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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.

rs6037146

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:25573172 (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
C>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.126930 (33597/264690, TOPMED)
C=0.123074 (17160/139428, GnomAD)
C=0.09728 (2749/28258, 14KJPN) (+ 15 more)
C=0.08926 (1686/18888, ALFA)
C=0.09618 (1612/16760, 8.3KJPN)
C=0.1410 (903/6404, 1000G_30x)
C=0.1380 (691/5008, 1000G)
C=0.0442 (198/4478, Estonian)
C=0.0363 (140/3854, ALSPAC)
C=0.0367 (136/3708, TWINSUK)
C=0.0748 (219/2928, KOREAN)
C=0.0557 (102/1832, Korea1K)
C=0.039 (39/998, GoNL)
C=0.038 (23/600, NorthernSweden)
C=0.098 (53/540, SGDP_PRJ)
C=0.148 (32/216, Qatari)
C=0.05 (3/56, Siberian)
C=0.12 (5/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NINL : Intron Variant
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 18888 C=0.08926 A=0.91074
European Sub 14284 C=0.04404 A=0.95596
African Sub 2946 C=0.3150 A=0.6850
African Others Sub 114 C=0.368 A=0.632
African American Sub 2832 C=0.3129 A=0.6871
Asian Sub 112 C=0.045 A=0.955
East Asian Sub 86 C=0.06 A=0.94
Other Asian Sub 26 C=0.00 A=1.00
Latin American 1 Sub 146 C=0.137 A=0.863
Latin American 2 Sub 610 C=0.051 A=0.949
South Asian Sub 98 C=0.03 A=0.97
Other Sub 692 C=0.101 A=0.899


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 C=0.126930 A=0.873070
gnomAD - Genomes Global Study-wide 139428 C=0.123074 A=0.876926
gnomAD - Genomes European Sub 75692 C=0.04444 A=0.95556
gnomAD - Genomes African Sub 41580 C=0.29658 A=0.70342
gnomAD - Genomes American Sub 13596 C=0.06583 A=0.93417
gnomAD - Genomes Ashkenazi Jewish Sub 3312 C=0.0435 A=0.9565
gnomAD - Genomes East Asian Sub 3110 C=0.0617 A=0.9383
gnomAD - Genomes Other Sub 2138 C=0.1090 A=0.8910
14KJPN JAPANESE Study-wide 28258 C=0.09728 A=0.90272
Allele Frequency Aggregator Total Global 18888 C=0.08926 A=0.91074
Allele Frequency Aggregator European Sub 14284 C=0.04404 A=0.95596
Allele Frequency Aggregator African Sub 2946 C=0.3150 A=0.6850
Allele Frequency Aggregator Other Sub 692 C=0.101 A=0.899
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.051 A=0.949
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.137 A=0.863
Allele Frequency Aggregator Asian Sub 112 C=0.045 A=0.955
Allele Frequency Aggregator South Asian Sub 98 C=0.03 A=0.97
8.3KJPN JAPANESE Study-wide 16760 C=0.09618 A=0.90382
1000Genomes_30x Global Study-wide 6404 C=0.1410 A=0.8590
1000Genomes_30x African Sub 1786 C=0.3516 A=0.6484
1000Genomes_30x Europe Sub 1266 C=0.0521 A=0.9479
1000Genomes_30x South Asian Sub 1202 C=0.0449 A=0.9551
1000Genomes_30x East Asian Sub 1170 C=0.0692 A=0.9308
1000Genomes_30x American Sub 980 C=0.076 A=0.924
1000Genomes Global Study-wide 5008 C=0.1380 A=0.8620
1000Genomes African Sub 1322 C=0.3533 A=0.6467
1000Genomes East Asian Sub 1008 C=0.0744 A=0.9256
1000Genomes Europe Sub 1006 C=0.0537 A=0.9463
1000Genomes South Asian Sub 978 C=0.047 A=0.953
1000Genomes American Sub 694 C=0.071 A=0.929
Genetic variation in the Estonian population Estonian Study-wide 4478 C=0.0442 A=0.9558
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.0363 A=0.9637
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.0367 A=0.9633
KOREAN population from KRGDB KOREAN Study-wide 2928 C=0.0748 A=0.9252, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 C=0.0557 A=0.9443
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.039 A=0.961
Northern Sweden ACPOP Study-wide 600 C=0.038 A=0.962
SGDP_PRJ Global Study-wide 540 C=0.098 A=0.902
Qatari Global Study-wide 216 C=0.148 A=0.852
Siberian Global Study-wide 56 C=0.05 A=0.95
The Danish reference pan genome Danish Study-wide 40 C=0.12 A=0.88
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 20 NC_000020.11:g.25573172C>A
GRCh38.p14 chr 20 NC_000020.11:g.25573172C>G
GRCh37.p13 chr 20 NC_000020.10:g.25553808C>A
GRCh37.p13 chr 20 NC_000020.10:g.25553808C>G
Gene: NINL, ninein like (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NINL transcript variant 2 NM_001318226.2:c.-12+1228…

NM_001318226.2:c.-12+12283G>T

N/A Intron Variant
NINL transcript variant 1 NM_025176.6:c.-12+12283G>T N/A Intron Variant
NINL transcript variant X5 XM_011529188.1:c.-12+1228…

XM_011529188.1:c.-12+12283G>T

N/A Intron Variant
NINL transcript variant X3 XM_047440019.1:c.10+11407…

XM_047440019.1:c.10+11407G>T

N/A Intron Variant
NINL transcript variant X4 XM_047440020.1:c.10+11407…

XM_047440020.1:c.10+11407G>T

N/A Intron Variant
NINL transcript variant X7 XM_047440021.1:c.-12+1228…

XM_047440021.1:c.-12+12283G>T

N/A Intron Variant
NINL transcript variant X8 XM_047440022.1:c.43+11436…

XM_047440022.1:c.43+11436G>T

N/A Intron Variant
NINL transcript variant X9 XM_047440023.1:c.67+1347G…

XM_047440023.1:c.67+1347G>T

N/A Intron Variant
NINL transcript variant X11 XM_047440025.1:c.10+11407…

XM_047440025.1:c.10+11407G>T

N/A Intron Variant
NINL transcript variant X12 XM_047440026.1:c.10+11407…

XM_047440026.1:c.10+11407G>T

N/A Intron Variant
NINL transcript variant X13 XM_047440027.1:c.-12+1228…

XM_047440027.1:c.-12+12283G>T

N/A Intron Variant
NINL transcript variant X22 XM_047440033.1:c.-12+1228…

XM_047440033.1:c.-12+12283G>T

N/A Intron Variant
NINL transcript variant X1 XM_011529186.3:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X2 XM_011529187.3:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X6 XM_011529189.2:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X14 XM_011529191.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X19 XM_011529192.3:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X23 XM_011529194.3:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X24 XM_011529195.3:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X28 XM_011529198.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X27 XM_017027735.2:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X10 XM_047440024.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X15 XM_047440028.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X16 XM_047440029.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X18 XM_047440030.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X20 XM_047440031.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X21 XM_047440032.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X25 XM_047440034.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X26 XM_047440035.1:c. N/A Genic Upstream Transcript Variant
NINL transcript variant X17 XR_007067445.1:n. N/A Intron Variant
NINL transcript variant X29 XR_007067446.1:n. N/A Intron 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

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 C= A G
GRCh38.p14 chr 20 NC_000020.11:g.25573172= NC_000020.11:g.25573172C>A NC_000020.11:g.25573172C>G
GRCh37.p13 chr 20 NC_000020.10:g.25553808= NC_000020.10:g.25553808C>A NC_000020.10:g.25553808C>G
NINL transcript variant 2 NM_001318226.2:c.-12+12283= NM_001318226.2:c.-12+12283G>T NM_001318226.2:c.-12+12283G>C
NINL transcript NM_025176.4:c.-12+12283= NM_025176.4:c.-12+12283G>T NM_025176.4:c.-12+12283G>C
NINL transcript variant 1 NM_025176.6:c.-12+12283= NM_025176.6:c.-12+12283G>T NM_025176.6:c.-12+12283G>C
NINL transcript variant X9 XM_005260679.1:c.-12+12283= XM_005260679.1:c.-12+12283G>T XM_005260679.1:c.-12+12283G>C
NINL transcript variant X5 XM_011529188.1:c.-12+12283= XM_011529188.1:c.-12+12283G>T XM_011529188.1:c.-12+12283G>C
NINL transcript variant X3 XM_047440019.1:c.10+11407= XM_047440019.1:c.10+11407G>T XM_047440019.1:c.10+11407G>C
NINL transcript variant X4 XM_047440020.1:c.10+11407= XM_047440020.1:c.10+11407G>T XM_047440020.1:c.10+11407G>C
NINL transcript variant X7 XM_047440021.1:c.-12+12283= XM_047440021.1:c.-12+12283G>T XM_047440021.1:c.-12+12283G>C
NINL transcript variant X8 XM_047440022.1:c.43+11436= XM_047440022.1:c.43+11436G>T XM_047440022.1:c.43+11436G>C
NINL transcript variant X9 XM_047440023.1:c.67+1347= XM_047440023.1:c.67+1347G>T XM_047440023.1:c.67+1347G>C
NINL transcript variant X11 XM_047440025.1:c.10+11407= XM_047440025.1:c.10+11407G>T XM_047440025.1:c.10+11407G>C
NINL transcript variant X12 XM_047440026.1:c.10+11407= XM_047440026.1:c.10+11407G>T XM_047440026.1:c.10+11407G>C
NINL transcript variant X13 XM_047440027.1:c.-12+12283= XM_047440027.1:c.-12+12283G>T XM_047440027.1:c.-12+12283G>C
NINL transcript variant X22 XM_047440033.1:c.-12+12283= XM_047440033.1:c.-12+12283G>T XM_047440033.1:c.-12+12283G>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#.

58 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8344854 Apr 21, 2003 (114)
2 CSHL-HAPMAP ss16899190 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19479366 Feb 27, 2004 (120)
4 SSAHASNP ss21801551 Apr 05, 2004 (121)
5 HGSV ss77493911 Dec 07, 2007 (129)
6 HGSV ss85399434 Dec 15, 2007 (130)
7 IGMI-SNU ss115467565 Feb 06, 2009 (130)
8 ENSEMBL ss135734672 Dec 01, 2009 (131)
9 BL ss255561627 May 09, 2011 (134)
10 GMI ss283343938 May 04, 2012 (137)
11 GMI ss287442439 Apr 25, 2013 (138)
12 PJP ss292637064 May 09, 2011 (134)
13 1000GENOMES ss340692683 May 09, 2011 (134)
14 SSMP ss662084191 Apr 25, 2013 (138)
15 EVA-GONL ss994659974 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1082162858 Aug 21, 2014 (142)
17 1000GENOMES ss1364514909 Aug 21, 2014 (142)
18 DDI ss1429031011 Apr 01, 2015 (144)
19 EVA_GENOME_DK ss1579485228 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1638655000 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1681649033 Apr 01, 2015 (144)
22 EVA_DECODE ss1698719243 Apr 01, 2015 (144)
23 WEILL_CORNELL_DGM ss1938167938 Feb 12, 2016 (147)
24 JJLAB ss2029869230 Sep 14, 2016 (149)
25 USC_VALOUEV ss2158421364 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2242241040 Dec 20, 2016 (150)
27 GRF ss2704098545 Nov 08, 2017 (151)
28 GNOMAD ss2966682619 Nov 08, 2017 (151)
29 SWEGEN ss3018044920 Nov 08, 2017 (151)
30 CSHL ss3352472118 Nov 08, 2017 (151)
31 URBANLAB ss3650995940 Oct 12, 2018 (152)
32 EGCUT_WGS ss3684771516 Jul 13, 2019 (153)
33 EVA_DECODE ss3706779985 Jul 13, 2019 (153)
34 ACPOP ss3743345316 Jul 13, 2019 (153)
35 EVA ss3758566325 Jul 13, 2019 (153)
36 PACBIO ss3788629415 Jul 13, 2019 (153)
37 PACBIO ss3793525342 Jul 13, 2019 (153)
38 PACBIO ss3798412526 Jul 13, 2019 (153)
39 KHV_HUMAN_GENOMES ss3821732228 Jul 13, 2019 (153)
40 EVA ss3835645227 Apr 27, 2020 (154)
41 EVA ss3841449036 Apr 27, 2020 (154)
42 EVA ss3846957303 Apr 27, 2020 (154)
43 SGDP_PRJ ss3888965963 Apr 27, 2020 (154)
44 KRGDB ss3939174987 Apr 27, 2020 (154)
45 KOGIC ss3982029249 Apr 27, 2020 (154)
46 TOPMED ss5086170144 Apr 27, 2021 (155)
47 TOMMO_GENOMICS ss5229334264 Apr 27, 2021 (155)
48 1000G_HIGH_COVERAGE ss5308471623 Oct 16, 2022 (156)
49 HUGCELL_USP ss5500835911 Oct 16, 2022 (156)
50 EVA ss5512197393 Oct 16, 2022 (156)
51 1000G_HIGH_COVERAGE ss5614754073 Oct 16, 2022 (156)
52 SANFORD_IMAGENETICS ss5663088522 Oct 16, 2022 (156)
53 TOMMO_GENOMICS ss5788461513 Oct 16, 2022 (156)
54 YY_MCH ss5817912546 Oct 16, 2022 (156)
55 EVA ss5845599084 Oct 16, 2022 (156)
56 EVA ss5853116837 Oct 16, 2022 (156)
57 EVA ss5923128615 Oct 16, 2022 (156)
58 EVA ss5958006278 Oct 16, 2022 (156)
59 1000Genomes NC_000020.10 - 25553808 Oct 12, 2018 (152)
60 1000Genomes_30x NC_000020.11 - 25573172 Oct 16, 2022 (156)
61 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 25553808 Oct 12, 2018 (152)
62 Genetic variation in the Estonian population NC_000020.10 - 25553808 Oct 12, 2018 (152)
63 The Danish reference pan genome NC_000020.10 - 25553808 Apr 27, 2020 (154)
64 gnomAD - Genomes NC_000020.11 - 25573172 Apr 27, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000020.10 - 25553808 Apr 27, 2020 (154)
66 KOREAN population from KRGDB NC_000020.10 - 25553808 Apr 27, 2020 (154)
67 Korean Genome Project NC_000020.11 - 25573172 Apr 27, 2020 (154)
68 Northern Sweden NC_000020.10 - 25553808 Jul 13, 2019 (153)
69 Qatari NC_000020.10 - 25553808 Apr 27, 2020 (154)
70 SGDP_PRJ NC_000020.10 - 25553808 Apr 27, 2020 (154)
71 Siberian NC_000020.10 - 25553808 Apr 27, 2020 (154)
72 8.3KJPN NC_000020.10 - 25553808 Apr 27, 2021 (155)
73 14KJPN NC_000020.11 - 25573172 Oct 16, 2022 (156)
74 TopMed NC_000020.11 - 25573172 Apr 27, 2021 (155)
75 UK 10K study - Twins NC_000020.10 - 25553808 Oct 12, 2018 (152)
76 ALFA NC_000020.11 - 25573172 Apr 27, 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)
rs60329493 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77493911, ss85399434, ss255561627, ss283343938, ss287442439, ss292637064, ss1698719243 NC_000020.9:25501807:C:A NC_000020.11:25573171:C:A (self)
77969347, 43169524, 30509764, 5650167, 19235693, 46352381, 16630181, 20209860, 40982943, 10937718, 87303571, 43169524, ss340692683, ss662084191, ss994659974, ss1082162858, ss1364514909, ss1429031011, ss1579485228, ss1638655000, ss1681649033, ss1938167938, ss2029869230, ss2158421364, ss2704098545, ss2966682619, ss3018044920, ss3352472118, ss3684771516, ss3743345316, ss3758566325, ss3788629415, ss3793525342, ss3798412526, ss3835645227, ss3841449036, ss3888965963, ss3939174987, ss5229334264, ss5512197393, ss5663088522, ss5845599084, ss5958006278 NC_000020.10:25553807:C:A NC_000020.11:25573171:C:A (self)
102280008, 549661557, 38407250, 122298617, 361279089, 3239068053, ss2242241040, ss3650995940, ss3706779985, ss3821732228, ss3846957303, ss3982029249, ss5086170144, ss5308471623, ss5500835911, ss5614754073, ss5788461513, ss5817912546, ss5853116837, ss5923128615 NC_000020.11:25573171:C:A NC_000020.11:25573171:C:A (self)
ss8344854, ss16899190, ss19479366, ss21801551, ss115467565, ss135734672 NT_011387.8:25493807:C:A NC_000020.11:25573171:C:A (self)
46352381, ss3939174987 NC_000020.10:25553807:C:G NC_000020.11:25573171:C: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 rs6037146

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