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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.

rs11075299

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:16152307 (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>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.213068 (56397/264690, TOPMED)
G=0.20906 (7762/37128, ALFA)
G=0.15994 (2680/16756, 8.3KJPN) (+ 11 more)
G=0.1795 (899/5008, 1000G)
G=0.3183 (1426/4480, Estonian)
G=0.2867 (1105/3854, ALSPAC)
G=0.2805 (1040/3708, TWINSUK)
G=0.1468 (430/2930, KOREAN)
G=0.286 (285/998, GoNL)
G=0.338 (203/600, NorthernSweden)
G=0.139 (30/216, Qatari)
T=0.406 (65/160, SGDP_PRJ)
G=0.40 (16/40, GENOME_DK)
T=0.45 (10/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABCC6 : 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 16 NC_000016.10:g.16152307T>A
GRCh38.p13 chr 16 NC_000016.10:g.16152307T>G
GRCh37.p13 chr 16 NC_000016.9:g.16246164T>A
GRCh37.p13 chr 16 NC_000016.9:g.16246164T>G
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.76311A>T
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.76311A>C
ABCC6 RefSeqGene NG_007558.2:g.76165A>T
ABCC6 RefSeqGene NG_007558.2:g.76165A>C
GRCh38.p13 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1810235G>T
GRCh38.p13 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1810235G>A
Gene: ABCC6, ATP binding cassette subfamily C member 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCC6 transcript variant 1 NM_001171.6:c.4209-1535A>T N/A Intron Variant
ABCC6 transcript variant 3 NM_001351800.1:c.3867-153…

NM_001351800.1:c.3867-1535A>T

N/A Intron Variant
ABCC6 transcript variant 2 NM_001079528.4:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant 4 NR_147784.1:n. N/A Intron Variant
ABCC6 transcript variant X1 XM_011522479.2:c.4176-153…

XM_011522479.2:c.4176-1535A>T

N/A Intron Variant
ABCC6 transcript variant X4 XM_011522480.1:c.3867-153…

XM_011522480.1:c.3867-1535A>T

N/A Intron Variant
ABCC6 transcript variant X5 XM_011522481.3:c.3867-153…

XM_011522481.3:c.3867-1535A>T

N/A Intron Variant
ABCC6 transcript variant X2 XM_017023212.1:c.4041-153…

XM_017023212.1:c.4041-1535A>T

N/A Intron Variant
ABCC6 transcript variant X10 XM_024450261.1:c.4245-153…

XM_024450261.1:c.4245-1535A>T

N/A Intron Variant
ABCC6 transcript variant X9 XM_011522482.3:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X8 XM_017023214.1:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X3 XR_932836.2:n. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X6 XR_932837.3:n. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X7 XR_932838.3: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 37128 T=0.79094 A=0.00000, G=0.20906
European Sub 26204 T=0.75901 A=0.00000, G=0.24099
African Sub 5900 T=0.9419 A=0.0000, G=0.0581
African Others Sub 212 T=0.972 A=0.000, G=0.028
African American Sub 5688 T=0.9408 A=0.0000, G=0.0592
Asian Sub 402 T=0.863 A=0.000, G=0.137
East Asian Sub 340 T=0.859 A=0.000, G=0.141
Other Asian Sub 62 T=0.89 A=0.00, G=0.11
Latin American 1 Sub 234 T=0.876 A=0.000, G=0.124
Latin American 2 Sub 1054 T=0.8027 A=0.0000, G=0.1973
South Asian Sub 122 T=0.885 A=0.000, G=0.115
Other Sub 3212 T=0.7516 A=0.0000, G=0.2484


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=0.786932 G=0.213068
8.3KJPN JAPANESE Study-wide 16756 T=0.84006 G=0.15994
1000Genomes Global Study-wide 5008 T=0.8205 G=0.1795
1000Genomes African Sub 1322 T=0.9448 G=0.0552
1000Genomes East Asian Sub 1008 T=0.8750 G=0.1250
1000Genomes Europe Sub 1006 T=0.6978 G=0.3022
1000Genomes South Asian Sub 978 T=0.805 G=0.195
1000Genomes American Sub 694 T=0.705 G=0.295
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6817 G=0.3183
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7133 G=0.2867
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7195 G=0.2805
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.8532 G=0.1468
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.714 G=0.286
Northern Sweden ACPOP Study-wide 600 T=0.662 G=0.338
Qatari Global Study-wide 216 T=0.861 G=0.139
SGDP_PRJ Global Study-wide 160 T=0.406 G=0.594
The Danish reference pan genome Danish Study-wide 40 T=0.60 G=0.40
Siberian Global Study-wide 22 T=0.45 G=0.55
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.p13 chr 16 NC_000016.10:g.16152307= NC_000016.10:g.16152307T>A NC_000016.10:g.16152307T>G
GRCh37.p13 chr 16 NC_000016.9:g.16246164= NC_000016.9:g.16246164T>A NC_000016.9:g.16246164T>G
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.76311= NG_007558.3:g.76311A>T NG_007558.3:g.76311A>C
ABCC6 RefSeqGene NG_007558.2:g.76165= NG_007558.2:g.76165A>T NG_007558.2:g.76165A>C
GRCh38.p13 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1810235G>T NT_187607.1:g.1810235G>A NT_187607.1:g.1810235=
ABCC6 transcript variant 1 NM_001171.5:c.4209-1535= NM_001171.5:c.4209-1535A>T NM_001171.5:c.4209-1535A>C
ABCC6 transcript variant 1 NM_001171.6:c.4209-1535= NM_001171.6:c.4209-1535A>T NM_001171.6:c.4209-1535A>C
ABCC6 transcript variant 3 NM_001351800.1:c.3867-1535= NM_001351800.1:c.3867-1535A>T NM_001351800.1:c.3867-1535A>C
ABCC6 transcript variant X1 XM_011522479.2:c.4176-1535= XM_011522479.2:c.4176-1535A>T XM_011522479.2:c.4176-1535A>C
ABCC6 transcript variant X4 XM_011522480.1:c.3867-1535= XM_011522480.1:c.3867-1535A>T XM_011522480.1:c.3867-1535A>C
ABCC6 transcript variant X5 XM_011522481.3:c.3867-1535= XM_011522481.3:c.3867-1535A>T XM_011522481.3:c.3867-1535A>C
ABCC6 transcript variant X2 XM_017023212.1:c.4041-1535= XM_017023212.1:c.4041-1535A>T XM_017023212.1:c.4041-1535A>C
ABCC6 transcript variant X10 XM_024450261.1:c.4245-1535= XM_024450261.1:c.4245-1535A>T XM_024450261.1:c.4245-1535A>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#.

65 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16713869 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss19345358 Feb 27, 2004 (120)
3 ABI ss43969347 Mar 14, 2006 (126)
4 HGSV ss78189695 Dec 06, 2007 (129)
5 HUMANGENOME_JCVI ss96628285 Feb 03, 2009 (130)
6 1000GENOMES ss109234856 Jan 23, 2009 (130)
7 1000GENOMES ss114911070 Jan 25, 2009 (130)
8 ENSEMBL ss132458198 Dec 01, 2009 (131)
9 ILLUMINA ss152536325 Dec 01, 2009 (131)
10 GMI ss157152887 Dec 01, 2009 (131)
11 ILLUMINA ss159102621 Dec 01, 2009 (131)
12 ILLUMINA ss159845999 Dec 01, 2009 (131)
13 ILLUMINA ss168870740 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss169308396 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss207686563 Jul 04, 2010 (132)
16 1000GENOMES ss227170893 Jul 14, 2010 (132)
17 1000GENOMES ss236973258 Jul 15, 2010 (132)
18 1000GENOMES ss243323805 Jul 15, 2010 (132)
19 BL ss255552054 May 09, 2011 (134)
20 GMI ss282457501 May 04, 2012 (137)
21 GMI ss287043568 Apr 25, 2013 (138)
22 PJP ss291928878 May 09, 2011 (134)
23 ILLUMINA ss479154430 Sep 08, 2015 (146)
24 ILLUMINA ss532727813 Sep 08, 2015 (146)
25 TISHKOFF ss564815825 Apr 25, 2013 (138)
26 SSMP ss660561953 Apr 25, 2013 (138)
27 ILLUMINA ss832615417 Aug 21, 2014 (142)
28 ILLUMINA ss833206106 Aug 21, 2014 (142)
29 EVA-GONL ss992337946 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1080525929 Aug 21, 2014 (142)
31 1000GENOMES ss1355597779 Aug 21, 2014 (142)
32 DDI ss1427794551 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1577857954 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1634121546 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1677115579 Apr 01, 2015 (144)
36 EVA_DECODE ss1696373162 Apr 01, 2015 (144)
37 WEILL_CORNELL_DGM ss1935755502 Feb 12, 2016 (147)
38 GENOMED ss1968232313 Jul 19, 2016 (147)
39 JJLAB ss2028664702 Sep 14, 2016 (149)
40 USC_VALOUEV ss2157076233 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2211036886 Dec 20, 2016 (150)
42 TOPMED ss2375725948 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2628826500 Nov 08, 2017 (151)
44 GRF ss2701575189 Nov 08, 2017 (151)
45 SWEGEN ss3014156639 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3028157948 Nov 08, 2017 (151)
47 TOPMED ss3241489325 Nov 08, 2017 (151)
48 TOPMED ss3241489326 Nov 08, 2017 (151)
49 CSHL ss3351362880 Nov 08, 2017 (151)
50 ILLUMINA ss3627490017 Oct 12, 2018 (152)
51 ILLUMINA ss3636325272 Oct 12, 2018 (152)
52 ILLUMINA ss3638116595 Oct 12, 2018 (152)
53 URBANLAB ss3650476009 Oct 12, 2018 (152)
54 EGCUT_WGS ss3681269800 Jul 13, 2019 (153)
55 ACPOP ss3741382263 Jul 13, 2019 (153)
56 EVA ss3753751348 Jul 13, 2019 (153)
57 KHV_HUMAN_GENOMES ss3819045243 Jul 13, 2019 (153)
58 EVA ss3834501445 Apr 27, 2020 (154)
59 EVA ss3840856224 Apr 27, 2020 (154)
60 EVA ss3846347601 Apr 27, 2020 (154)
61 SGDP_PRJ ss3884057753 Apr 27, 2020 (154)
62 KRGDB ss3933369364 Apr 27, 2020 (154)
63 VINODS ss4032512633 Apr 27, 2021 (155)
64 TOPMED ss5009584113 Apr 27, 2021 (155)
65 TOMMO_GENOMICS ss5218676483 Apr 27, 2021 (155)
66 1000Genomes NC_000016.9 - 16246164 Oct 12, 2018 (152)
67 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 16246164 Oct 12, 2018 (152)
68 Genetic variation in the Estonian population NC_000016.9 - 16246164 Oct 12, 2018 (152)
69 The Danish reference pan genome NC_000016.9 - 16246164 Apr 27, 2020 (154)
70 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 484390044 (NC_000016.10:16152306:T:A 2/139250)
Row 484390045 (NC_000016.10:16152306:T:G 31529/139184)

- Apr 27, 2021 (155)
71 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 484390044 (NC_000016.10:16152306:T:A 2/139250)
Row 484390045 (NC_000016.10:16152306:T:G 31529/139184)

- Apr 27, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000016.9 - 16246164 Apr 27, 2020 (154)
73 KOREAN population from KRGDB NC_000016.9 - 16246164 Apr 27, 2020 (154)
74 Northern Sweden NC_000016.9 - 16246164 Jul 13, 2019 (153)
75 Qatari NC_000016.9 - 16246164 Apr 27, 2020 (154)
76 SGDP_PRJ NC_000016.9 - 16246164 Apr 27, 2020 (154)
77 Siberian NC_000016.9 - 16246164 Apr 27, 2020 (154)
78 8.3KJPN NC_000016.9 - 16246164 Apr 27, 2021 (155)
79 TopMed NC_000016.10 - 16152307 Apr 27, 2021 (155)
80 UK 10K study - Twins NC_000016.9 - 16246164 Oct 12, 2018 (152)
81 ALFA NC_000016.10 - 16152307 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10384507450, ss3241489325 NC_000016.10:16152306:T:A NC_000016.10:16152306:T:A (self)
ss78189695, ss109234856, ss114911070, ss159845999, ss169308396, ss207686563, ss255552054, ss282457501, ss287043568, ss291928878, ss1696373162 NC_000016.8:16153664:T:G NC_000016.10:16152306:T:G (self)
68739476, 38166427, 27008048, 4072657, 17024996, 40546758, 14667128, 17797424, 36074733, 9592587, 76645790, 38166427, ss227170893, ss236973258, ss243323805, ss479154430, ss532727813, ss564815825, ss660561953, ss832615417, ss833206106, ss992337946, ss1080525929, ss1355597779, ss1427794551, ss1577857954, ss1634121546, ss1677115579, ss1935755502, ss1968232313, ss2028664702, ss2157076233, ss2375725948, ss2628826500, ss2701575189, ss3014156639, ss3351362880, ss3627490017, ss3636325272, ss3638116595, ss3681269800, ss3741382263, ss3753751348, ss3834501445, ss3840856224, ss3884057753, ss3933369364, ss5218676483 NC_000016.9:16246163:T:G NC_000016.10:16152306:T:G (self)
140704650, 225129774, 10384507450, ss2211036886, ss3028157948, ss3241489326, ss3650476009, ss3819045243, ss3846347601, ss5009584113 NC_000016.10:16152306:T:G NC_000016.10:16152306:T:G (self)
ss16713869, ss19345358 NT_010393.14:7558297:T:G NC_000016.10:16152306:T:G (self)
ss43969347, ss96628285, ss132458198, ss152536325, ss157152887, ss159102621, ss168870740 NT_010393.16:16186163:T:G NC_000016.10:16152306:T:G (self)
ss4032512633 NT_187607.1:1810234:G:G NC_000016.10:16152306:T:G
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 rs11075299

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