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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs10195871

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr2:60493454 (GRCh38.p7) 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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.3624 (11181/30852, GnomAD)
G=0.481 (2407/5008, 1000G)
A=0.310 (1194/3854, ALSPAC) (+ 1 more)
A=0.296 (1096/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCL11A : Intron Variant
Publications
2 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.p7 chr 2 NC_000002.12:g.60493454A>G
GRCh38.p7 chr 2 NC_000002.12:g.60493454A>T
GRCh37.p13 chr 2 NC_000002.11:g.60720589A>G
GRCh37.p13 chr 2 NC_000002.11:g.60720589A>T
BCL11A RefSeqGene NG_011968.1:g.65045T>C
BCL11A RefSeqGene NG_011968.1:g.65045T>A
Gene: BCL11A, B-cell CLL/lymphoma 11A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BCL11A transcript variant 2 NM_018014.3:c. N/A Intron Variant
BCL11A transcript variant 1 NM_022893.3:c. N/A Intron Variant
BCL11A transcript variant 3 NM_138559.1:c. N/A Intron Variant
BCL11A transcript variant X1 XM_011532909.1:c. N/A Intron Variant
BCL11A transcript variant X3 XM_011532910.1:c. N/A Intron Variant
BCL11A transcript variant X6 XM_011532912.1:c. N/A Intron Variant
BCL11A transcript variant X2 XM_017004333.1:c. N/A Intron Variant
BCL11A transcript variant X4 XM_017004334.1:c. N/A Intron Variant
BCL11A transcript variant X5 XM_017004335.1:c. N/A Intron Variant
BCL11A transcript variant X9 XM_017004336.1:c. N/A Intron Variant
BCL11A transcript variant X8 XM_017004337.1:c. N/A Intron Variant
BCL11A transcript variant X9 XM_017004338.1:c. 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

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
The Genome Aggregation Database Global Study-wide 30852 A=0.3624 G=0.6376
The Genome Aggregation Database European Sub 18430 A=0.3260 G=0.6740
The Genome Aggregation Database African Sub 8686 A=0.297 G=0.703
The Genome Aggregation Database East Asian Sub 1618 A=0.980 G=0.020
The Genome Aggregation Database Other Sub 978 A=0.39 G=0.61
The Genome Aggregation Database American Sub 838 A=0.60 G=0.40
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=0.43 G=0.57
1000Genomes Global Study-wide 5008 A=0.519 G=0.481
1000Genomes African Sub 1322 A=0.278 G=0.722
1000Genomes East Asian Sub 1008 A=0.968 G=0.032
1000Genomes Europe Sub 1006 A=0.307 G=0.693
1000Genomes South Asian Sub 978 A=0.59 G=0.41
1000Genomes American Sub 694 A=0.54 G=0.46
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.310 G=0.690
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.296 G=0.704
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 A= G T Note
GRCh38.p7 chr 2 NC_000002.12:g.60...

NC_000002.12:g.60493454A=

NC_000002.12:g.60...

NC_000002.12:g.60493454A>G

NC_000002.12:g.60...

NC_000002.12:g.60493454A>T

GRCh37.p13 chr 2 NC_000002.11:g.60...

NC_000002.11:g.60720589A=

NC_000002.11:g.60...

NC_000002.11:g.60720589A>G

NC_000002.11:g.60...

NC_000002.11:g.60720589A>T

BCL11A RefSeqGene NG_011968.1:g.650...

NG_011968.1:g.65045T=

NG_011968.1:g.650...

NG_011968.1:g.65045T>C

NG_011968.1:g.650...

NG_011968.1:g.65045T>A

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#.

4 Frequency, 89 SubSNP submissions
No Submitter Submission ID Date (Build)
1 WUGSC_SSAHASNP ss14060254 Dec 05, 2003 (119)
2 SSAHASNP ss21622555 Apr 05, 2004 (121)
3 PERLEGEN ss23177038 Sep 20, 2004 (123)
4 ABI ss44331958 Mar 14, 2006 (126)
5 ILLUMINA ss66875395 Nov 30, 2006 (127)
6 ILLUMINA ss66958273 Nov 30, 2006 (127)
7 ILLUMINA ss68080909 Dec 12, 2006 (127)
8 PERLEGEN ss68816483 May 17, 2007 (127)
9 ILLUMINA ss70470974 May 23, 2008 (130)
10 ILLUMINA ss70992700 May 17, 2007 (127)
11 ILLUMINA ss75838517 Dec 07, 2007 (129)
12 KRIBB_YJKIM ss84920327 Dec 14, 2007 (130)
13 BCMHGSC_JDW ss91182749 Mar 24, 2008 (129)
14 HUMANGENOME_JCVI ss96400307 Feb 04, 2009 (130)
15 1000GENOMES ss109566749 Jan 24, 2009 (130)
16 1000GENOMES ss110356928 Jan 24, 2009 (130)
17 ILLUMINA-UK ss117729987 Feb 14, 2009 (130)
18 ENSEMBL ss135839437 Dec 01, 2009 (131)
19 ENSEMBL ss138453914 Dec 01, 2009 (131)
20 ILLUMINA ss152599654 Dec 01, 2009 (131)
21 ILLUMINA ss159115133 Dec 01, 2009 (131)
22 ILLUMINA ss159876521 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss163503610 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss164502118 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss166669408 Jul 04, 2010 (132)
26 ILLUMINA ss169833746 Jul 04, 2010 (132)
27 BUSHMAN ss200518995 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss205712516 Jul 04, 2010 (132)
29 1000GENOMES ss219281729 Jul 14, 2010 (132)
30 1000GENOMES ss231193996 Jul 14, 2010 (132)
31 1000GENOMES ss238742970 Jul 15, 2010 (132)
32 ILLUMINA ss244268238 Jul 04, 2010 (132)
33 BL ss253142610 May 09, 2011 (134)
34 GMI ss276493445 May 04, 2012 (137)
35 GMI ss284355793 Apr 25, 2013 (138)
36 PJP ss292279924 May 09, 2011 (134)
37 ILLUMINA ss479220199 May 04, 2012 (137)
38 ILLUMINA ss479222749 May 04, 2012 (137)
39 ILLUMINA ss479572205 Sep 08, 2015 (146)
40 ILLUMINA ss484410966 May 04, 2012 (137)
41 ILLUMINA ss536588247 Sep 08, 2015 (146)
42 TISHKOFF ss555605569 Apr 25, 2013 (138)
43 SSMP ss649193024 Apr 25, 2013 (138)
44 ILLUMINA ss778350912 Sep 08, 2015 (146)
45 ILLUMINA ss782651910 Sep 08, 2015 (146)
46 ILLUMINA ss783621124 Sep 08, 2015 (146)
47 ILLUMINA ss831902254 Sep 08, 2015 (146)
48 ILLUMINA ss833805600 Sep 08, 2015 (146)
49 EVA-GONL ss976898495 Aug 21, 2014 (142)
50 JMKIDD_LAB ss1069166611 Aug 21, 2014 (142)
51 1000GENOMES ss1297479860 Aug 21, 2014 (142)
52 DDI ss1428596670 Apr 01, 2015 (144)
53 EVA_GENOME_DK ss1578905934 Apr 01, 2015 (144)
54 EVA_DECODE ss1586312088 Apr 01, 2015 (144)
55 EVA_UK10K_ALSPAC ss1603647113 Apr 01, 2015 (144)
56 EVA_UK10K_TWINSUK ss1646641146 Apr 01, 2015 (144)
57 EVA_SVP ss1712460519 Apr 01, 2015 (144)
58 ILLUMINA ss1752364034 Sep 08, 2015 (146)
59 HAMMER_LAB ss1796832117 Sep 08, 2015 (146)
60 WEILL_CORNELL_DGM ss1920130017 Feb 12, 2016 (147)
61 GENOMED ss1968785667 Jul 19, 2016 (147)
62 JJLAB ss2020599139 Sep 14, 2016 (149)
63 USC_VALOUEV ss2148642891 Dec 20, 2016 (150)
64 HUMAN_LONGEVITY ss2230803030 Dec 20, 2016 (150)
65 TOPMED ss2396745603 Dec 20, 2016 (150)
66 ILLUMINA ss2633622517 Nov 08, 2017 (151)
67 GRF ss2703213450 Nov 08, 2017 (151)
68 GNOMAD ss2774156009 Nov 08, 2017 (151)
69 AFFY ss2985797454 Nov 08, 2017 (151)
70 SWEGEN ss2989598454 Nov 08, 2017 (151)
71 ILLUMINA ss3021976790 Nov 08, 2017 (151)
72 BIOINF_KMB_FNS_UNIBA ss3024066440 Nov 08, 2017 (151)
73 TOPMED ss3309531236 Nov 08, 2017 (151)
74 TOPMED ss3309531237 Nov 08, 2017 (151)
75 CSHL ss3344257010 Nov 08, 2017 (151)
76 ILLUMINA ss3628077013 Jul 19, 2018 (151)
77 ILLUMINA ss3631588882 Jul 19, 2018 (151)
78 ILLUMINA ss3633202559 Jul 19, 2018 (151)
79 ILLUMINA ss3633914316 Jul 19, 2018 (151)
80 ILLUMINA ss3634769043 Jul 19, 2018 (151)
81 ILLUMINA ss3635600533 Jul 19, 2018 (151)
82 ILLUMINA ss3636455575 Jul 19, 2018 (151)
83 ILLUMINA ss3637352405 Jul 19, 2018 (151)
84 ILLUMINA ss3638263441 Jul 19, 2018 (151)
85 ILLUMINA ss3639136987 Jul 19, 2018 (151)
86 ILLUMINA ss3639873396 Jul 19, 2018 (151)
87 ILLUMINA ss3640476345 Jul 19, 2018 (151)
88 ILLUMINA ss3643233153 Jul 19, 2018 (151)
89 ILLUMINA ss3643921893 Jul 19, 2018 (151)
90 1000Genomes NC_000002.11 - 60720589 Jul 19, 2018 (151)
91 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 60720589 Jul 19, 2018 (151)
92 The Genome Aggregation Database NC_000002.11 - 60720589 Jul 19, 2018 (151)
93 UK 10K study - Twins NC_000002.11 - 60720589 Jul 19, 2018 (151)
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)
rs57600883 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3639136987, ss3639873396, ss3643921893 NC_000002.9:60632239:A= NC_000002.12:60493453:A=
ss91182749, ss109566749, ss110356928, ss117729987, ss163503610, ss164502118, ss166669408, ss200518995, ss205712516, ss253142610, ss276493445, ss284355793, ss292279924, ss479220199, ss1586312088, ss1712460519, ss3643233153 NC_000002.10:60574092:A= NC_000002.12:60493453:A= (self)
8431612, 4688210, 103645870, 4688210, ss219281729, ss231193996, ss238742970, ss479222749, ss479572205, ss484410966, ss536588247, ss555605569, ss649193024, ss778350912, ss782651910, ss783621124, ss831902254, ss833805600, ss976898495, ss1069166611, ss1297479860, ss1428596670, ss1578905934, ss1603647113, ss1646641146, ss1752364034, ss1796832117, ss1920130017, ss1968785667, ss2020599139, ss2148642891, ss2396745603, ss2633622517, ss2703213450, ss2774156009, ss2985797454, ss2989598454, ss3021976790, ss3344257010, ss3628077013, ss3631588882, ss3633202559, ss3633914316, ss3634769043, ss3635600533, ss3636455575, ss3637352405, ss3638263441, ss3640476345 NC_000002.11:60720588:A= NC_000002.12:60493453:A= (self)
ss2230803030, ss3024066440, ss3309531236, ss3309531237 NC_000002.12:60493453:A= NC_000002.12:60493453:A= (self)
ss14060254, ss21622555 NT_022184.13:39536520:A= NC_000002.12:60493453:A= (self)
ss23177038, ss44331958, ss66875395, ss66958273, ss68080909, ss68816483, ss70470974, ss70992700, ss75838517, ss84920327, ss96400307, ss135839437, ss138453914, ss152599654, ss159115133, ss159876521, ss169833746, ss244268238 NT_022184.15:39542475:A= NC_000002.12:60493453:A= (self)
ss3639136987, ss3639873396, ss3643921893 NC_000002.9:60632239:A>G NC_000002.12:60493453:A>G
ss91182749, ss109566749, ss110356928, ss117729987, ss163503610, ss164502118, ss166669408, ss200518995, ss205712516, ss253142610, ss276493445, ss284355793, ss292279924, ss479220199, ss1586312088, ss1712460519, ss3643233153 NC_000002.10:60574092:A>G NC_000002.12:60493453:A>G (self)
8431612, 4688210, 103645870, 4688210, ss219281729, ss231193996, ss238742970, ss479222749, ss479572205, ss484410966, ss536588247, ss555605569, ss649193024, ss778350912, ss782651910, ss783621124, ss831902254, ss833805600, ss976898495, ss1069166611, ss1297479860, ss1428596670, ss1578905934, ss1603647113, ss1646641146, ss1752364034, ss1796832117, ss1920130017, ss1968785667, ss2020599139, ss2148642891, ss2396745603, ss2633622517, ss2703213450, ss2774156009, ss2985797454, ss2989598454, ss3021976790, ss3344257010, ss3628077013, ss3631588882, ss3633202559, ss3633914316, ss3634769043, ss3635600533, ss3636455575, ss3637352405, ss3638263441, ss3640476345 NC_000002.11:60720588:A>G NC_000002.12:60493453:A>G (self)
ss2230803030, ss3024066440, ss3309531236 NC_000002.12:60493453:A>G NC_000002.12:60493453:A>G (self)
ss14060254, ss21622555 NT_022184.13:39536520:A>G NC_000002.12:60493453:A>G (self)
ss23177038, ss44331958, ss66875395, ss66958273, ss68080909, ss68816483, ss70470974, ss70992700, ss75838517, ss84920327, ss96400307, ss135839437, ss138453914, ss152599654, ss159115133, ss159876521, ss169833746, ss244268238 NT_022184.15:39542475:A>G NC_000002.12:60493453:A>G (self)
ss3309531237 NC_000002.12:60493453:A>T NC_000002.12:60493453:A>T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs10195871
PMID Title Author Year Journal
26663441 Protein Quantitative Trait Loci Analysis Identifies Genetic Variation in the Innate Immune Regulator TOLLIP in Post-Lung Transplant Primary Graft Dysfunction Risk. Cantu E et al. 2016 American journal of transplantation
27022141 Original Research: A case-control genome-wide association study identifies genetic modifiers of fetal hemoglobin in sickle cell disease. Liu L et al. 2016 Experimental biology and medicine (Maywood, N.J.)

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: 0.1.4.post833+d3ba21e