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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.

rs2507981

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:31378470 (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>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.452340 (119730/264690, TOPMED)
T=0.450610 (63052/139926, GnomAD)
T=0.39118 (11054/28258, 14KJPN) (+ 15 more)
T=0.42837 (8092/18890, ALFA)
T=0.38544 (6460/16760, 8.3KJPN)
T=0.4463 (2858/6404, 1000G_30x)
T=0.4423 (2215/5008, 1000G)
T=0.4498 (2015/4480, Estonian)
T=0.3557 (1371/3854, ALSPAC)
T=0.3676 (1363/3708, TWINSUK)
T=0.4215 (1235/2930, KOREAN)
T=0.385 (384/998, GoNL)
T=0.398 (239/600, NorthernSweden)
T=0.301 (124/412, SGDP_PRJ)
T=0.333 (72/216, Qatari)
A=0.45 (37/82, HapMap)
T=0.39 (17/44, Siberian)
T=0.42 (17/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
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 18890 T=0.42837 A=0.57163
European Sub 14286 T=0.40599 A=0.59401
African Sub 2946 T=0.4956 A=0.5044
African Others Sub 114 T=0.561 A=0.439
African American Sub 2832 T=0.4929 A=0.5071
Asian Sub 112 T=0.464 A=0.536
East Asian Sub 86 T=0.49 A=0.51
Other Asian Sub 26 T=0.38 A=0.62
Latin American 1 Sub 146 T=0.425 A=0.575
Latin American 2 Sub 610 T=0.603 A=0.397
South Asian Sub 98 T=0.38 A=0.62
Other Sub 692 T=0.452 A=0.548


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 264690 T=0.452340 A=0.547660
gnomAD - Genomes Global Study-wide 139926 T=0.450610 A=0.549390
gnomAD - Genomes European Sub 75796 T=0.40435 A=0.59565
gnomAD - Genomes African Sub 41898 T=0.50783 A=0.49217
gnomAD - Genomes American Sub 13644 T=0.52228 A=0.47772
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.5897 A=0.4103
gnomAD - Genomes East Asian Sub 3120 T=0.3587 A=0.6413
gnomAD - Genomes Other Sub 2144 T=0.4300 A=0.5700
14KJPN JAPANESE Study-wide 28258 T=0.39118 A=0.60882
Allele Frequency Aggregator Total Global 18890 T=0.42837 A=0.57163
Allele Frequency Aggregator European Sub 14286 T=0.40599 A=0.59401
Allele Frequency Aggregator African Sub 2946 T=0.4956 A=0.5044
Allele Frequency Aggregator Other Sub 692 T=0.452 A=0.548
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.603 A=0.397
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.425 A=0.575
Allele Frequency Aggregator Asian Sub 112 T=0.464 A=0.536
Allele Frequency Aggregator South Asian Sub 98 T=0.38 A=0.62
8.3KJPN JAPANESE Study-wide 16760 T=0.38544 A=0.61456
1000Genomes_30x Global Study-wide 6404 T=0.4463 A=0.5537
1000Genomes_30x African Sub 1786 T=0.5034 A=0.4966
1000Genomes_30x Europe Sub 1266 T=0.3934 A=0.6066
1000Genomes_30x South Asian Sub 1202 T=0.3943 A=0.6057
1000Genomes_30x East Asian Sub 1170 T=0.3778 A=0.6222
1000Genomes_30x American Sub 980 T=0.556 A=0.444
1000Genomes Global Study-wide 5008 T=0.4423 A=0.5577
1000Genomes African Sub 1322 T=0.5015 A=0.4985
1000Genomes East Asian Sub 1008 T=0.3889 A=0.6111
1000Genomes Europe Sub 1006 T=0.4016 A=0.5984
1000Genomes South Asian Sub 978 T=0.387 A=0.613
1000Genomes American Sub 694 T=0.545 A=0.455
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.4498 A=0.5502
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.3557 A=0.6443
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.3676 A=0.6324
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.4215 A=0.5785, G=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.385 A=0.615
Northern Sweden ACPOP Study-wide 600 T=0.398 A=0.602
SGDP_PRJ Global Study-wide 412 T=0.301 A=0.699
Qatari Global Study-wide 216 T=0.333 A=0.667
HapMap Global Study-wide 82 T=0.55 A=0.45
HapMap Asian Sub 82 T=0.55 A=0.45
Siberian Global Study-wide 44 T=0.39 A=0.61
The Danish reference pan genome Danish Study-wide 40 T=0.42 A=0.57
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.31378470T>A
GRCh38.p14 chr 6 NC_000006.12:g.31378470T>G
GRCh37.p13 chr 6 NC_000006.11:g.31346247T>A
GRCh37.p13 chr 6 NC_000006.11:g.31346247T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2858800A>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2858800A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2858906A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2858906A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2634160A>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2634160A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2639756A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2639756A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2680690A>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2680690A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2679988A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2679988A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2687073A>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2687073A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2692693A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2692693A>G
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 T= A G
GRCh38.p14 chr 6 NC_000006.12:g.31378470= NC_000006.12:g.31378470T>A NC_000006.12:g.31378470T>G
GRCh37.p13 chr 6 NC_000006.11:g.31346247= NC_000006.11:g.31346247T>A NC_000006.11:g.31346247T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2858800A>T NT_113891.3:g.2858800= NT_113891.3:g.2858800A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2858906A>T NT_113891.2:g.2858906= NT_113891.2:g.2858906A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2634160A>T NT_167248.2:g.2634160= NT_167248.2:g.2634160A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2639756A>T NT_167248.1:g.2639756= NT_167248.1:g.2639756A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2680690A>T NT_167249.2:g.2680690= NT_167249.2:g.2680690A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2679988A>T NT_167249.1:g.2679988= NT_167249.1:g.2679988A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2687073A>T NT_167246.2:g.2687073= NT_167246.2:g.2687073A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2692693A>T NT_167246.1:g.2692693= NT_167246.1:g.2692693A>G
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#.

80 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3516030 Sep 28, 2001 (100)
2 SI_MHC_SNP ss12690189 Oct 31, 2003 (119)
3 CSHL-HAPMAP ss17100929 Feb 27, 2004 (120)
4 SSAHASNP ss22384654 Apr 05, 2004 (123)
5 ABI ss42648909 Mar 14, 2006 (126)
6 HGSV ss83149304 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss93435983 Mar 24, 2008 (129)
8 BGI ss104296379 Dec 01, 2009 (131)
9 1000GENOMES ss109897816 Feb 13, 2009 (137)
10 1000GENOMES ss114138472 Jan 25, 2009 (137)
11 ILLUMINA-UK ss116393149 Feb 14, 2009 (130)
12 GMI ss156740309 Dec 01, 2009 (131)
13 ILLUMINA ss160554038 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss162195389 Jul 04, 2010 (137)
15 COMPLETE_GENOMICS ss163343015 Jul 04, 2010 (137)
16 COMPLETE_GENOMICS ss166423954 Jul 04, 2010 (137)
17 BUSHMAN ss201621087 Jul 04, 2010 (137)
18 BCM-HGSC-SUB ss207380186 Jul 04, 2010 (137)
19 1000GENOMES ss222302260 Jul 14, 2010 (137)
20 1000GENOMES ss233397182 Jul 14, 2010 (137)
21 1000GENOMES ss240468172 Jul 15, 2010 (137)
22 BL ss254183921 May 09, 2011 (137)
23 GMI ss278724870 May 04, 2012 (137)
24 GMI ss285373490 Apr 25, 2013 (138)
25 PJP ss293825079 May 09, 2011 (137)
26 ILLUMINA ss481430428 Sep 08, 2015 (146)
27 ILLUMINA ss537098633 Sep 08, 2015 (146)
28 TISHKOFF ss559112420 Apr 25, 2013 (138)
29 SSMP ss653032851 Apr 25, 2013 (138)
30 ILLUMINA ss778656595 Sep 08, 2015 (146)
31 ILLUMINA ss834114545 Sep 08, 2015 (146)
32 EVA-GONL ss982762942 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1073503838 Aug 21, 2014 (142)
34 1000GENOMES ss1319552320 Aug 21, 2014 (142)
35 EVA_GENOME_DK ss1581604933 Apr 01, 2015 (144)
36 EVA_DECODE ss1592307362 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1615274003 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1658268036 Apr 01, 2015 (144)
39 HAMMER_LAB ss1804356665 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1926014947 Feb 12, 2016 (147)
41 GENOMED ss1970356284 Jul 19, 2016 (147)
42 JJLAB ss2023640010 Sep 14, 2016 (149)
43 USC_VALOUEV ss2151806174 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2282938679 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2626306976 Nov 08, 2017 (151)
46 ILLUMINA ss2634429013 Nov 08, 2017 (151)
47 GRF ss2707399579 Nov 08, 2017 (151)
48 SWEGEN ss2998791635 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3025606804 Nov 08, 2017 (151)
50 ILLUMINA ss3629501862 Oct 12, 2018 (152)
51 ILLUMINA ss3632347689 Oct 12, 2018 (152)
52 ILLUMINA ss3636777451 Oct 12, 2018 (152)
53 EGCUT_WGS ss3666707916 Jul 13, 2019 (153)
54 EVA_DECODE ss3716903812 Jul 13, 2019 (153)
55 ACPOP ss3733358676 Jul 13, 2019 (153)
56 EVA ss3764819188 Jul 13, 2019 (153)
57 KHV_HUMAN_GENOMES ss3807974573 Jul 13, 2019 (153)
58 EVA ss3829830721 Apr 26, 2020 (154)
59 EVA ss3838393346 Apr 26, 2020 (154)
60 EVA ss3843835447 Apr 26, 2020 (154)
61 SGDP_PRJ ss3864248805 Apr 26, 2020 (154)
62 KRGDB ss3911023944 Apr 26, 2020 (154)
63 VINODS ss4025187016 Apr 26, 2021 (155)
64 VINODS ss4025265748 Apr 26, 2021 (155)
65 VINODS ss4025285989 Apr 26, 2021 (155)
66 TOPMED ss4698355787 Apr 26, 2021 (155)
67 TOMMO_GENOMICS ss5176828997 Apr 26, 2021 (155)
68 1000G_HIGH_COVERAGE ss5267930918 Oct 13, 2022 (156)
69 EVA ss5315141636 Oct 13, 2022 (156)
70 EVA ss5364715443 Oct 13, 2022 (156)
71 HUGCELL_USP ss5465666174 Oct 13, 2022 (156)
72 EVA ss5508426151 Oct 13, 2022 (156)
73 1000G_HIGH_COVERAGE ss5553585804 Oct 13, 2022 (156)
74 SANFORD_IMAGENETICS ss5640085169 Oct 13, 2022 (156)
75 TOMMO_GENOMICS ss5714681739 Oct 13, 2022 (156)
76 YY_MCH ss5807304160 Oct 13, 2022 (156)
77 EVA ss5842022998 Oct 13, 2022 (156)
78 EVA ss5855282139 Oct 13, 2022 (156)
79 EVA ss5883238574 Oct 13, 2022 (156)
80 EVA ss5968587318 Oct 13, 2022 (156)
81 1000Genomes NC_000006.11 - 31346247 Oct 12, 2018 (152)
82 1000Genomes_30x NC_000006.12 - 31378470 Oct 13, 2022 (156)
83 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 31346247 Oct 12, 2018 (152)
84 Genetic variation in the Estonian population NC_000006.11 - 31346247 Oct 12, 2018 (152)
85 The Danish reference pan genome NC_000006.11 - 31346247 Apr 26, 2020 (154)
86 gnomAD - Genomes NC_000006.12 - 31378470 Apr 26, 2021 (155)
87 Genome of the Netherlands Release 5 NC_000006.11 - 31346247 Apr 26, 2020 (154)
88 HapMap NC_000006.12 - 31378470 Apr 26, 2020 (154)
89 KOREAN population from KRGDB NC_000006.11 - 31346247 Apr 26, 2020 (154)
90 Northern Sweden NC_000006.11 - 31346247 Jul 13, 2019 (153)
91 Qatari NC_000006.11 - 31346247 Apr 26, 2020 (154)
92 SGDP_PRJ NC_000006.11 - 31346247 Apr 26, 2020 (154)
93 Siberian NC_000006.11 - 31346247 Apr 26, 2020 (154)
94 8.3KJPN NC_000006.11 - 31346247 Apr 26, 2021 (155)
95 14KJPN NC_000006.12 - 31378470 Oct 13, 2022 (156)
96 TopMed NC_000006.12 - 31378470 Apr 26, 2021 (155)
97 UK 10K study - Twins NC_000006.11 - 31346247 Oct 12, 2018 (152)
98 ALFA NC_000006.12 - 31378470 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)
rs9266620 Dec 04, 2003 (119)
rs13194110 Oct 08, 2004 (123)
rs59402657 May 25, 2008 (130)
rs113532934 May 04, 2012 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83149304 NC_000006.9:31454225:T:A NC_000006.12:31378469:T:A (self)
ss93435983, ss109897816, ss114138472, ss116393149, ss162195389, ss163343015, ss166423954, ss201621087, ss207380186, ss254183921, ss278724870, ss285373490, ss293825079, ss1592307362 NC_000006.10:31454225:T:A NC_000006.12:31378469:T:A (self)
31319445, 17463087, 12446164, 7769872, 7761955, 18201338, 6643541, 8056877, 16265785, 4322528, 34798304, 17463087, ss222302260, ss233397182, ss240468172, ss481430428, ss537098633, ss559112420, ss653032851, ss778656595, ss834114545, ss982762942, ss1073503838, ss1319552320, ss1581604933, ss1615274003, ss1658268036, ss1804356665, ss1926014947, ss1970356284, ss2023640010, ss2151806174, ss2626306976, ss2634429013, ss2707399579, ss2998791635, ss3629501862, ss3632347689, ss3636777451, ss3666707916, ss3733358676, ss3764819188, ss3829830721, ss3838393346, ss3864248805, ss3911023944, ss5176828997, ss5315141636, ss5364715443, ss5508426151, ss5640085169, ss5842022998, ss5968587318 NC_000006.11:31346246:T:A NC_000006.12:31378469:T:A (self)
41111739, 221183145, 3099379, 48518843, 535733345, 10055336697, ss2282938679, ss3025606804, ss3716903812, ss3807974573, ss3843835447, ss4698355787, ss5267930918, ss5465666174, ss5553585804, ss5714681739, ss5807304160, ss5855282139, ss5883238574 NC_000006.12:31378469:T:A NC_000006.12:31378469:T:A (self)
ss17100929, ss22384654 NT_007592.13:22200679:A:A NC_000006.12:31378469:T:A (self)
ss3516030, ss12690189, ss42648909, ss104296379, ss156740309, ss160554038 NT_007592.15:31286246:T:A NC_000006.12:31378469:T:A (self)
ss4025187016 NT_113891.3:2858799:A:A NC_000006.12:31378469:T:A (self)
ss4025265748 NT_167248.2:2634159:A:A NC_000006.12:31378469:T:A (self)
ss4025285989 NT_167249.2:2680689:A:A NC_000006.12:31378469:T:A (self)
18201338, ss3911023944 NC_000006.11:31346246:T:G NC_000006.12:31378469:T:G (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 rs2507981

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