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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.

rs2077551

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:46137522 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.125559 (17354/138214, GnomAD)
C=0.16105 (4939/30668, ALFA)
C=0.00053 (15/28258, 14KJPN) (+ 13 more)
C=0.00042 (7/16760, 8.3KJPN)
C=0.0781 (500/6404, 1000G_30x)
C=0.0787 (394/5008, 1000G)
C=0.0003 (1/2922, KOREAN)
C=0.214 (214/998, GoNL)
C=0.112 (67/600, NorthernSweden)
C=0.072 (23/320, HapMap)
C=0.162 (35/216, Qatari)
T=0.50 (40/80, SGDP_PRJ)
C=0.50 (40/80, SGDP_PRJ)
C=0.15 (6/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KANSL1 : 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 30668 T=0.83895 C=0.16105
European Sub 22500 T=0.81480 C=0.18520
African Sub 3520 T=0.9594 C=0.0406
African Others Sub 120 T=0.992 C=0.008
African American Sub 3400 T=0.9582 C=0.0418
Asian Sub 200 T=0.990 C=0.010
East Asian Sub 144 T=1.000 C=0.000
Other Asian Sub 56 T=0.96 C=0.04
Latin American 1 Sub 276 T=0.826 C=0.174
Latin American 2 Sub 2702 T=0.8620 C=0.1380
South Asian Sub 106 T=0.915 C=0.085
Other Sub 1364 T=0.8556 C=0.1444


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 138214 T=0.874441 C=0.125559
gnomAD - Genomes European Sub 74412 T=0.83160 C=0.16840
gnomAD - Genomes African Sub 41872 T=0.95790 C=0.04210
gnomAD - Genomes American Sub 13450 T=0.84491 C=0.15509
gnomAD - Genomes Ashkenazi Jewish Sub 3234 T=0.7975 C=0.2025
gnomAD - Genomes East Asian Sub 3130 T=0.9990 C=0.0010
gnomAD - Genomes Other Sub 2116 T=0.8507 C=0.1493
Allele Frequency Aggregator Total Global 30668 T=0.83895 C=0.16105
Allele Frequency Aggregator European Sub 22500 T=0.81480 C=0.18520
Allele Frequency Aggregator African Sub 3520 T=0.9594 C=0.0406
Allele Frequency Aggregator Latin American 2 Sub 2702 T=0.8620 C=0.1380
Allele Frequency Aggregator Other Sub 1364 T=0.8556 C=0.1444
Allele Frequency Aggregator Latin American 1 Sub 276 T=0.826 C=0.174
Allele Frequency Aggregator Asian Sub 200 T=0.990 C=0.010
Allele Frequency Aggregator South Asian Sub 106 T=0.915 C=0.085
14KJPN JAPANESE Study-wide 28258 T=0.99947 C=0.00053
8.3KJPN JAPANESE Study-wide 16760 T=0.99958 C=0.00042
1000Genomes_30x Global Study-wide 6404 T=0.9219 C=0.0781
1000Genomes_30x African Sub 1786 T=0.9860 C=0.0140
1000Genomes_30x Europe Sub 1266 T=0.7891 C=0.2109
1000Genomes_30x South Asian Sub 1202 T=0.9401 C=0.0599
1000Genomes_30x East Asian Sub 1170 T=0.9991 C=0.0009
1000Genomes_30x American Sub 980 T=0.862 C=0.138
1000Genomes Global Study-wide 5008 T=0.9213 C=0.0787
1000Genomes African Sub 1322 T=0.9849 C=0.0151
1000Genomes East Asian Sub 1008 T=0.9990 C=0.0010
1000Genomes Europe Sub 1006 T=0.7873 C=0.2127
1000Genomes South Asian Sub 978 T=0.941 C=0.059
1000Genomes American Sub 694 T=0.854 C=0.146
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9997 C=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.786 C=0.214
Northern Sweden ACPOP Study-wide 600 T=0.888 C=0.112
HapMap Global Study-wide 320 T=0.928 C=0.072
HapMap American Sub 120 T=0.808 C=0.192
HapMap African Sub 114 T=1.000 C=0.000
HapMap Asian Sub 86 T=1.00 C=0.00
Qatari Global Study-wide 216 T=0.838 C=0.162
SGDP_PRJ Global Study-wide 80 T=0.50 C=0.50
The Danish reference pan genome Danish Study-wide 40 T=0.85 C=0.15
Siberian Global Study-wide 4 T=0.5 C=0.5
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 17 NC_000017.11:g.46137522T>C
GRCh37.p13 chr 17 NC_000017.10:g.44214888T>C
KANSL1 RefSeqGene NG_032784.1:g.92853A>G
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5 NT_187663.1:g.839628T>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.2:g.649165G>A
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.1:g.651158G>A
Gene: KANSL1, KAT8 regulatory NSL complex subunit 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KANSL1 transcript variant 3 NM_001193465.2:c.1289+333…

NM_001193465.2:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant 1 NM_001193466.2:c.1289+333…

NM_001193466.2:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant 4 NM_001379198.1:c.1289+333…

NM_001379198.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant 2 NM_015443.4:c.1289+33333A…

NM_015443.4:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X1 XM_006721824.5:c.1289+333…

XM_006721824.5:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X2 XM_011524628.4:c.1289+333…

XM_011524628.4:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X8 XM_017024488.3:c.1289+333…

XM_017024488.3:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X1 XM_047435794.1:c.1289+333…

XM_047435794.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X4 XM_047435795.1:c.1289+333…

XM_047435795.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X5 XM_047435796.1:c.1289+333…

XM_047435796.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X6 XM_047435797.1:c.1289+333…

XM_047435797.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X7 XM_047435798.1:c.1289+333…

XM_047435798.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X9 XM_047435799.1:c.1289+333…

XM_047435799.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X3 XM_047435800.1:c.1289+333…

XM_047435800.1:c.1289+33333A>G

N/A Intron Variant
KANSL1 transcript variant X4 XM_047435801.1:c.59+24955…

XM_047435801.1:c.59+24955A>G

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 T= C
GRCh38.p14 chr 17 NC_000017.11:g.46137522= NC_000017.11:g.46137522T>C
GRCh37.p13 chr 17 NC_000017.10:g.44214888= NC_000017.10:g.44214888T>C
KANSL1 RefSeqGene NG_032784.1:g.92853= NG_032784.1:g.92853A>G
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5 NT_187663.1:g.839628= NT_187663.1:g.839628T>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.2:g.649165G>A NT_167251.2:g.649165=
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.1:g.651158G>A NT_167251.1:g.651158=
KANSL1 transcript variant 3 NM_001193465.1:c.1289+33333= NM_001193465.1:c.1289+33333A>G
KANSL1 transcript variant 3 NM_001193465.2:c.1289+33333= NM_001193465.2:c.1289+33333A>G
KANSL1 transcript variant 1 NM_001193466.1:c.1289+33333= NM_001193466.1:c.1289+33333A>G
KANSL1 transcript variant 1 NM_001193466.2:c.1289+33333= NM_001193466.2:c.1289+33333A>G
KANSL1 transcript variant 4 NM_001379198.1:c.1289+33333= NM_001379198.1:c.1289+33333A>G
KANSL1 transcript variant 2 NM_015443.3:c.1289+33333= NM_015443.3:c.1289+33333A>G
KANSL1 transcript variant 2 NM_015443.4:c.1289+33333= NM_015443.4:c.1289+33333A>G
KANSL1 transcript variant X1 XM_005257232.1:c.1289+33333= XM_005257232.1:c.1289+33333A>G
KANSL1 transcript variant X2 XM_005257233.1:c.1289+33333= XM_005257233.1:c.1289+33333A>G
KANSL1 transcript variant X3 XM_005257234.1:c.1289+33333= XM_005257234.1:c.1289+33333A>G
KANSL1 transcript variant X4 XM_005257235.1:c.1289+33333= XM_005257235.1:c.1289+33333A>G
KANSL1 transcript variant X2 XM_005275644.1:c.1289+33036G>A XM_005275644.1:c.1289+33036=
KANSL1 transcript variant X1 XM_005275645.1:c.1289+33036G>A XM_005275645.1:c.1289+33036=
KANSL1 transcript variant X1 XM_006721824.5:c.1289+33333= XM_006721824.5:c.1289+33333A>G
KANSL1 transcript variant X2 XM_011524628.4:c.1289+33333= XM_011524628.4:c.1289+33333A>G
KANSL1 transcript variant X8 XM_017024488.3:c.1289+33333= XM_017024488.3:c.1289+33333A>G
KANSL1 transcript variant X1 XM_047435794.1:c.1289+33333= XM_047435794.1:c.1289+33333A>G
KANSL1 transcript variant X4 XM_047435795.1:c.1289+33333= XM_047435795.1:c.1289+33333A>G
KANSL1 transcript variant X5 XM_047435796.1:c.1289+33333= XM_047435796.1:c.1289+33333A>G
KANSL1 transcript variant X6 XM_047435797.1:c.1289+33333= XM_047435797.1:c.1289+33333A>G
KANSL1 transcript variant X7 XM_047435798.1:c.1289+33333= XM_047435798.1:c.1289+33333A>G
KANSL1 transcript variant X9 XM_047435799.1:c.1289+33333= XM_047435799.1:c.1289+33333A>G
KANSL1 transcript variant X3 XM_047435800.1:c.1289+33333= XM_047435800.1:c.1289+33333A>G
KANSL1 transcript variant X4 XM_047435801.1:c.59+24955= XM_047435801.1:c.59+24955A>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#.

51 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2993168 Jun 15, 2001 (96)
2 SC_JCM ss3809911 Sep 28, 2001 (100)
3 TSC-CSHL ss5538842 Oct 08, 2002 (108)
4 PERLEGEN ss24574996 Sep 20, 2004 (123)
5 ABI ss44004678 Mar 13, 2006 (126)
6 AFFY ss66218702 Apr 01, 2015 (144)
7 AFFY ss76365040 Apr 01, 2015 (144)
8 KRIBB_YJKIM ss81682131 Dec 14, 2007 (130)
9 BCMHGSC_JDW ss90598748 Apr 01, 2015 (144)
10 COMPLETE_GENOMICS ss168221166 Apr 01, 2015 (144)
11 COMPLETE_GENOMICS ss171454088 Apr 01, 2015 (144)
12 AFFY ss173391406 Apr 01, 2015 (144)
13 BUSHMAN ss202549544 Apr 01, 2015 (144)
14 BCM-HGSC-SUB ss207797405 Apr 01, 2015 (144)
15 1000GENOMES ss237251996 Jul 15, 2010 (137)
16 PJP ss292056461 Apr 01, 2015 (144)
17 SSMP ss661091361 Apr 25, 2013 (138)
18 EVA-GONL ss993132595 Aug 21, 2014 (144)
19 JMKIDD_LAB ss1081074692 Aug 21, 2014 (144)
20 1000GENOMES ss1358753154 Aug 21, 2014 (144)
21 EVA_GENOME_DK ss1578167052 Apr 01, 2015 (144)
22 EVA_SVP ss1713584099 Apr 01, 2015 (144)
23 HAMMER_LAB ss1808794095 Sep 08, 2015 (146)
24 WEILL_CORNELL_DGM ss1936593693 Feb 12, 2016 (147)
25 JJLAB ss2029073441 Sep 14, 2016 (149)
26 USC_VALOUEV ss2157546554 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2217033546 Dec 20, 2016 (150)
28 ILLUMINA ss2710850826 Nov 08, 2017 (151)
29 SWEGEN ss3015577638 Nov 08, 2017 (151)
30 BIOINF_KMB_FNS_UNIBA ss3028358031 Nov 08, 2017 (151)
31 EVA_DECODE ss3700517228 Jul 13, 2019 (153)
32 ACPOP ss3742047279 Jul 13, 2019 (153)
33 EVA ss3754696705 Jul 13, 2019 (153)
34 PACBIO ss3788213268 Jul 13, 2019 (153)
35 PACBIO ss3793169127 Jul 13, 2019 (153)
36 PACBIO ss3798054991 Jul 13, 2019 (153)
37 KHV_HUMAN_GENOMES ss3819964515 Jul 13, 2019 (153)
38 EVA ss3834880693 Apr 27, 2020 (154)
39 EVA ss3841051069 Apr 27, 2020 (154)
40 EVA ss3846548192 Apr 27, 2020 (154)
41 SGDP_PRJ ss3885801399 Apr 27, 2020 (154)
42 KRGDB ss3935501327 Apr 27, 2020 (154)
43 TOMMO_GENOMICS ss5222539191 Apr 27, 2021 (155)
44 1000G_HIGH_COVERAGE ss5303222907 Oct 16, 2022 (156)
45 EVA ss5427753188 Oct 16, 2022 (156)
46 HUGCELL_USP ss5496266553 Oct 16, 2022 (156)
47 1000G_HIGH_COVERAGE ss5606984612 Oct 16, 2022 (156)
48 SANFORD_IMAGENETICS ss5660152554 Oct 16, 2022 (156)
49 TOMMO_GENOMICS ss5778790105 Oct 16, 2022 (156)
50 EVA ss5834018820 Oct 16, 2022 (156)
51 EVA ss5951543984 Oct 16, 2022 (156)
52 1000Genomes NC_000017.10 - 44214888 Oct 12, 2018 (152)
53 1000Genomes_30x NC_000017.11 - 46137522 Oct 16, 2022 (156)
54 The Danish reference pan genome NC_000017.10 - 44214888 Apr 27, 2020 (154)
55 gnomAD - Genomes NC_000017.11 - 46137522 Apr 27, 2021 (155)
56 Genome of the Netherlands Release 5 NC_000017.10 - 44214888 Apr 27, 2020 (154)
57 HapMap NC_000017.11 - 46137522 Apr 27, 2020 (154)
58 KOREAN population from KRGDB NC_000017.10 - 44214888 Apr 27, 2020 (154)
59 Northern Sweden NC_000017.10 - 44214888 Jul 13, 2019 (153)
60 Qatari NC_000017.10 - 44214888 Apr 27, 2020 (154)
61 SGDP_PRJ NC_000017.10 - 44214888 Apr 27, 2020 (154)
62 Siberian NC_000017.10 - 44214888 Apr 27, 2020 (154)
63 8.3KJPN NC_000017.10 - 44214888 Apr 27, 2021 (155)
64 14KJPN NC_000017.11 - 46137522 Oct 16, 2022 (156)
65 ALFA NC_000017.11 - 46137522 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)
rs17661638 Oct 08, 2004 (123)
rs57896044 Feb 27, 2009 (130)
rs117043708 May 04, 2012 (137)
rs575074983 Apr 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66218702, ss76365040, ss90598748, ss168221166, ss171454088, ss173391406, ss202549544, ss207797405, ss292056461, ss1713584099 NC_000017.9:41570664:T:C NC_000017.11:46137521:T:C (self)
71998661, 4369004, 17783164, 42678721, 15332144, 18635615, 37818379, 10062908, 80508498, ss237251996, ss661091361, ss993132595, ss1081074692, ss1358753154, ss1578167052, ss1808794095, ss1936593693, ss2029073441, ss2157546554, ss2710850826, ss3015577638, ss3742047279, ss3754696705, ss3788213268, ss3793169127, ss3798054991, ss3834880693, ss3841051069, ss3885801399, ss3935501327, ss5222539191, ss5427753188, ss5660152554, ss5834018820, ss5951543984 NC_000017.10:44214887:T:C NC_000017.11:46137521:T:C (self)
94510547, 507992541, 1491944, 112627209, 2553100950, ss2217033546, ss3028358031, ss3700517228, ss3819964515, ss3846548192, ss5303222907, ss5496266553, ss5606984612, ss5778790105 NC_000017.11:46137521:T:C NC_000017.11:46137521:T:C (self)
ss2993168, ss3809911, ss5538842, ss24574996, ss44004678, ss81682131 NT_010783.15:9489039:T:C NC_000017.11:46137521: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 rs2077551

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