sub	164	T=0.982	G=0.018
Allele Frequency Aggregator	South Asian	Sub	94	T=0.99	G=0.01
14KJPN	JAPANESE	Study-wide	23694	T=0.98751	G=0.01249
8.3KJPN	JAPANESE	Study-wide	16760	T=0.85650	G=0.14350
1000Genomes_30x	Global	Study-wide	6404	T=0.9969	G=0.0031
1000Genomes_30x	African	Sub	1786	T=0.9972	G=0.0028
1000Genomes_30x	Europe	Sub	1266	T=0.9968	G=0.0032
1000Genomes_30x	South Asian	Sub	1202	T=0.9942	G=0.0058
1000Genomes_30x	East Asian	Sub	1170	T=0.9974	G=0.0026
1000Genomes_30x	American	Sub	980	T=0.999	G=0.001
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8051	G=0.1949
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.901	G=0.099
Northern Sweden	ACPOP	Study-wide	600	T=0.918	G=0.082
Qatari	Global	Study-wide	216	T=0.903	G=0.097
SGDP_PRJ	Global	Study-wide	134	T=0.485	G=0.515

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.29944596T>G
GRCh37.p13 chr 6	NC_000006.11:g.29912373T>G
HLA-A RefSeqGene	NG_029217.2:g.7132T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.1424019T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.1424125T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.2:g.1202344T>G
GRCh37.p13 chr 6 fix patch HG1322_PATCH	NW_003871063.1:g.178521T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.1199574T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.1205170T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.1200168T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.1205753T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.1242428G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.1241726G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.1199156G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.1204776G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.1288695T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.1294280T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.1:g.1152260T>G

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.992T>G	M [ATG] > R [AGG]	Coding Sequence Variant
HLA class I histocompatibility antigen, A alpha chain isoform A*03:01:01:01 precursor	NP_002107.3:p.Met331Arg	M (Met) > R (Arg)	Missense 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

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=	G
GRCh38.p14 chr 6	NC_000006.12:g.29944596=	NC_000006.12:g.29944596T>G
GRCh37.p13 chr 6	NC_000006.11:g.29912373=	NC_000006.11:g.29912373T>G
HLA-A RefSeqGene	NG_029217.2:g.7132=	NG_029217.2:g.7132T>G
HLA-A transcript variant 1 (A*03:01:01:01)	NM_002116.8:c.992=	NM_002116.8:c.992T>G
HLA-A transcript variant 1 (A*03:01:0:01)	NM_002116.7:c.992=	NM_002116.7:c.992T>G
HLA-A transcript variant 2 (A*01:01:01:01)	NM_001242758.1:c.992=	NM_001242758.1:c.992T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.1424019=	NT_113891.3:g.1424019T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.1424125=	NT_113891.2:g.1424125T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.2:g.1202344=	NT_167244.2:g.1202344T>G
GRCh37.p13 chr 6 fix patch HG1322_PATCH	NW_003871063.1:g.178521=	NW_003871063.1:g.178521T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.1199574=	NT_167248.2:g.1199574T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.1205170=	NT_167248.1:g.1205170T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.1200168=	NT_167245.2:g.1200168T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.1205753=	NT_167245.1:g.1205753T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.1242428G>T	NT_167249.2:g.1242428=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.1241726G>T	NT_167249.1:g.1241726=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.1199156G>T	NT_167246.2:g.1199156=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.1204776G>T	NT_167246.1:g.1204776=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.1288695=	NT_167247.2:g.1288695T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.1294280=	NT_167247.1:g.1294280T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.1:g.1152260=	NT_167244.1:g.1152260T>G
HLA-A29.1 transcript	NM_001080840.1:c.992G>T	NM_001080840.1:c.992=
HLA-A transcript variant X1	XM_041680768.2:c.983=	XM_041680768.2:c.983T>G
HLA-A transcript variant X2	XM_041680768.1:c.983=	XM_041680768.1:c.983T>G
HLA-A transcript variant X2	XM_041680767.1:c.983=	XM_041680767.1:c.983T>G
HLA class I histocompatibility antigen, A alpha chain isoform A*03:01:01:01 precursor	NP_002107.3:p.Met331=	NP_002107.3:p.Met331Arg
HLA class I histocompatibility antigen, A alpha chain isoform A*01:01:01:01 precursor	NP_001229687.1:p.Met331=	NP_001229687.1:p.Met331Arg
HLA class I histocompatibility antigen, A alpha chain isoform X1	XP_041536701.1:p.Met328=	XP_041536701.1:p.Met328Arg
HLA class I histocompatibility antigen, A alpha chain isoform X2	XP_041536702.1:p.Met328=	XP_041536702.1:p.Met328Arg

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#.

39 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	LEE	ss1543156	Oct 13, 2000 (86)
2	LEE	ss4399330	May 29, 2002 (136)
3	LEE	ss4429558	May 29, 2002 (108)
4	SI_MHC_SNP	ss12681237	Oct 31, 2003 (136)
5	1000GENOMES	ss333174532	May 09, 2011 (136)
6	EXOME_CHIP	ss491379948	May 04, 2012 (137)
7	CLINSEQ_SNP	ss491883639	May 04, 2012 (137)
8	DBMHC	ss539215475	Oct 04, 2012 (137)
9	TISHKOFF	ss559099197	Apr 25, 2013 (138)
10	SSMP	ss653015547	Apr 25, 2013 (138)
11	EVA-GONL	ss982740573	Aug 21, 2014 (142)
12	EVA_EXAC	ss1688212347	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1925992639	Feb 12, 2016 (147)
14	ILLUMINA	ss1958879337	Feb 12, 2016 (147)
15	JJLAB	ss2023623432	Sep 14, 2016 (149)
16	GRF	ss2707380654	Nov 08, 2017 (151)
17	GNOMAD	ss2735619664	Nov 08, 2017 (151)
18	GNOMAD	ss2747572182	Nov 08, 2017 (151)
19	SWEGEN	ss2998758378	Nov 08, 2017 (151)
20	ILLUMINA	ss3022591259	Nov 08, 2017 (151)
21	ILLUMINA	ss3653101623	Oct 12, 2018 (152)
22	ACPOP	ss3733335718	Jul 13, 2019 (153)
23	EVA	ss3764794925	Jul 13, 2019 (153)
24	SGDP_PRJ	ss3864212230	Apr 26, 2020 (154)
25	KRGDB	ss3910987236	Apr 26, 2020 (154)
26	TOMMO_GENOMICS	ss5176771142	Apr 26, 2021 (155)
27	EVA	ss5237021368	Apr 26, 2021 (155)
28	EVA	ss5364649015	Oct 13, 2022 (156)
29	1000G_HIGH_COVERAGE	ss5553525779	Oct 13, 2022 (156)
30	SANFORD_IMAGENETICS	ss5640050685	Oct 13, 2022 (156)
31	TOMMO_GENOMICS	ss5714608580	Oct 13, 2022 (156)
32	EVA	ss5799402417	Oct 13, 2022 (156)
33	EVA	ss5800128249	Oct 13, 2022 (156)
34	YY_MCH	ss5807281855	Oct 13, 2022 (156)
35	EVA	ss5841995959	Oct 13, 2022 (156)
36	EVA	ss5848649123	Oct 13, 2022 (156)
37	EVA	ss5883192536	Oct 13, 2022 (156)
38	EVA	ss5968556080	Oct 13, 2022 (156)
39	EVA	ss5980353262	Oct 13, 2022 (156)
40	1000Genomes_30x	NC_000006.12 - 29944596	Oct 13, 2022 (156)
41	ExAC	NC_000006.11 - 29912373	Oct 12, 2018 (152)
42	gnomAD - Genomes	NC_000006.12 - 29944596	Apr 26, 2021 (155)
43	Genome of the Netherlands Release 5	NC_000006.11 - 29912373	Apr 26, 2020 (154)
44	KOREAN population from KRGDB	NC_000006.11 - 29912373	Apr 26, 2020 (154)
45	Northern Sweden	NC_000006.11 - 29912373	Jul 13, 2019 (153)
46	Qatari	NC_000006.11 - 29912373	Apr 26, 2020 (154)
47	SGDP_PRJ	NC_000006.11 - 29912373	Apr 26, 2020 (154)
48	8.3KJPN	NC_000006.11 - 29912373	Apr 26, 2021 (155)
49	14KJPN	NC_000006.12 - 29944596	Oct 13, 2022 (156)
50	ALFA	NC_000006.12 - 29944596	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)
rs2231114	Mar 28, 2012 (136)
rs3179292	Sep 24, 2004 (123)
rs3200890	Oct 09, 2002 (108)
rs9260190	May 25, 2008 (130)
rs41561813	Sep 21, 2007 (128)
rs138805162	Mar 28, 2012 (136)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss491883639	NC_000006.10:30020351:T:G	NC_000006.12:29944595:T:G	(self)
8235907, 7740697, 18164630, 6620583, 8034569, 16229210, 34740449, ss333174532, ss491379948, ss559099197, ss653015547, ss982740573, ss1688212347, ss1925992639, ss1958879337, ss2023623432, ss2707380654, ss2735619664, ss2747572182, ss2998758378, ss3022591259, ss3653101623, ss3733335718, ss3764794925, ss3864212230, ss3910987236, ss5176771142, ss5364649015, ss5640050685, ss5799402417, ss5800128249, ss5841995959, ss5848649123, ss5968556080, ss5980353262	NC_000006.11:29912372:T:G	NC_000006.12:29944595:T:G	(self)
41051714, 220908169, 48445684, 1417477535, ss539215475, ss5237021368, ss5553525779, ss5714608580, ss5807281855, ss5883192536	NC_000006.12:29944595:T:G	NC_000006.12:29944595:T:G	(self)
ss1543156, ss4399330, ss4429558, ss12681237	NT_007592.15:29852372:T:G	NC_000006.12:29944595:T:G	(self)

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

1 citation for rs1137110

PMID	Title	Author	Year	Journal
21108794	Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.	Zhao Q et al.	2010	Genome biology

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

rs1137110