Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

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.

rs61740966

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:25317062 (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
T=0.1532 (5989/39082, GnomAD)
T=0.345 (1727/5008, 1000G)
C=0.058 (253/4348, GO-ESP) (+ 2 more)
C=0.012 (50/4150, ExAC)
C=0.124 (231/1858, GnomAD)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RHD : Missense Variant
RSRP1 : 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.p12 chr 1 NC_000001.11:g.25317062T>C
GRCh37.p13 chr 1 NC_000001.10:g.25643553T>C
RHD RefSeqGene NG_007494.1:g.49573C>T
Gene: RHD, Rh blood group D antigen (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RHD transcript variant 1 NM_016124.4:c.1136C>T T [ACG] > M [ATG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Thr379Met T (Thr) > M (Met) Missense Variant
RHD transcript variant 3 NM_001282867.1:c.638C>T T [ACG] > M [ATG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Thr213Met T (Thr) > M (Met) Missense Variant
RHD transcript variant 6 NM_001282870.1:c.1136C>T T [ACG] > M [ATG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Thr379Met T (Thr) > M (Met) Missense Variant
RHD transcript variant 4 NM_001282868.1:c.1002C>T H [CAC] > H [CAT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.His334= H (His) > H (His) Synonymous Variant
RHD transcript variant 2 NM_001127691.2:c. N/A Intron Variant
RHD transcript variant 5 NM_001282869.1:c. N/A Intron Variant
RHD transcript variant 7 NM_001282871.1:c. N/A Intron Variant
RHD transcript variant 8 NM_001282872.1:c. N/A 3 Prime UTR Variant
RHD transcript variant X1 XM_017002015.1:c. N/A Genic Downstream Transcript Variant
RHD transcript variant X3 XR_946737.2:n.1157T>C N/A Non Coding Transcript Variant
RHD transcript variant X2 XR_946736.1:n. N/A Intron Variant
Gene: RSRP1, arginine and serine rich protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RSRP1 transcript variant 14 NM_001321772.1:c. N/A Intron Variant
RSRP1 transcript variant 2 NM_020317.4:c. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 15 NR_135787.1:n. N/A Intron Variant
RSRP1 transcript variant 16 NR_135788.1:n. N/A Intron Variant
RSRP1 transcript variant 17 NR_135789.1:n. N/A Intron Variant
RSRP1 transcript variant 18 NR_135790.1:n. N/A Intron Variant
RSRP1 transcript variant 19 NR_135791.1:n. N/A Intron Variant
RSRP1 transcript variant 20 NR_135792.1:n. N/A Intron Variant
RSRP1 transcript variant 21 NR_135793.1:n. N/A Intron Variant
RSRP1 transcript variant 3 NR_135143.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 4 NR_135144.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 5 NR_135777.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 6 NR_135778.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 7 NR_135780.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 8 NR_135781.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 9 NR_135782.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 10 NR_135783.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 11 NR_135784.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 12 NR_135785.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 13 NR_135786.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant X1 XM_011541797.1:c. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant X2 XR_946709.2:n. N/A Genic Upstream 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 39082 T=0.1532 C=0.8468
gnomAD - Exomes Asian Sub 11094 T=0.0051 C=0.9949
gnomAD - Exomes European Sub 10856 T=0.0184 C=0.9816
gnomAD - Exomes American Sub 7626 T=0.081 C=0.919
gnomAD - Exomes African Sub 7526 T=0.649 C=0.351
gnomAD - Exomes Other Sub 1048 T=0.093 C=0.907
gnomAD - Exomes Ashkenazi Jewish Sub 932 T=0.14 C=0.86
1000Genomes Global Study-wide 5008 T=0.345 C=0.655
1000Genomes African Sub 1322 T=0.703 C=0.297
1000Genomes East Asian Sub 1008 T=0.150 C=0.850
1000Genomes Europe Sub 1006 T=0.270 C=0.730
1000Genomes South Asian Sub 978 T=0.19 C=0.81
1000Genomes American Sub 694 T=0.27 C=0.73
GO Exome Sequencing Project Global Study-wide 4348 T=0.942 C=0.058
GO Exome Sequencing Project African American Sub 2422 T=0.967 C=0.033
GO Exome Sequencing Project European American Sub 1926 T=0.910 C=0.090
ExAC Global Study-wide 4150 T=0.988 C=0.012
ExAC African Sub 3644 T=0.995 C=0.005
ExAC American Sub 260 T=1.00 C=0.00
ExAC Europe Sub 196 T=0.86 C=0.14
ExAC Asian Sub 32 T=0.9 C=0.1
ExAC Other Sub 18 T=1.0 C=0.0
gnomAD - Genomes Global Study-wide 1858 T=0.876 C=0.124
gnomAD - Genomes African Sub 1736 T=0.901 C=0.099
gnomAD - Genomes European Sub 70 T=0.3 C=0.7
gnomAD - Genomes American Sub 30 T=0.8 C=0.2
gnomAD - Genomes Other Sub 22 T=0.9 C=0.1
gnomAD - Genomes Ashkenazi Jewish Sub 0 T=0 C=0
gnomAD - Genomes East Asian Sub 0 T=0 C=0
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 1 NC_000001.11:g.25317062T= NC_000001.11:g.25317062T>C
GRCh37.p13 chr 1 NC_000001.10:g.25643553T= NC_000001.10:g.25643553T>C
RHD RefSeqGene NG_007494.1:g.49573C>T NG_007494.1:g.49573C=
RHD transcript variant 1 NM_016124.4:c.1136C>T NM_016124.4:c.1136C=
RHD transcript variant 1 NM_016124.3:c.1136C>T NM_016124.3:c.1136C=
RHD transcript variant 8 NM_001282872.1:c.*10C>T NM_001282872.1:c.*10C=
RHD transcript variant 3 NM_001282867.1:c.638C>T NM_001282867.1:c.638C=
RHD transcript variant 6 NM_001282870.1:c.1136C>T NM_001282870.1:c.1136C=
RHD transcript variant 4 NM_001282868.1:c.1002C>T NM_001282868.1:c.1002C=
RHD transcript variant X3 XR_946737.2:n.1157T= XR_946737.2:n.1157T>C
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Thr379Met NP_057208.2:p.Thr379=
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Thr213Met NP_001269796.1:p.Thr213=
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Thr379Met NP_001269799.1:p.Thr379=
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.His334= NP_001269797.1:p.His334=
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#.

26 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 CORNELL ss86262274 Mar 23, 2008 (129)
2 HUMANGENOME_JCVI ss97926536 Feb 04, 2009 (130)
3 ENSEMBL ss133788265 Dec 01, 2009 (131)
4 ILLUMINA ss161047297 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss166262992 Jul 04, 2010 (132)
6 GMI ss475582097 May 04, 2012 (142)
7 ILLUMINA ss479218605 Sep 08, 2015 (146)
8 ILLUMINA ss534050862 Sep 08, 2015 (146)
9 BILGI_BIOE ss538310711 Apr 25, 2013 (142)
10 SSMP ss647648299 Apr 25, 2013 (142)
11 NHLBI-ESP ss712285212 Apr 25, 2013 (142)
12 1000GENOMES ss1290089856 Aug 21, 2014 (142)
13 EVA_GENOME_DK ss1573949055 Apr 01, 2015 (144)
14 EVA_EXAC ss1685398982 Apr 01, 2015 (144)
15 HAMMER_LAB ss1794082207 Sep 08, 2015 (146)
16 WEILL_CORNELL_DGM ss1918172304 Feb 12, 2016 (147)
17 SYSTEMSBIOZJU ss2624316042 Nov 08, 2017 (151)
18 GRF ss2697509861 Nov 08, 2017 (151)
19 GNOMAD ss2731265090 Nov 08, 2017 (151)
20 GNOMAD ss2746262221 Nov 08, 2017 (151)
21 GNOMAD ss2752824295 Nov 08, 2017 (151)
22 SWEGEN ss2986489041 Nov 08, 2017 (151)
23 TOPMED ss3071296915 Nov 08, 2017 (151)
24 CSHL ss3343373513 Nov 08, 2017 (151)
25 ILLUMINA ss3626051786 Oct 11, 2018 (152)
26 ILLUMINA ss3635989575 Oct 11, 2018 (152)
27 1000Genomes NC_000001.10 - 25643553 Oct 11, 2018 (152)
28 ExAC NC_000001.10 - 25643553 Oct 11, 2018 (152)
29 gnomAD - Genomes NC_000001.10 - 25643553 Oct 11, 2018 (152)
30 gnomAD - Exomes NC_000001.10 - 25643553 Oct 11, 2018 (152)
31 GO Exome Sequencing Project NC_000001.10 - 25643553 Oct 11, 2018 (152)
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)
rs199998930 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss166262992, ss475582097 NC_000001.9:25516139:T= NC_000001.11:25317061:T= (self)
779840, 4584699, 2223494, 209779, 38553, ss479218605, ss534050862, ss538310711, ss647648299, ss712285212, ss1290089856, ss1573949055, ss1685398982, ss1794082207, ss1918172304, ss2624316042, ss2697509861, ss2731265090, ss2746262221, ss2752824295, ss2986489041, ss3343373513, ss3626051786, ss3635989575 NC_000001.10:25643552:T= NC_000001.11:25317061:T= (self)
ss3071296915 NC_000001.11:25317061:T= NC_000001.11:25317061:T= (self)
ss86262274, ss97926536, ss133788265, ss161047297 NT_004610.19:12323640:T= NC_000001.11:25317061:T= (self)
ss166262992, ss475582097 NC_000001.9:25516139:T>C NC_000001.11:25317061:T>C (self)
779840, 4584699, 2223494, 209779, 38553, ss479218605, ss534050862, ss538310711, ss647648299, ss712285212, ss1290089856, ss1573949055, ss1685398982, ss1794082207, ss1918172304, ss2624316042, ss2697509861, ss2731265090, ss2746262221, ss2752824295, ss2986489041, ss3343373513, ss3626051786, ss3635989575 NC_000001.10:25643552:T>C NC_000001.11:25317061:T>C (self)
ss3071296915 NC_000001.11:25317061:T>C NC_000001.11:25317061:T>C (self)
ss86262274, ss97926536, ss133788265, ss161047297 NT_004610.19:12323640:T>C NC_000001.11:25317061: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 rs61740966

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.post104+4a6ee9c