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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.

rs1360756

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:130828276 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.37118 (46608/125568, TOPMED)
T=0.3800 (11745/30904, GnomAD)
T=0.480 (2402/5008, 1000G) (+ 3 more)
T=0.343 (1538/4480, Estonian)
T=0.293 (1128/3854, ALSPAC)
T=0.309 (1144/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EPB41L2 : Non Coding Transcript Variant
SMLR1 : Intron Variant
Publications
1 citation
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 6 NC_000006.12:g.130828276C>T
GRCh37.p13 chr 6 NC_000006.11:g.131149416C>T
Gene: SMLR1, small leucine rich protein 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SMLR1 transcript NM_001195597.1:c. N/A Intron Variant
Gene: EPB41L2, erythrocyte membrane protein band 4.1 like 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EPB41L2 transcript variant 3 NM_001135554.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 2 NM_001135555.3:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 4 NM_001199388.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 6 NM_001252660.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 7 NM_001350299.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 8 NM_001350301.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 9 NM_001350302.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 10 NM_001350303.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 11 NM_001350304.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 12 NM_001350305.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 13 NM_001350306.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 14 NM_001350307.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 15 NM_001350308.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 16 NM_001350309.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 17 NM_001350310.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 18 NM_001350311.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 19 NM_001350312.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 20 NM_001350313.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 21 NM_001350314.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 22 NM_001350315.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 23 NM_001350320.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 1 NM_001431.3:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant 24 NR_146620.1:n. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X1 XM_011535524.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X7 XM_011535525.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X8 XM_011535527.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X10 XM_011535528.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X2 XM_017010350.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X3 XM_017010351.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X4 XM_017010352.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X6 XM_017010353.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X9 XM_017010356.2:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X14 XM_017010364.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X15 XM_024446349.1:c. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X5 XR_001743213.2:n.4523G>A N/A Non Coding Transcript Variant
EPB41L2 transcript variant X11 XR_001743215.2:n. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X12 XR_001743216.2:n. N/A Genic Downstream Transcript Variant
EPB41L2 transcript variant X13 XR_001743217.2: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
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 125568 C=0.62882 T=0.37118
gnomAD - Genomes Global Study-wide 30904 C=0.6200 T=0.3800
gnomAD - Genomes European Sub 18478 C=0.6729 T=0.3271
gnomAD - Genomes African Sub 8696 C=0.566 T=0.434
gnomAD - Genomes East Asian Sub 1616 C=0.347 T=0.653
gnomAD - Genomes Other Sub 980 C=0.62 T=0.38
gnomAD - Genomes American Sub 832 C=0.51 T=0.49
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.72 T=0.28
1000Genomes Global Study-wide 5008 C=0.520 T=0.480
1000Genomes African Sub 1322 C=0.533 T=0.467
1000Genomes East Asian Sub 1008 C=0.325 T=0.675
1000Genomes Europe Sub 1006 C=0.686 T=0.314
1000Genomes South Asian Sub 978 C=0.48 T=0.52
1000Genomes American Sub 694 C=0.59 T=0.41
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.657 T=0.343
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.707 T=0.293
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.691 T=0.309
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= T Note
GRCh38.p12 chr 6 NC_000006.12:g.130828276C= NC_000006.12:g.13082827...

NC_000006.12:g.130828276C>T

GRCh37.p13 chr 6 NC_000006.11:g.131149416C= NC_000006.11:g.13114941...

NC_000006.11:g.131149416C>T

EPB41L2 transcript variant X5 XR_001743213.2:n.4523G= XR_001743213.2:n.4523G>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#.

51 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2143732 Oct 23, 2000 (88)
2 SC_JCM ss6267061 Feb 20, 2003 (111)
3 WI_SSAHASNP ss6767760 Feb 20, 2003 (111)
4 SC_SNP ss12854818 Dec 05, 2003 (119)
5 SC_SNP ss15743236 Feb 27, 2004 (120)
6 PERLEGEN ss23502926 Sep 20, 2004 (123)
7 ABI ss44680976 Mar 14, 2006 (126)
8 AFFY ss66079383 Dec 02, 2006 (127)
9 AFFY ss76018561 Dec 08, 2007 (130)
10 KRIBB_YJKIM ss81462393 Dec 14, 2007 (130)
11 HUMANGENOME_JCVI ss98541843 Feb 03, 2009 (130)
12 BGI ss104360414 Dec 01, 2009 (131)
13 1000GENOMES ss110927518 Jan 25, 2009 (130)
14 1000GENOMES ss115111929 Jan 25, 2009 (130)
15 ENSEMBL ss143210408 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss164556023 Jul 04, 2010 (132)
17 AFFY ss170486534 Jul 04, 2010 (132)
18 BUSHMAN ss202426196 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss207529909 Jul 04, 2010 (132)
20 1000GENOMES ss222679496 Jul 14, 2010 (132)
21 1000GENOMES ss233687481 Jul 15, 2010 (132)
22 1000GENOMES ss240700545 Jul 15, 2010 (132)
23 GMI ss279025164 May 04, 2012 (137)
24 GMI ss285506460 Apr 25, 2013 (138)
25 PJP ss293726120 May 09, 2011 (134)
26 TISHKOFF ss559529375 Apr 25, 2013 (138)
27 SSMP ss653778365 Apr 25, 2013 (138)
28 EVA-GONL ss983511192 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1074041922 Aug 21, 2014 (142)
30 1000GENOMES ss1322312702 Aug 21, 2014 (142)
31 DDI ss1430898445 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1581901916 Apr 01, 2015 (144)
33 EVA_DECODE ss1593079641 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1616715657 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1659709690 Apr 01, 2015 (144)
36 EVA_SVP ss1712900617 Apr 01, 2015 (144)
37 HAMMER_LAB ss1804675632 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1926754758 Feb 12, 2016 (147)
39 GENOMED ss1970528452 Jul 19, 2016 (147)
40 JJLAB ss2024034371 Sep 14, 2016 (149)
41 USC_VALOUEV ss2152228185 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2288474145 Dec 20, 2016 (150)
43 TOPMED ss2457145060 Dec 20, 2016 (150)
44 SYSTEMSBIOZJU ss2626511347 Nov 08, 2017 (151)
45 GRF ss2707858702 Nov 08, 2017 (151)
46 GNOMAD ss2845240756 Nov 08, 2017 (151)
47 SWEGEN ss2999968337 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3025810706 Nov 08, 2017 (151)
49 CSHL ss3347233682 Nov 08, 2017 (151)
50 TOPMED ss3512163320 Nov 08, 2017 (151)
51 URBANLAB ss3648474220 Oct 12, 2018 (152)
52 1000Genomes NC_000006.11 - 131149416 Oct 12, 2018 (152)
53 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 131149416 Oct 12, 2018 (152)
54 Genetic variation in the Estonian population NC_000006.11 - 131149416 Oct 12, 2018 (152)
55 gnomAD - Genomes NC_000006.11 - 131149416 Oct 12, 2018 (152)
56 TopMed NC_000006.12 - 130828276 Oct 12, 2018 (152)
57 UK 10K study - Twins NC_000006.11 - 131149416 Oct 12, 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)
rs56641350 May 27, 2008 (130)
rs57945778 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss110927518, ss115111929, ss164556023, ss202426196, ss207529909, ss279025164, ss285506460, ss293726120, ss1593079641, ss1712900617 NC_000006.10:131191108:C:T NC_000006.12:130828275:C:T (self)
34183366, 19049034, 13623419, 185868513, 19049034, ss222679496, ss233687481, ss240700545, ss559529375, ss653778365, ss983511192, ss1074041922, ss1322312702, ss1430898445, ss1581901916, ss1616715657, ss1659709690, ss1804675632, ss1926754758, ss1970528452, ss2024034371, ss2152228185, ss2457145060, ss2626511347, ss2707858702, ss2845240756, ss2999968337, ss3347233682 NC_000006.11:131149415:C:T NC_000006.12:130828275:C:T (self)
350031140, ss2288474145, ss3025810706, ss3512163320, ss3648474220 NC_000006.12:130828275:C:T NC_000006.12:130828275:C:T (self)
ss12854818 NT_025741.12:35253844:C:T NC_000006.12:130828275:C:T (self)
ss15743236 NT_025741.13:35253844:C:T NC_000006.12:130828275:C:T (self)
ss2143732, ss6267061, ss6767760, ss23502926, ss44680976, ss66079383, ss76018561, ss81462393, ss98541843, ss104360414, ss143210408, ss170486534 NT_025741.15:35318872:C:T NC_000006.12:130828275:C:T (self)
Help

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

1 citation for rs1360756
PMID Title Author Year Journal
20189245 Genome-wide association study of childhood acute lymphoblastic leukemia in Korea. Han S et al. 2010 Leukemia research

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