SNP Links for Gene (Select 677775) - SNP

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Select item 14882060561.

rs1488206056 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G,T [Show Flanks]
Chromosome:: 2:233276348 (GRCh38)
2:234184994 (GRCh37)
Canonical SPDI:: NC_000002.12:233276347:A:G,NC_000002.12:233276347:A:T
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
G=0.00004/1 (TOMMO)
HGVS:: NC_000002.12:g.233276348A>G, NC_000002.12:g.233276348A>T, NC_000002.11:g.234184994A>G, NC_000002.11:g.234184994A>T, NG_023038.1:g.29778A>G, NG_023038.1:g.29778A>T, NW_011332690.1:g.221686A>G, NW_011332690.1:g.221686A>T

Select item 14875269372.

rs1487526937 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:233275318 (GRCh38)
2:234183964 (GRCh37)
Canonical SPDI:: NC_000002.12:233275317:G:A
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000011/3 (TOPMED)
A=0.000014/2 (GnomAD)
HGVS:: NC_000002.12:g.233275318G>A, NC_000002.11:g.234183964G>A, NG_023038.1:g.28748G>A, NW_011332690.1:g.220656G>A

Select item 14870257803.

rs1487025780 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:233274828 (GRCh38)
2:234183474 (GRCh37)
Canonical SPDI:: NC_000002.12:233274827:G:A
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000071/1 (ALFA)
A=0.000004/1 (GnomAD_exomes)
A=0.000007/1 (GnomAD)
A=0.000008/2 (TOPMED)
HGVS:: NC_000002.12:g.233274828G>A, NC_000002.11:g.234183474G>A, NG_023038.1:g.28258G>A, NW_011332690.1:g.220166G>A

Select item 14844210604.

rs1484421060 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 2:233275875 (GRCh38)
2:234184521 (GRCh37)
Canonical SPDI:: NC_000002.12:233275874:C:T
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by cluster
MAF:: T=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.233275875C>T, NC_000002.11:g.234184521C>T, NG_023038.1:g.29305C>T, NW_011332690.1:g.221213C>T, NR_003008.2:n.150C>T

Select item 14808982495.

rs1480898249 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:233275838 (GRCh38)
2:234184484 (GRCh37)
Canonical SPDI:: NC_000002.12:233275837:A:G
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by cluster
MAF:: G=0.000004/1 (GnomAD_exomes)
G=0.000546/1 (Korea1K)
HGVS:: NC_000002.12:g.233275838A>G, NC_000002.11:g.234184484A>G, NG_023038.1:g.29268A>G, NW_011332690.1:g.221176A>G, NR_003008.2:n.113A>G

Select item 14803268076.

rs1480326807 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->GACTGGCTGAGTGATG [Show Flanks]
Chromosome:: 2:233275585 (GRCh38)
2:234184232 (GRCh37)
Canonical SPDI:: NC_000002.12:233275585:TGGACTGGCTGAGTGATG:TGGACTGGCTGAGTGATGGACTGGCTGAGTGATG
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGGACTGGCTGAGTGATGGACTGGCTGAGTGATG=0./0 (ALFA)
TGGACTGGCTGAGTGA=0.000004/1 (TOPMED)
TGGACTGGCTGAGTGA=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.233275588_233275603dup, NC_000002.11:g.234184234_234184249dup, NG_023038.1:g.29018_29033dup, NW_011332690.1:g.220926_220941dup

Select item 14789632797.

rs1478963279 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G,T [Show Flanks]
Chromosome:: 2:233273905 (GRCh38)
2:234182551 (GRCh37)
Canonical SPDI:: NC_000002.12:233273904:A:C,NC_000002.12:233273904:A:G,NC_000002.12:233273904:A:T
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
C=0.000004/1 (TOPMED)
HGVS:: NC_000002.12:g.233273905A>C, NC_000002.12:g.233273905A>G, NC_000002.12:g.233273905A>T, NC_000002.11:g.234182551A>C, NC_000002.11:g.234182551A>G, NC_000002.11:g.234182551A>T, NG_023038.1:g.27335A>C, NG_023038.1:g.27335A>G, NG_023038.1:g.27335A>T, NW_011332690.1:g.219243A>C, NW_011332690.1:g.219243A>G, NW_011332690.1:g.219243A>T

Select item 14756872948.

rs1475687294 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 2:233274801 (GRCh38)
2:234183447 (GRCh37)
Canonical SPDI:: NC_000002.12:233274800:C:G
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000015/4 (TOPMED)
HGVS:: NC_000002.12:g.233274801C>G, NC_000002.11:g.234183447C>G, NG_023038.1:g.28231C>G, NW_011332690.1:g.220139C>G

Select item 14707367299.

rs1470736729 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 2:233274545 (GRCh38)
2:234183191 (GRCh37)
Canonical SPDI:: NC_000002.12:233274544:A:T
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0.000071/1 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000002.12:g.233274545A>T, NC_000002.11:g.234183191A>T, NG_023038.1:g.27975A>T, NW_011332690.1:g.219883A>T

Select item 146972744910.

rs1469727449 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 2:233274528 (GRCh38)
2:234183174 (GRCh37)
Canonical SPDI:: NC_000002.12:233274527:T:C
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000007/1 (GnomAD)
C=0.000342/1 (KOREAN)
HGVS:: NC_000002.12:g.233274528T>C, NC_000002.11:g.234183174T>C, NG_023038.1:g.27958T>C, NW_011332690.1:g.219866T>C

Select item 146662374911.

rs1466623749 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:233274093 (GRCh38)
2:234182739 (GRCh37)
Canonical SPDI:: NC_000002.12:233274092:A:G
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000008/2 (TOPMED)
HGVS:: NC_000002.12:g.233274093A>G, NC_000002.11:g.234182739A>G, NG_023038.1:g.27523A>G, NW_011332690.1:g.219431A>G

Select item 146459985012.

rs1464599850 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->AAAAAAA [Show Flanks]
Chromosome:: 2:233274322 (GRCh38)
2:234182969 (GRCh37)
Canonical SPDI:: NC_000002.12:233274322:AAAAAA:AAAAAAAAAAAAA
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: AAAAAAAAAAAAA=0.0004/2 (ALFA)
AAAAAAA=0.0004/2 (Estonian)
HGVS:: NC_000002.12:g.233274328_233274329insAAAAAAA, NC_000002.11:g.234182974_234182975insAAAAAAA, NG_023038.1:g.27758_27759insAAAAAAA, NW_011332690.1:g.219666_219667insAAAAAAA

Select item 146451014413.

rs1464510144 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:233275558 (GRCh38)
2:234184204 (GRCh37)
Canonical SPDI:: NC_000002.12:233275557:A:G
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000011/3 (TOPMED)
G=0.000071/2 (TOMMO)
G=0.000342/1 (KOREAN)
HGVS:: NC_000002.12:g.233275558A>G, NC_000002.11:g.234184204A>G, NG_023038.1:g.28988A>G, NW_011332690.1:g.220896A>G

Select item 146430690714.

rs1464306907 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 2:233275145 (GRCh38)
2:234183791 (GRCh37)
Canonical SPDI:: NC_000002.12:233275144:G:C
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.233275145G>C, NC_000002.11:g.234183791G>C, NG_023038.1:g.28575G>C, NW_011332690.1:g.220483G>C

Select item 146213036515.

rs1462130365 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:233275078 (GRCh38)
2:234183724 (GRCh37)
Canonical SPDI:: NC_000002.12:233275077:A:G
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000008/2 (TOPMED)
HGVS:: NC_000002.12:g.233275078A>G, NC_000002.11:g.234183724A>G, NG_023038.1:g.28508A>G, NW_011332690.1:g.220416A>G

Select item 146138572916.

rs1461385729 [Homo sapiens]

Variant type:: DEL
Alleles:: T>- [Show Flanks]
Chromosome:: 2:233274003 (GRCh38)
2:234182649 (GRCh37)
Canonical SPDI:: NC_000002.12:233274002:T:
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,frameshift_variant,2KB_upstream_variant,coding_sequence_variant,intron_variant
Validated:: by frequency
MAF:: -=0.000007/1 (GnomAD_exomes)
HGVS:: NC_000002.12:g.233274003del, NC_000002.11:g.234182649del, NG_023038.1:g.27433del, NM_001363742.2:c.864del, NM_001363742.1:c.864del, NW_011332690.1:g.219341del, XM_006712608.4:c.612del, XM_006712608.3:c.612del, XM_006712608.2:c.612del, XM_006712608.1:c.612del, XM_005246084.3:c.432del, XM_005246084.2:c.432del, XM_005246084.1:c.432del, XM_047444850.1:c.864del, NP_001350671.1:p.Leu290fs, XP_006712671.1:p.Leu206fs, XP_005246141.1:p.Leu146fs, XP_047300806.1:p.Leu290fs

Select item 146132635917.

rs1461326359 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 2:233274086 (GRCh38)
2:234182732 (GRCh37)
Canonical SPDI:: NC_000002.12:233274085:C:T
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000002.12:g.233274086C>T, NC_000002.11:g.234182732C>T, NG_023038.1:g.27516C>T, NW_011332690.1:g.219424C>T

Select item 146084539318.

rs1460845393 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 2:233276498 (GRCh38)
2:234185144 (GRCh37)
Canonical SPDI:: NC_000002.12:233276497:T:C
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: downstream_transcript_variant,500B_downstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.233276498T>C, NC_000002.11:g.234185144T>C, NG_023038.1:g.29928T>C, NW_011332690.1:g.221836T>C

Select item 146079802219.

rs1460798022 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 2:233274581 (GRCh38)
2:234183227 (GRCh37)
Canonical SPDI:: NC_000002.12:233274580:C:T
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000002.12:g.233274581C>T, NC_000002.11:g.234183227C>T, NG_023038.1:g.28011C>T, NW_011332690.1:g.219919C>T

Select item 146006079420.

rs1460060794 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:233274385 (GRCh38)
2:234183031 (GRCh37)
Canonical SPDI:: NC_000002.12:233274384:A:G
Gene:: ATG16L1 (Varview), SCARNA5 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000002.12:g.233274385A>G, NC_000002.11:g.234183031A>G, NG_023038.1:g.27815A>G, NW_011332690.1:g.219723A>G

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