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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 Aliases 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.

rs6931763

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr6:30344155 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.13933 (17495/125568, TOPMED)
C=0.1293 (10172/78700, PAGE_STUDY)
C=0.1260 (3947/31324, GnomAD) (+ 6 more)
C=0.154 (769/5008, 1000G)
C=0.100 (448/4480, Estonian)
C=0.125 (483/3854, ALSPAC)
C=0.128 (473/3708, TWINSUK)
C=0.11 (64/600, NorthernSweden)
C=0.21 (45/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM39-RPP21 : Intron Variant
RPP21 : 2KB Upstream Variant
TRIM39 : 500B Downstream 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.p12 chr 6 NC_000006.12:g.30344155A>C
GRCh37.p13 chr 6 NC_000006.11:g.30311932A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1823836A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1823942A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1599237A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1604833A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1600001C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1605586C>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1642612A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1641910A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1654387A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1660007A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1673651C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1623567C>A
Gene: TRIM39-RPP21, TRIM39-RPP21 readthrough (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM39-RPP21 transcript NM_001199119.1:c. N/A Intron Variant
Gene: RPP21, ribonuclease P/MRP subunit p21 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
RPP21 transcript variant 1 NM_001199120.2:c. N/A Upstream Transcript Variant
RPP21 transcript variant 3 NM_001199121.2:c. N/A Upstream Transcript Variant
RPP21 transcript variant 2 NM_024839.3:c. N/A Upstream Transcript Variant
Gene: TRIM39, tripartite motif containing 39 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TRIM39 transcript variant 3 NM_001369521.1:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 4 NM_001369522.1:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 5 NM_001369523.1:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 1 NM_021253.4:c. N/A Downstream Transcript Variant
TRIM39 transcript variant 2 NM_172016.2:c. N/A Downstream 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
TopMed Global Study-wide 125568 A=0.86067 C=0.13933
The PAGE Study Global Study-wide 78700 A=0.8707 C=0.1293
The PAGE Study AfricanAmerican Sub 32516 A=0.8703 C=0.1297
The PAGE Study Mexican Sub 10810 A=0.8967 C=0.1033
The PAGE Study Asian Sub 8316 A=0.922 C=0.078
The PAGE Study PuertoRican Sub 7918 A=0.857 C=0.143
The PAGE Study NativeHawaiian Sub 4534 A=0.793 C=0.207
The PAGE Study Cuban Sub 4230 A=0.840 C=0.160
The PAGE Study Dominican Sub 3828 A=0.836 C=0.164
The PAGE Study CentralAmerican Sub 2450 A=0.889 C=0.111
The PAGE Study SouthAmerican Sub 1982 A=0.896 C=0.104
The PAGE Study NativeAmerican Sub 1260 A=0.896 C=0.104
The PAGE Study SouthAsian Sub 856 A=0.76 C=0.24
gnomAD - Genomes Global Study-wide 31324 A=0.8740 C=0.1260
gnomAD - Genomes European Sub 18870 A=0.8794 C=0.1206
gnomAD - Genomes African Sub 8680 A=0.871 C=0.129
gnomAD - Genomes East Asian Sub 1554 A=0.844 C=0.156
gnomAD - Genomes Other Sub 1082 A=0.867 C=0.133
gnomAD - Genomes American Sub 848 A=0.88 C=0.12
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.78 C=0.22
1000Genomes Global Study-wide 5008 A=0.846 C=0.154
1000Genomes African Sub 1322 A=0.888 C=0.112
1000Genomes East Asian Sub 1008 A=0.857 C=0.143
1000Genomes Europe Sub 1006 A=0.854 C=0.146
1000Genomes South Asian Sub 978 A=0.74 C=0.26
1000Genomes American Sub 694 A=0.88 C=0.12
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.900 C=0.100
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.875 C=0.125
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.872 C=0.128
Northern Sweden ACPOP Study-wide 600 A=0.89 C=0.11
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.79 C=0.21
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 A= C Note
GRCh38.p12 chr 6 NC_000006.12:g.30344155= NC_000006.12:g.30344155A>C
GRCh37.p13 chr 6 NC_000006.11:g.30311932= NC_000006.11:g.30311932A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1823836= NT_113891.3:g.1823836A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1823942= NT_113891.2:g.1823942A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1599237= NT_167248.2:g.1599237A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1604833= NT_167248.1:g.1604833A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1600001C>A NT_167245.2:g.1600001=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1605586C>A NT_167245.1:g.1605586=
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1642612= NT_167249.2:g.1642612A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1641910= NT_167249.1:g.1641910A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1654387= NT_167246.2:g.1654387A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1660007= NT_167246.1:g.1660007A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1673651C>A NT_167244.2:g.1673651=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1623567C>A NT_167244.1:g.1623567=
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#.

98 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10329968 Jul 11, 2003 (116)
2 SI_MHC_SNP ss35524166 May 24, 2005 (125)
3 KRIBB_YJKIM ss65846866 Nov 30, 2006 (127)
4 ILLUMINA ss75315808 Dec 07, 2007 (129)
5 HGSV ss78871898 Dec 07, 2007 (129)
6 BGI ss104293737 Feb 23, 2009 (131)
7 ILLUMINA-UK ss116382990 Feb 14, 2009 (130)
8 KRIBB_YJKIM ss119532843 Dec 01, 2009 (131)
9 ILLUMINA ss123434581 Dec 01, 2009 (131)
10 ILLUMINA ss154392676 Dec 01, 2009 (131)
11 ILLUMINA ss160826884 Dec 01, 2009 (131)
12 ILLUMINA ss172219785 Jul 04, 2010 (132)
13 ILLUMINA ss174171915 Jul 04, 2010 (132)
14 1000GENOMES ss222292720 Jul 14, 2010 (137)
15 1000GENOMES ss233387793 Jul 14, 2010 (137)
16 1000GENOMES ss240459481 Jul 15, 2010 (137)
17 BL ss254165640 May 09, 2011 (137)
18 GMI ss278715143 May 04, 2012 (137)
19 ILLUMINA ss481403990 May 04, 2012 (137)
20 ILLUMINA ss481430681 May 04, 2012 (137)
21 ILLUMINA ss482410360 Sep 08, 2015 (146)
22 ILLUMINA ss485496935 May 04, 2012 (137)
23 EXOME_CHIP ss491380329 May 04, 2012 (137)
24 ILLUMINA ss537411744 Sep 08, 2015 (146)
25 TISHKOFF ss559102795 Apr 25, 2013 (138)
26 SSMP ss653020139 Apr 25, 2013 (138)
27 ILLUMINA ss779047175 Sep 08, 2015 (146)
28 ILLUMINA ss780686194 Sep 08, 2015 (146)
29 ILLUMINA ss783194013 Sep 08, 2015 (146)
30 ILLUMINA ss783359704 Sep 08, 2015 (146)
31 ILLUMINA ss784149106 Sep 08, 2015 (146)
32 ILLUMINA ss825675030 Jul 19, 2016 (147)
33 ILLUMINA ss832453875 Sep 08, 2015 (146)
34 ILLUMINA ss834510096 Sep 08, 2015 (146)
35 EVA-GONL ss982746216 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1073493901 Aug 21, 2014 (142)
37 1000GENOMES ss1319517125 Aug 21, 2014 (142)
38 HAMMER_LAB ss1397447880 Sep 08, 2015 (146)
39 EVA_GENOME_DK ss1581597047 Apr 01, 2015 (144)
40 EVA_DECODE ss1592293634 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1615254082 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1658248115 Apr 01, 2015 (144)
43 EVA_SVP ss1712848857 Apr 01, 2015 (144)
44 ILLUMINA ss1752625710 Sep 08, 2015 (146)
45 ILLUMINA ss1752625711 Sep 08, 2015 (146)
46 ILLUMINA ss1917801357 Feb 12, 2016 (147)
47 WEILL_CORNELL_DGM ss1925998408 Feb 12, 2016 (147)
48 ILLUMINA ss1946172007 Feb 12, 2016 (147)
49 ILLUMINA ss1958881989 Feb 12, 2016 (147)
50 JJLAB ss2023627667 Sep 14, 2016 (149)
51 ILLUMINA ss2094822709 Dec 20, 2016 (150)
52 ILLUMINA ss2095175310 Dec 20, 2016 (150)
53 USC_VALOUEV ss2151792976 Nov 08, 2017 (151)
54 HUMAN_LONGEVITY ss2282881948 Dec 20, 2016 (150)
55 TOPMED ss2451251947 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2626299927 Nov 08, 2017 (151)
57 ILLUMINA ss2634424939 Nov 08, 2017 (151)
58 GRF ss2707385174 Nov 08, 2017 (151)
59 GNOMAD ss2837326329 Nov 08, 2017 (151)
60 AFFY ss2985358903 Nov 08, 2017 (151)
61 AFFY ss2985990870 Nov 08, 2017 (151)
62 SWEGEN ss2998768263 Nov 08, 2017 (151)
63 ILLUMINA ss3022593639 Nov 08, 2017 (151)
64 BIOINF_KMB_FNS_UNIBA ss3025599017 Nov 08, 2017 (151)
65 TOPMED ss3493627897 Nov 08, 2017 (151)
66 ILLUMINA ss3629493554 Oct 12, 2018 (152)
67 ILLUMINA ss3629493555 Oct 12, 2018 (152)
68 ILLUMINA ss3632344069 Oct 12, 2018 (152)
69 ILLUMINA ss3633413610 Oct 12, 2018 (152)
70 ILLUMINA ss3634135947 Oct 12, 2018 (152)
71 ILLUMINA ss3635054083 Oct 12, 2018 (152)
72 ILLUMINA ss3635054084 Oct 12, 2018 (152)
73 ILLUMINA ss3635817060 Oct 12, 2018 (152)
74 ILLUMINA ss3636773997 Oct 12, 2018 (152)
75 ILLUMINA ss3637569819 Oct 12, 2018 (152)
76 ILLUMINA ss3638617441 Oct 12, 2018 (152)
77 ILLUMINA ss3640761379 Oct 12, 2018 (152)
78 ILLUMINA ss3640761380 Oct 12, 2018 (152)
79 ILLUMINA ss3643558686 Oct 12, 2018 (152)
80 ILLUMINA ss3644905076 Oct 12, 2018 (152)
81 ILLUMINA ss3653104994 Oct 12, 2018 (152)
82 ILLUMINA ss3653104995 Oct 12, 2018 (152)
83 ILLUMINA ss3654126747 Oct 12, 2018 (152)
84 EGCUT_WGS ss3666690799 Jul 13, 2019 (153)
85 EVA_DECODE ss3716879041 Jul 13, 2019 (153)
86 ILLUMINA ss3726326133 Jul 13, 2019 (153)
87 ACPOP ss3733341929 Jul 13, 2019 (153)
88 ILLUMINA ss3744548490 Jul 13, 2019 (153)
89 ILLUMINA ss3745354130 Jul 13, 2019 (153)
90 ILLUMINA ss3745354131 Jul 13, 2019 (153)
91 EVA ss3764801083 Jul 13, 2019 (153)
92 PAGE_CC ss3771275505 Jul 13, 2019 (153)
93 ILLUMINA ss3772847856 Jul 13, 2019 (153)
94 ILLUMINA ss3772847857 Jul 13, 2019 (153)
95 PACBIO ss3785417197 Jul 13, 2019 (153)
96 PACBIO ss3790777028 Jul 13, 2019 (153)
97 PACBIO ss3795654392 Jul 13, 2019 (153)
98 KHV_HUMAN_GENOMES ss3807956434 Jul 13, 2019 (153)
99 1000Genomes NC_000006.11 - 30311932 Oct 12, 2018 (152)
100 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 30311932 Oct 12, 2018 (152)
101 Genetic variation in the Estonian population NC_000006.11 - 30311932 Oct 12, 2018 (152)
102 gnomAD - Genomes NC_000006.11 - 30311932 Jul 13, 2019 (153)
103 Northern Sweden NC_000006.11 - 30311932 Jul 13, 2019 (153)
104 The PAGE Study NC_000006.12 - 30344155 Jul 13, 2019 (153)
105 TopMed NC_000006.12 - 30344155 Oct 12, 2018 (152)
106 UK 10K study - Twins NC_000006.11 - 30311932 Oct 12, 2018 (152)
107 A Vietnamese Genetic Variation Database NC_000006.11 - 30311932 Jul 13, 2019 (153)
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)
rs74295277 Dec 02, 2009 (131)
rs114200728 May 04, 2012 (137)
rs117347362 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78871898 NC_000006.9:30419910:A:C NC_000006.12:30344154:A:C (self)
ss116382990, ss254165640, ss278715143, ss481403990, ss825675030, ss1397447880, ss1592293634, ss1712848857, ss3643558686 NC_000006.10:30419910:A:C NC_000006.12:30344154:A:C (self)
31282761, 17440873, 12429047, 85575253, 6626794, 17440873, 3864125, ss222292720, ss233387793, ss240459481, ss481430681, ss482410360, ss485496935, ss491380329, ss537411744, ss559102795, ss653020139, ss779047175, ss780686194, ss783194013, ss783359704, ss784149106, ss832453875, ss834510096, ss982746216, ss1073493901, ss1319517125, ss1581597047, ss1615254082, ss1658248115, ss1752625710, ss1752625711, ss1917801357, ss1925998408, ss1946172007, ss1958881989, ss2023627667, ss2094822709, ss2095175310, ss2151792976, ss2451251947, ss2626299927, ss2634424939, ss2707385174, ss2837326329, ss2985358903, ss2985990870, ss2998768263, ss3022593639, ss3629493554, ss3629493555, ss3632344069, ss3633413610, ss3634135947, ss3635054083, ss3635054084, ss3635817060, ss3636773997, ss3637569819, ss3638617441, ss3640761379, ss3640761380, ss3644905076, ss3653104994, ss3653104995, ss3654126747, ss3666690799, ss3733341929, ss3744548490, ss3745354130, ss3745354131, ss3764801083, ss3772847856, ss3772847857, ss3785417197, ss3790777028, ss3795654392 NC_000006.11:30311931:A:C NC_000006.12:30344154:A:C (self)
496974, 334886026, ss2282881948, ss3025599017, ss3493627897, ss3716879041, ss3726326133, ss3771275505, ss3807956434 NC_000006.12:30344154:A:C NC_000006.12:30344154:A:C (self)
ss10329968 NT_007592.13:21168351:A:C NC_000006.12:30344154:A:C (self)
ss35524166, ss65846866, ss75315808, ss104293737, ss119532843, ss123434581, ss154392676, ss160826884, ss172219785, ss174171915 NT_007592.15:30251931:A:C NC_000006.12:30344154:A:C (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 rs6931763
PMID Title Author Year Journal
19143817 Effect of linkage status of affected sib-pairs on the search for novel type 1 diabetes susceptibility genes in the HLA complex. Morahan G et al. 2009 Diabetes, obesity & metabolism

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.post308+0fe9b3b