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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.

rs1042178

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr6:33069745 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.24040 (57844/240620, GnomAD)
C=0.31070 (39014/125568, TOPMED)
C=0.24670 (28646/116118, ExAC) (+ 5 more)
C=0.2817 (8702/30894, GnomAD)
C=0.280 (2365/8440, GO-ESP)
C=0.438 (2196/5008, 1000G)
C=0.185 (712/3854, ALSPAC)
C=0.158 (585/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HLA-DPA1 : Missense Variant
Publications
0 citations
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.33069745T>C
GRCh37.p13 chr 6 NC_000006.11:g.33037522T>C
HLA-DPA1 RefSeqGene NG_033241.1:g.16034A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4518728T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4518026T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.4489442T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.4495062T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4264377T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4269973T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4313276T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4318861T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4368810T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4374395T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.4374425T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.4324341T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4481596T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4481702T>C
Gene: HLA-DPA1, major histocompatibility complex, class II, DP alpha 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HLA-DPA1 transcript variant 1 NM_033554.3:c.242A>G Q [CAA] > R [CGA] Coding Sequence Variant
HLA class II histocompatibility antigen, DP alpha 1 chain precursor NP_291032.2:p.Gln...

NP_291032.2:p.Gln81Arg

Q (Gln) > R (Arg) Missense Variant
HLA-DPA1 transcript variant 2 NM_001242524.1:c....

NM_001242524.1:c.242A>G

Q [CAA] > R [CGA] Coding Sequence Variant
HLA class II histocompatibility antigen, DP alpha 1 chain precursor NP_001229453.1:p....

NP_001229453.1:p.Gln81Arg

Q (Gln) > R (Arg) Missense Variant
HLA-DPA1 transcript variant 3 NM_001242525.1:c....

NM_001242525.1:c.242A>G

Q [CAA] > R [CGA] Coding Sequence Variant
HLA class II histocompatibility antigen, DP alpha 1 chain precursor NP_001229454.1:p....

NP_001229454.1:p.Gln81Arg

Q (Gln) > R (Arg) Missense 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 240620 T=0.75960 C=0.24040
The Genome Aggregation Database European Sub 130368 T=0.84216 C=0.15784
The Genome Aggregation Database Asian Sub 47594 T=0.5501 C=0.4499
The Genome Aggregation Database American Sub 33410 T=0.8283 C=0.1717
The Genome Aggregation Database African Sub 14138 T=0.4881 C=0.5119
The Genome Aggregation Database Ashkenazi Jewish Sub 9708 T=0.817 C=0.183
The Genome Aggregation Database Other Sub 5402 T=0.795 C=0.205
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.68930 C=0.31070
The Genome Aggregation Database Global Study-wide 30894 T=0.7183 C=0.2817
The Genome Aggregation Database European Sub 18480 T=0.8467 C=0.1533
The Genome Aggregation Database African Sub 8678 T=0.507 C=0.493
The Genome Aggregation Database East Asian Sub 1616 T=0.267 C=0.733
The Genome Aggregation Database Other Sub 980 T=0.80 C=0.20
The Genome Aggregation Database American Sub 838 T=0.81 C=0.19
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.83 C=0.17
GO Exome Sequencing Project Global Study-wide 8440 T=0.720 C=0.280
GO Exome Sequencing Project European American Sub 5418 T=0.824 C=0.176
GO Exome Sequencing Project African American Sub 3022 T=0.533 C=0.467
1000Genomes Global Study-wide 5008 T=0.562 C=0.438
1000Genomes African Sub 1322 T=0.419 C=0.581
1000Genomes East Asian Sub 1008 T=0.320 C=0.680
1000Genomes Europe Sub 1006 T=0.813 C=0.187
1000Genomes South Asian Sub 978 T=0.63 C=0.37
1000Genomes American Sub 694 T=0.72 C=0.28
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.815 C=0.185
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.842 C=0.158
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 T= C Note
GRCh38.p7 chr 6 NC_000006.12:g.33069745T= NC_000006.12:g.33069745T>C
GRCh37.p13 chr 6 NC_000006.11:g.33037522T= NC_000006.11:g.33037522T>C
HLA-DPA1 RefSeqGene NG_033241.1:g.16034A= NG_033241.1:g.16034A>G
HLA-DPA1 transcript variant 1 NM_033554.3:c.242A= NM_033554.3:c.242A>G
HLA-DPA1 transcript variant 2 NM_001242524.1:c.242A= NM_001242524.1:c.242A>G
HLA-DPA1 transcript variant 3 NM_001242525.1:c.242A= NM_001242525.1:c.242A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4518728T= NT_167249.2:g.4518728T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4518026T= NT_167249.1:g.4518026T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.4489442T= NT_167246.2:g.4489442T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.4495062T= NT_167246.1:g.4495062T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4264377T= NT_167248.2:g.4264377T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4269973T= NT_167248.1:g.4269973T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4313276T= NT_167245.2:g.4313276T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4318861T= NT_167245.1:g.4318861T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4368810T= NT_167247.2:g.4368810T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4374395T= NT_167247.1:g.4374395T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.4374425T= NT_167244.2:g.4374425T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.4324341T= NT_167244.1:g.4324341T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4481596T= NT_113891.3:g.4481596T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4481702T= NT_113891.2:g.4481702T>C
HLA class II histocompatibility antigen, DP alpha 1 chain precursor NP_291032.2:p.Gln81= NP_291032.2:p.Gln81Arg
HLA class II histocompatibility antigen, DP alpha 1 chain precursor NP_001229453.1:p.Gln81= NP_001229453.1:p.Gln81Arg
HLA class II histocompatibility antigen, DP alpha 1 chain precursor NP_001229454.1:p.Gln81= NP_001229454.1:p.Gln81Arg
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#.

8 Frequency, 73 SubSNP submissions
No Submitter Submission ID Date (Build)
1 LEE ss1509157 Oct 05, 2000 (86)
2 LEE ss4390596 May 29, 2002 (106)
3 LEE ss4403450 May 29, 2002 (106)
4 DBMHC ss20422208 Dec 12, 2006 (127)
5 PERLEGEN ss23718763 Sep 20, 2004 (123)
6 SEQUENOM ss24819982 Sep 20, 2004 (123)
7 ABI ss42701887 Mar 13, 2006 (126)
8 APPLERA_GI ss48408522 Mar 13, 2006 (126)
9 PERLEGEN ss68972546 May 18, 2007 (130)
10 ILLUMINA ss70365410 May 18, 2007 (130)
11 ILLUMINA ss70478255 May 25, 2008 (130)
12 ILLUMINA ss71001518 May 18, 2007 (130)
13 AFFY ss74815595 Aug 16, 2007 (130)
14 ILLUMINA ss75469085 Dec 07, 2007 (129)
15 KRIBB_YJKIM ss83672150 Dec 15, 2007 (130)
16 BGI ss104300853 Feb 13, 2009 (130)
17 1000GENOMES ss109929005 Feb 13, 2009 (137)
18 1000GENOMES ss114178263 Jan 25, 2009 (137)
19 ILLUMINA-UK ss116408794 Feb 14, 2009 (130)
20 ILLUMINA ss121304177 Dec 01, 2009 (131)
21 GMI ss156778566 Dec 01, 2009 (131)
22 SEATTLESEQ ss159712361 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss163379519 Jul 04, 2010 (132)
24 BUSHMAN ss201659387 Jul 04, 2010 (132)
25 1000GENOMES ss222322578 Jul 14, 2010 (137)
26 1000GENOMES ss233419997 Jul 14, 2010 (137)
27 1000GENOMES ss240486298 Jul 15, 2010 (137)
28 BL ss254221362 May 09, 2011 (137)
29 GMI ss278745228 May 04, 2012 (137)
30 PJP ss293833030 May 09, 2011 (137)
31 NHLBI-ESP ss342208670 May 09, 2011 (137)
32 ILLUMINA ss479633867 Sep 08, 2015 (146)
33 ILLUMINA ss483459431 May 04, 2012 (137)
34 ILLUMINA ss485229820 May 04, 2012 (137)
35 CLINSEQ_SNP ss491887407 May 04, 2012 (137)
36 ILLUMINA ss535669192 Sep 08, 2015 (146)
37 TISHKOFF ss559123995 Apr 25, 2013 (138)
38 SSMP ss653056866 Apr 25, 2013 (138)
39 ILLUMINA ss779507692 Aug 21, 2014 (142)
40 ILLUMINA ss782173084 Aug 21, 2014 (142)
41 ILLUMINA ss825335141 Apr 01, 2015 (144)
42 ILLUMINA ss834978007 Aug 21, 2014 (142)
43 EVA-GONL ss982792285 Aug 21, 2014 (142)
44 JMKIDD_LAB ss1067478016 Aug 21, 2014 (142)
45 JMKIDD_LAB ss1073516356 Aug 21, 2014 (142)
46 1000GENOMES ss1319610266 Aug 21, 2014 (142)
47 EVA_GENOME_DK ss1581618334 Apr 01, 2015 (144)
48 EVA_FINRISK ss1584045860 Apr 01, 2015 (144)
49 EVA_DECODE ss1592325448 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1615299218 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1658293251 Apr 01, 2015 (144)
52 EVA_EXAC ss1688263486 Apr 01, 2015 (144)
53 EVA_MGP ss1711124884 Apr 01, 2015 (144)
54 WEILL_CORNELL_DGM ss1926050099 Feb 12, 2016 (147)
55 ILLUMINA ss1958897260 Feb 12, 2016 (147)
56 JJLAB ss2023661411 Sep 14, 2016 (149)
57 USC_VALOUEV ss2151837353 Dec 20, 2016 (150)
58 HUMAN_LONGEVITY ss2283012590 Dec 20, 2016 (150)
59 TOPMED ss2451395011 Dec 20, 2016 (150)
60 SYSTEMSBIOZJU ss2626318960 Nov 08, 2017 (151)
61 ILLUMINA ss2634435620 Nov 08, 2017 (151)
62 GRF ss2707432396 Nov 08, 2017 (151)
63 GNOMAD ss2735699585 Nov 08, 2017 (151)
64 GNOMAD ss2747597395 Nov 08, 2017 (151)
65 GNOMAD ss2837546970 Nov 08, 2017 (151)
66 SWEGEN ss2998849815 Nov 08, 2017 (151)
67 ILLUMINA ss3022608096 Nov 08, 2017 (151)
68 BIOINF_KMB_FNS_UNIBA ss3025622441 Nov 08, 2017 (151)
69 TOPMED ss3494114179 Nov 08, 2017 (151)
70 ILLUMINA ss3629515403 Jul 20, 2018 (151)
71 ILLUMINA ss3632353403 Jul 20, 2018 (151)
72 ILLUMINA ss3636783111 Jul 20, 2018 (151)
73 ILLUMINA ss3643564278 Jul 20, 2018 (151)
74 1000Genomes NC_000006.11 - 33037522 Jul 20, 2018 (151)
75 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 33037522 Jul 20, 2018 (151)
76 The Exome Aggregation Consortium NC_000006.11 - 33037522 Jul 20, 2018 (151)
77 The Genome Aggregation Database NC_000006.11 - 33037522 Jul 20, 2018 (151)
78 The Genome Aggregation Database NC_000006.11 - 33037522 Jul 20, 2018 (151)
79 GO Exome Sequencing Project NC_000006.11 - 33037522 Jul 20, 2018 (151)
80 Trans-Omics for Precision Medicine NC_000006.12 - 33069745 Jul 20, 2018 (151)
81 UK 10K study - Twins NC_000006.11 - 33037522 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)
rs2308915 Sep 24, 2004 (123)
rs3173302 Jul 03, 2002 (106)
rs16868557 Oct 08, 2004 (123)
rs16868559 Oct 08, 2004 (123)
rs45614833 May 25, 2008 (130)
rs52792876 Sep 21, 2007 (128)
rs60098014 May 25, 2008 (130)
rs114025661 May 04, 2012 (137)
rs117006873 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss109929005, ss114178263, ss116408794, ss163379519, ss201659387, ss254221362, ss278745228, ss293833030, ss485229820, ss491887407, ss825335141, ss1592325448, ss3643564278 NC_000006.10:33145499:T= NC_000006.12:33069744:T= (self)
31379711, 17491613, 8291570, 178174727, 4714320, 633960, 17491613, ss222322578, ss233419997, ss240486298, ss342208670, ss479633867, ss483459431, ss535669192, ss559123995, ss653056866, ss779507692, ss782173084, ss834978007, ss982792285, ss1067478016, ss1073516356, ss1319610266, ss1581618334, ss1584045860, ss1615299218, ss1658293251, ss1688263486, ss1711124884, ss1926050099, ss1958897260, ss2023661411, ss2151837353, ss2451395011, ss2626318960, ss2634435620, ss2707432396, ss2735699585, ss2747597395, ss2837546970, ss2998849815, ss3022608096, ss3629515403, ss3632353403, ss3636783111 NC_000006.11:33037521:T= NC_000006.12:33069744:T= (self)
335211927, ss2283012590, ss3025622441, ss3494114179 NC_000006.12:33069744:T= NC_000006.12:33069744:T= (self)
ss1509157, ss4390596, ss4403450, ss20422208, ss23718763, ss24819982, ss42701887, ss48408522, ss68972546, ss70365410, ss70478255, ss71001518, ss74815595, ss75469085, ss83672150, ss104300853, ss121304177, ss156778566, ss159712361 NT_007592.15:32977521:T= NC_000006.12:33069744:T= (self)
ss109929005, ss114178263, ss116408794, ss163379519, ss201659387, ss254221362, ss278745228, ss293833030, ss485229820, ss491887407, ss825335141, ss1592325448, ss3643564278 NC_000006.10:33145499:T>C NC_000006.12:33069744:T>C (self)
31379711, 17491613, 8291570, 178174727, 4714320, 633960, 17491613, ss222322578, ss233419997, ss240486298, ss342208670, ss479633867, ss483459431, ss535669192, ss559123995, ss653056866, ss779507692, ss782173084, ss834978007, ss982792285, ss1067478016, ss1073516356, ss1319610266, ss1581618334, ss1584045860, ss1615299218, ss1658293251, ss1688263486, ss1711124884, ss1926050099, ss1958897260, ss2023661411, ss2151837353, ss2451395011, ss2626318960, ss2634435620, ss2707432396, ss2735699585, ss2747597395, ss2837546970, ss2998849815, ss3022608096, ss3629515403, ss3632353403, ss3636783111 NC_000006.11:33037521:T>C NC_000006.12:33069744:T>C (self)
335211927, ss2283012590, ss3025622441, ss3494114179 NC_000006.12:33069744:T>C NC_000006.12:33069744:T>C (self)
ss1509157, ss4390596, ss4403450, ss20422208, ss23718763, ss24819982, ss42701887, ss48408522, ss68972546, ss70365410, ss70478255, ss71001518, ss74815595, ss75469085, ss83672150, ss104300853, ss121304177, ss156778566, ss159712361 NT_007592.15:32977521:T>C NC_000006.12:33069744:T>C (self)
Help

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

No publications for rs1042178

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