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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.

rs9861097

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:107928048 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.43368 (55202/127288, GnomAD_exome)
C=0.35818 (44976/125568, TOPMED)
C=0.3533 (27787/78646, PAGE_STUDY) (+ 8 more)
C=0.3565 (11062/31028, GnomAD)
C=0.4237 (4617/10896, ExAC)
C=0.439 (2197/5008, 1000G)
C=0.358 (1602/4476, Estonian)
C=0.424 (1633/3854, ALSPAC)
C=0.430 (1593/3708, TWINSUK)
C=0.40 (240/600, NorthernSweden)
T=0.13 (27/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC00636 : Non Coding Transcript 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.p12 chr 3 NC_000003.12:g.107928048T>C
GRCh37.p13 chr 3 NC_000003.11:g.107646895T>C
Gene: LINC00636, long intergenic non-protein coding RNA 636 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC00636 transcript NR_015394.1:n.448T>C N/A Non Coding 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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 127288 T=0.56632 C=0.43368
gnomAD - Exomes European Sub 56746 T=0.5935 C=0.4065
gnomAD - Exomes Asian Sub 30812 T=0.4247 C=0.5753
gnomAD - Exomes American Sub 22182 T=0.5930 C=0.4070
gnomAD - Exomes Ashkenazi Jewish Sub 8008 T=0.633 C=0.367
gnomAD - Exomes African Sub 5722 T=0.843 C=0.157
gnomAD - Exomes Other Sub 3818 T=0.597 C=0.403
TopMed Global Study-wide 125568 T=0.64182 C=0.35818
The PAGE Study Global Study-wide 78646 T=0.6467 C=0.3533
The PAGE Study AfricanAmerican Sub 32486 T=0.8220 C=0.1780
The PAGE Study Mexican Sub 10804 T=0.6053 C=0.3947
The PAGE Study Asian Sub 8318 T=0.147 C=0.853
The PAGE Study PuertoRican Sub 7910 T=0.677 C=0.323
The PAGE Study NativeHawaiian Sub 4530 T=0.322 C=0.678
The PAGE Study Cuban Sub 4228 T=0.645 C=0.355
The PAGE Study Dominican Sub 3826 T=0.723 C=0.277
The PAGE Study CentralAmerican Sub 2446 T=0.655 C=0.345
The PAGE Study SouthAmerican Sub 1982 T=0.625 C=0.375
The PAGE Study NativeAmerican Sub 1260 T=0.612 C=0.388
The PAGE Study SouthAsian Sub 856 T=0.55 C=0.45
gnomAD - Genomes Global Study-wide 31028 T=0.6435 C=0.3565
gnomAD - Genomes European Sub 18654 T=0.6030 C=0.3970
gnomAD - Genomes African Sub 8618 T=0.831 C=0.169
gnomAD - Genomes East Asian Sub 1552 T=0.144 C=0.856
gnomAD - Genomes Other Sub 1072 T=0.600 C=0.400
gnomAD - Genomes American Sub 844 T=0.61 C=0.39
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=0.62 C=0.38
ExAC Global Study-wide 10896 T=0.5763 C=0.4237
ExAC Asian Sub 7530 T=0.552 C=0.448
ExAC Europe Sub 2876 T=0.617 C=0.383
ExAC African Sub 260 T=0.80 C=0.20
ExAC Other Sub 116 T=0.58 C=0.42
ExAC American Sub 114 T=0.62 C=0.38
1000Genomes Global Study-wide 5008 T=0.561 C=0.439
1000Genomes African Sub 1322 T=0.880 C=0.120
1000Genomes East Asian Sub 1008 T=0.121 C=0.879
1000Genomes Europe Sub 1006 T=0.592 C=0.408
1000Genomes South Asian Sub 978 T=0.48 C=0.52
1000Genomes American Sub 694 T=0.66 C=0.34
Genetic variation in the Estonian population Estonian Study-wide 4476 T=0.642 C=0.358
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.576 C=0.424
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.570 C=0.430
Northern Sweden ACPOP Study-wide 600 T=0.60 C=0.40
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.13 C=0.87
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.p12 chr 3 NC_000003.12:g.107928048= NC_000003.12:g.10792804...

NC_000003.12:g.107928048T>C

GRCh37.p13 chr 3 NC_000003.11:g.107646895= NC_000003.11:g.10764689...

NC_000003.11:g.107646895T>C

LINC00636 transcript NR_015394.1:n.448= NR_015394.1:n.448T>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#.

59 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss13695820 Dec 05, 2003 (119)
2 PERLEGEN ss23256737 Sep 20, 2004 (123)
3 ABI ss44378121 Mar 15, 2006 (126)
4 PERLEGEN ss68871108 May 16, 2007 (127)
5 HGSV ss77772199 Dec 07, 2007 (129)
6 HUMANGENOME_JCVI ss96040430 Feb 04, 2009 (130)
7 BGI ss103969706 Dec 01, 2009 (131)
8 ENSEMBL ss135560483 Dec 01, 2009 (131)
9 GMI ss156003885 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss167003471 Jul 04, 2010 (132)
11 1000GENOMES ss210545120 Jul 14, 2010 (132)
12 1000GENOMES ss220340364 Jul 14, 2010 (132)
13 1000GENOMES ss231968365 Jul 14, 2010 (132)
14 1000GENOMES ss239352956 Jul 15, 2010 (132)
15 GMI ss277284513 May 04, 2012 (137)
16 PJP ss292881172 May 09, 2011 (134)
17 ILLUMINA ss536269366 Sep 08, 2015 (146)
18 TISHKOFF ss556843399 Apr 25, 2013 (138)
19 SSMP ss650551339 Apr 25, 2013 (138)
20 EVA-GONL ss978992280 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1070707261 Aug 21, 2014 (142)
22 1000GENOMES ss1305514984 Aug 21, 2014 (142)
23 DDI ss1429535183 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1580114139 Apr 01, 2015 (144)
25 EVA_DECODE ss1588470294 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1607870534 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1650864567 Apr 01, 2015 (144)
28 EVA_EXAC ss1687127017 Apr 01, 2015 (144)
29 EVA_MGP ss1711027179 Apr 01, 2015 (144)
30 HAMMER_LAB ss1799813423 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1922220772 Feb 12, 2016 (147)
32 ILLUMINA ss1958591656 Feb 12, 2016 (147)
33 JJLAB ss2021673800 Sep 14, 2016 (149)
34 USC_VALOUEV ss2149765356 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2254527844 Dec 20, 2016 (150)
36 TOPMED ss2421852002 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2625339058 Nov 08, 2017 (151)
38 GRF ss2705165592 Nov 08, 2017 (151)
39 GNOMAD ss2733942341 Nov 08, 2017 (151)
40 GNOMAD ss2747063469 Nov 08, 2017 (151)
41 GNOMAD ss2797298295 Nov 08, 2017 (151)
42 SWEGEN ss2992935934 Nov 08, 2017 (151)
43 ILLUMINA ss3022271146 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3024603248 Nov 08, 2017 (151)
45 CSHL ss3345189802 Nov 08, 2017 (151)
46 TOPMED ss3401336643 Nov 08, 2017 (151)
47 ILLUMINA ss3628738787 Oct 12, 2018 (152)
48 OMUKHERJEE_ADBS ss3646290425 Oct 12, 2018 (152)
49 URBANLAB ss3647491037 Oct 12, 2018 (152)
50 ILLUMINA ss3652748298 Oct 12, 2018 (152)
51 EGCUT_WGS ss3660854942 Jul 13, 2019 (153)
52 EVA_DECODE ss3709974692 Jul 13, 2019 (153)
53 ACPOP ss3730209514 Jul 13, 2019 (153)
54 EVA ss3760491445 Jul 13, 2019 (153)
55 PAGE_CC ss3771052904 Jul 13, 2019 (153)
56 PACBIO ss3784417999 Jul 13, 2019 (153)
57 PACBIO ss3789919588 Jul 13, 2019 (153)
58 PACBIO ss3794794006 Jul 13, 2019 (153)
59 KHV_HUMAN_GENOMES ss3803627867 Jul 13, 2019 (153)
60 1000Genomes NC_000003.11 - 107646895 Oct 12, 2018 (152)
61 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 107646895 Oct 12, 2018 (152)
62 Genetic variation in the Estonian population NC_000003.11 - 107646895 Oct 12, 2018 (152)
63 ExAC NC_000003.11 - 107646895 Oct 12, 2018 (152)
64 gnomAD - Genomes NC_000003.11 - 107646895 Jul 13, 2019 (153)
65 gnomAD - Exomes NC_000003.11 - 107646895 Jul 13, 2019 (153)
66 Northern Sweden NC_000003.11 - 107646895 Jul 13, 2019 (153)
67 The PAGE Study NC_000003.12 - 107928048 Jul 13, 2019 (153)
68 TopMed NC_000003.12 - 107928048 Oct 12, 2018 (152)
69 UK 10K study - Twins NC_000003.11 - 107646895 Oct 12, 2018 (152)
70 A Vietnamese Genetic Variation Database NC_000003.11 - 107646895 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77772199 NC_000003.9:109129584:T:C NC_000003.12:107928047:T:C (self)
ss167003471, ss210545120, ss277284513, ss292881172, ss1588470294 NC_000003.10:109129584:T:C NC_000003.12:107928047:T:C (self)
16754599, 9324234, 6593190, 7060219, 45837623, 3025646, 3494379, 9324234, 2030315, ss220340364, ss231968365, ss239352956, ss536269366, ss556843399, ss650551339, ss978992280, ss1070707261, ss1305514984, ss1429535183, ss1580114139, ss1607870534, ss1650864567, ss1687127017, ss1711027179, ss1799813423, ss1922220772, ss1958591656, ss2021673800, ss2149765356, ss2421852002, ss2625339058, ss2705165592, ss2733942341, ss2747063469, ss2797298295, ss2992935934, ss3022271146, ss3345189802, ss3628738787, ss3646290425, ss3652748298, ss3660854942, ss3730209514, ss3760491445, ss3784417999, ss3789919588, ss3794794006 NC_000003.11:107646894:T:C NC_000003.12:107928047:T:C (self)
274373, 259617392, ss2254527844, ss3024603248, ss3401336643, ss3647491037, ss3709974692, ss3771052904, ss3803627867 NC_000003.12:107928047:T:C NC_000003.12:107928047:T:C (self)
ss13695820 NT_005612.14:14142040:T:C NC_000003.12:107928047:T:C (self)
ss23256737, ss44378121, ss68871108, ss96040430, ss103969706, ss135560483, ss156003885 NT_005612.16:14142040:T:C NC_000003.12:107928047: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 rs9861097

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