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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.

rs866348371

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:136635 (GRCh38.p13) 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=0.13717 (6489/47306, GnomAD)
G=0.13111 (2056/15682, 8.3KJPN)
G=0.21000 (2491/11862, ALFA) (+ 7 more)
G=0.4426 (1287/2908, KOREAN)
G=0.0259 (38/1466, Korea1K)
T=0.500 (142/284, SGDP_PRJ)
G=0.500 (142/284, SGDP_PRJ)
G=0.255 (55/216, Qatari)
T=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC729737 : Non Coding Transcript Variant
LOC100996442 : Intron 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.p13 chr 1 NC_000001.11:g.136635T>G
GRCh37.p13 chr 1 NC_000001.10:g.136635T>G
Gene: LOC729737, uncharacterized LOC729737 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC729737 transcript NR_039983.2:n.3612A>C N/A Non Coding Transcript Variant
Gene: LOC100996442, uncharacterized LOC100996442 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC100996442 transcript variant X4 XR_001737578.2:n. N/A Intron Variant
LOC100996442 transcript variant X5 XR_001737579.2:n. N/A Intron Variant
LOC100996442 transcript variant X8 XR_001737580.2:n. N/A Intron Variant
LOC100996442 transcript variant X12 XR_001737582.2:n. N/A Intron Variant
LOC100996442 transcript variant X13 XR_001737583.2:n. N/A Intron Variant
LOC100996442 transcript variant X11 XR_001737581.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X14 XR_001737584.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X1 XR_002958514.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X2 XR_002958515.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X3 XR_002958516.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X6 XR_002958517.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X7 XR_002958518.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X9 XR_002958519.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X10 XR_002958520.1:n. N/A Genic 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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 T=0.79000 G=0.21000
European Sub 7618 T=0.7611 G=0.2389
African Sub 2816 T=0.8775 G=0.1225
African Others Sub 108 T=0.926 G=0.074
African American Sub 2708 T=0.8756 G=0.1244
Asian Sub 108 T=0.546 G=0.454
East Asian Sub 84 T=0.52 G=0.48
Other Asian Sub 24 T=0.62 G=0.38
Latin American 1 Sub 146 T=0.815 G=0.185
Latin American 2 Sub 610 T=0.795 G=0.205
South Asian Sub 94 T=0.65 G=0.35
Other Sub 470 T=0.804 G=0.196


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
gnomAD - Genomes Global Study-wide 47306 T=0.86283 G=0.13717
gnomAD - Genomes European Sub 24828 T=0.83430 G=0.16570
gnomAD - Genomes African Sub 15078 T=0.93447 G=0.06553
gnomAD - Genomes American Sub 4554 T=0.8483 G=0.1517
gnomAD - Genomes Ashkenazi Jewish Sub 1308 T=0.8609 G=0.1391
gnomAD - Genomes East Asian Sub 878 T=0.532 G=0.468
gnomAD - Genomes Other Sub 660 T=0.844 G=0.156
8.3KJPN JAPANESE Study-wide 15682 T=0.86889 G=0.13111
KOREAN population from KRGDB KOREAN Study-wide 2908 T=0.5574 G=0.4426
Korean Genome Project KOREAN Study-wide 1466 T=0.9741 G=0.0259
SGDP_PRJ Global Study-wide 284 T=0.500 G=0.500
Qatari Global Study-wide 216 T=0.745 G=0.255
Siberian Global Study-wide 2 T=0.5 G=0.5
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= G
GRCh38.p13 chr 1 NC_000001.11:g.136635= NC_000001.11:g.136635T>G
GRCh37.p13 chr 1 NC_000001.10:g.136635= NC_000001.10:g.136635T>G
LOC729737 transcript NR_039983.2:n.3612= NR_039983.2:n.3612A>C
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#.

17 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 WEILL_CORNELL_DGM ss1917958764 Feb 12, 2016 (147)
2 TMC_SNPDB ss1997003431 Jul 19, 2016 (147)
3 USC_VALOUEV ss2147483751 Dec 20, 2016 (150)
4 GRF ss2697373311 Nov 08, 2017 (151)
5 GNOMAD ss2750611426 Nov 08, 2017 (151)
6 SWEGEN ss2986143444 Nov 08, 2017 (151)
7 TOPMED ss3066337540 Nov 08, 2017 (151)
8 CSHL ss3343271745 Nov 08, 2017 (151)
9 OMUKHERJEE_ADBS ss3646218250 Oct 11, 2018 (152)
10 URBANLAB ss3646580556 Oct 11, 2018 (152)
11 PACBIO ss3783301489 Jul 12, 2019 (153)
12 PACBIO ss3788979500 Jul 12, 2019 (153)
13 PACBIO ss3793852086 Jul 12, 2019 (153)
14 SGDP_PRJ ss3847986220 Apr 25, 2020 (154)
15 KRGDB ss3892826182 Apr 25, 2020 (154)
16 KOGIC ss3943624115 Apr 25, 2020 (154)
17 TOMMO_GENOMICS ss5142037463 Apr 25, 2021 (155)
18 gnomAD - Genomes NC_000001.11 - 136635 Apr 25, 2021 (155)
19 KOREAN population from KRGDB NC_000001.10 - 136635 Apr 25, 2020 (154)
20 Korean Genome Project NC_000001.11 - 136635 Apr 25, 2020 (154)
21 Qatari NC_000001.10 - 136635 Apr 25, 2020 (154)
22 SGDP_PRJ NC_000001.10 - 136635 Apr 25, 2020 (154)
23 Siberian NC_000001.10 - 136635 Apr 25, 2020 (154)
24 8.3KJPN NC_000001.10 - 136635 Apr 25, 2021 (155)
25 ALFA NC_000001.11 - 136635 Apr 25, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3576, 694, 3200, 105, 6770, ss1917958764, ss1997003431, ss2147483751, ss2697373311, ss2750611426, ss2986143444, ss3343271745, ss3646218250, ss3783301489, ss3788979500, ss3793852086, ss3847986220, ss3892826182, ss5142037463 NC_000001.10:136634:T:G NC_000001.11:136634:T:G (self)
17786, 2116, 13211580857, ss3066337540, ss3646580556, ss3943624115 NC_000001.11:136634:T:G NC_000001.11:136634: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 rs866348371

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.post596+ae089ad