SNP Links for Gene (Select 1136) - SNP

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Select item 14915216961.

rs1491521696 [Homo sapiens]

Variant type:: DEL
Alleles:: CA>- [Show Flanks]
Chromosome:: 15:78607218 (GRCh38)
15:78899560 (GRCh37)
Canonical SPDI:: NC_000015.10:78607217:CA:
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: -=0.00118/14 (ALFA)
HGVS:: NC_000015.10:g.78607218_78607219del, NC_000015.9:g.78899560_78899561del, NG_016143.1:g.19077_19078del

Select item 14914581872.

rs1491458187 [Homo sapiens]

Variant type:: DELINS
Alleles:: AG>- [Show Flanks]
Chromosome:: 15:78608639 (GRCh38)
15:78900981 (GRCh37)
Canonical SPDI:: NC_000015.10:78608636:AGAG:AG
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AGAG=0./0 (ALFA)
-=0.000008/2 (TOPMED)
-=0.000021/3 (GnomAD)
HGVS:: NC_000015.10:g.78608637AG[1], NC_000015.9:g.78900979AG[1], NG_016143.1:g.17656CT[1]

Select item 14913027003.

rs1491302700 has merged into rs1412843868 [Homo sapiens]

Variant type:: DELINS
Alleles:: A>-,AA,AAAA,AAAAA [Show Flanks]
Chromosome:: 15:78613778 (GRCh38)
15:78906120 (GRCh37)
Canonical SPDI:: NC_000015.10:78613777:AAAAAAAA:AAAAAAA,NC_000015.10:78613777:AAAAAAAA:AAAAAAAAA,NC_000015.10:78613777:AAAAAAAA:AAAAAAAAAAA,NC_000015.10:78613777:AAAAAAAA:AAAAAAAAAAAA
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAA=0./0 (ALFA)
-=0.00059/13 (TOMMO)
HGVS:: NC_000015.10:g.78613785del, NC_000015.10:g.78613785dup, NC_000015.10:g.78613783_78613785dup, NC_000015.10:g.78613782_78613785dup, NC_000015.9:g.78906127del, NC_000015.9:g.78906127dup, NC_000015.9:g.78906125_78906127dup, NC_000015.9:g.78906124_78906127dup, NG_016143.1:g.12518del, NG_016143.1:g.12518dup, NG_016143.1:g.12516_12518dup, NG_016143.1:g.12515_12518dup

Select item 14912823354.

rs1491282335 has merged into rs60628146 [Homo sapiens]

Variant type:: DELINS
Alleles:: TG>- [Show Flanks]
Chromosome:: 15:78595374 (GRCh38)
15:78887716 (GRCh37)
Canonical SPDI:: NC_000015.10:78595371:TGTG:TG
Gene:: CHRNA3 (Varview), CHRNA5 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant,intron_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGTG=0.003203/45 (ALFA)
-=0.002967/19 (1000Genomes)
-=0.004941/689 (GnomAD)
-=0.005421/1435 (TOPMED)
HGVS:: NC_000015.10:g.78595372TG[1], NC_000015.9:g.78887714TG[1], NG_023328.1:g.34853TG[1], NG_016143.1:g.30921CA[1], NM_000743.5:c.*1229CA[1], NM_000743.4:c.*1229CA[1], XM_006720382.4:c.*1229CA[1], XM_006720382.3:c.*1229CA[1], XM_006720382.2:c.*1229CA[1], XM_006720382.1:c.*1229CA[1]

Select item 14912516435.

rs1491251643 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->G [Show Flanks]
Chromosome:: 15:78601734 (GRCh38)
15:78894077 (GRCh37)
Canonical SPDI:: NC_000015.10:78601734:GGGGG:GGGGGG
Gene:: CHRNA3 (Varview)
Functional Consequence:: coding_sequence_variant,non_coding_transcript_variant,frameshift_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGGGGG=0./0 (ALFA)
G=0.000007/1 (GnomAD)
HGVS:: NC_000015.10:g.78601739dup, NC_000015.9:g.78894081dup, NG_016143.1:g.24561dup, NM_000743.5:c.907dup, NM_000743.4:c.907dup, NR_046313.2:n.1109dup, NR_046313.1:n.1408dup, NM_001166694.2:c.907dup, NM_001166694.1:c.907dup, XM_006720382.4:c.706dup, XM_006720382.3:c.706dup, XM_006720382.2:c.706dup, XM_006720382.1:c.706dup, NP_000734.2:p.Leu303fs, NP_001160166.1:p.Leu303fs, XP_006720445.1:p.Leu236fs

Select item 14912362816.

rs1491236281 [Homo sapiens]

Variant type:: INS
Alleles:: ->AA,AAA [Show Flanks]
Chromosome:: 15:78613776 (GRCh38)
15:78906119 (GRCh37)
Canonical SPDI:: NC_000015.10:78613776::AA,NC_000015.10:78613776::AAA
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAA=0./0 (ALFA)
AAA=0.0003/18 (GnomAD)
AA=0.00161/19 (TOMMO)
HGVS:: NC_000015.10:g.78613776_78613777insAA, NC_000015.10:g.78613776_78613777insAAA, NC_000015.9:g.78906118_78906119insAA, NC_000015.9:g.78906118_78906119insAAA, NG_016143.1:g.12519_12520insTT, NG_016143.1:g.12519_12520insTTT

Select item 14911963107.

rs1491196310 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->CCTC [Show Flanks]
Chromosome:: 15:78595368 (GRCh38)
15:78887711 (GRCh37)
Canonical SPDI:: NC_000015.10:78595368:CTC:CTCCCTC
Gene:: CHRNA3 (Varview), CHRNA5 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant,downstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CTCCCTC=0./0 (ALFA)
CTCC=0.00007/1 (GnomAD)
CTCC=0.0006/2 (TOMMO)
CTCC=0.00236/1 (Korea1K)
HGVS:: NC_000015.10:g.78595371_78595372insCCTC, NC_000015.9:g.78887713_78887714insCCTC, NG_023328.1:g.34852_34853insCCTC, NG_016143.1:g.30927_30928insGGAG, NM_000743.5:c.*1235_*1236insGGAG, NM_000743.4:c.*1235_*1236insGGAG, XM_006720382.4:c.*1235_*1236insGGAG, XM_006720382.3:c.*1235_*1236insGGAG, XM_006720382.2:c.*1235_*1236insGGAG, XM_006720382.1:c.*1235_*1236insGGAG

Select item 14911907748.

rs1491190774 has merged into rs57005476 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAAA>-,A,AA,AAA,AAAA,AAAAAA,AAAAAAA,AAAAAAAA,AAAAAAAAA,AAAAAAAAAAA [Show Flanks]
Chromosome:: 15:78600027 (GRCh38)
15:78892369 (GRCh37)
Canonical SPDI:: NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAA,NC_000015.10:78600016:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAA=0./0 (ALFA)
AA=0.3137/1571 (1000Genomes)
AA=0.3166/183 (NorthernSweden)
AA=0.325/13 (GENOME_DK)
HGVS:: NC_000015.10:g.78600027_78600031del, NC_000015.10:g.78600028_78600031del, NC_000015.10:g.78600029_78600031del, NC_000015.10:g.78600030_78600031del, NC_000015.10:g.78600031del, NC_000015.10:g.78600031dup, NC_000015.10:g.78600030_78600031dup, NC_000015.10:g.78600029_78600031dup, NC_000015.10:g.78600028_78600031dup, NC_000015.10:g.78600026_78600031dup, NC_000015.9:g.78892369_78892373del, NC_000015.9:g.78892370_78892373del, NC_000015.9:g.78892371_78892373del, NC_000015.9:g.78892372_78892373del, NC_000015.9:g.78892373del, NC_000015.9:g.78892373dup, NC_000015.9:g.78892372_78892373dup, NC_000015.9:g.78892371_78892373dup, NC_000015.9:g.78892370_78892373dup, NC_000015.9:g.78892368_78892373dup, NG_016143.1:g.26275_26279del, NG_016143.1:g.26276_26279del, NG_016143.1:g.26277_26279del, NG_016143.1:g.26278_26279del, NG_016143.1:g.26279del, NG_016143.1:g.26279dup, NG_016143.1:g.26278_26279dup, NG_016143.1:g.26277_26279dup, NG_016143.1:g.26276_26279dup, NG_016143.1:g.26274_26279dup

Select item 14911698029.

rs1491169802 [Homo sapiens]

Variant type:: DELINS
Alleles:: GA>- [Show Flanks]
Chromosome:: 15:78596754 (GRCh38)
15:78889096 (GRCh37)
Canonical SPDI:: NC_000015.10:78596752:AGA:A
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
-=0.000007/1 (GnomAD)
-=0.000008/2 (TOPMED)
HGVS:: NC_000015.10:g.78596754_78596755del, NC_000015.9:g.78889096_78889097del, NG_023328.1:g.36235_36236del, NG_016143.1:g.29542_29543del

Select item 149114595810.

rs1491145958 [Homo sapiens]

Variant type:: INS
Alleles:: ->CTGGAAACTG [Show Flanks]
Chromosome:: 15:78608637 (GRCh38)
15:78900980 (GRCh37)
Canonical SPDI:: NC_000015.10:78608637::CTGGAAACTG
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: CTGGAAACTG=0./0 (ALFA)
CTGGAAACTG=0.000036/5 (GnomAD)
HGVS:: NC_000015.10:g.78608637_78608638insCTGGAAACTG, NC_000015.9:g.78900979_78900980insCTGGAAACTG, NG_016143.1:g.17658_17659insCAGTTTCCAG

Select item 149114122111.

rs1491141221 [Homo sapiens]

Variant type:: DEL
Alleles:: CC>- [Show Flanks]
Chromosome:: 15:78613776 (GRCh38)
15:78906118 (GRCh37)
Canonical SPDI:: NC_000015.10:78613775:CC:
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.02115/311 (TOMMO)
HGVS:: NC_000015.10:g.78613776_78613777del, NC_000015.9:g.78906118_78906119del, NG_016143.1:g.12519_12520del

Select item 149105211112.

rs1491052111 has merged into rs34573245 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTT>-,TT,TTT,TTTTT,TTTTTT,TTTTTTT [Show Flanks]
Chromosome:: 15:78623037 (GRCh38)
15:78915379 (GRCh37)
Canonical SPDI:: NC_000015.10:78623028:TTTTTTTTTTTT:TTTTTTTT,NC_000015.10:78623028:TTTTTTTTTTTT:TTTTTTTTTT,NC_000015.10:78623028:TTTTTTTTTTTT:TTTTTTTTTTT,NC_000015.10:78623028:TTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000015.10:78623028:TTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000015.10:78623028:TTTTTTTTTTTT:TTTTTTTTTTTTTTT
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTT=0./0 (ALFA)
T=0.2186/393 (1000Genomes)
-=0.3913/1508 (ALSPAC)
-=0.3943/1462 (TWINSUK)
T=0.5/20 (GENOME_DK)
HGVS:: NC_000015.10:g.78623037_78623040del, NC_000015.10:g.78623039_78623040del, NC_000015.10:g.78623040del, NC_000015.10:g.78623040dup, NC_000015.10:g.78623039_78623040dup, NC_000015.10:g.78623038_78623040dup, NC_000015.9:g.78915379_78915382del, NC_000015.9:g.78915381_78915382del, NC_000015.9:g.78915382del, NC_000015.9:g.78915382dup, NC_000015.9:g.78915381_78915382dup, NC_000015.9:g.78915380_78915382dup, NG_016143.1:g.3264_3267del, NG_016143.1:g.3266_3267del, NG_016143.1:g.3267del, NG_016143.1:g.3267dup, NG_016143.1:g.3266_3267dup, NG_016143.1:g.3265_3267dup

Select item 149100795913.

rs1491007959 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->AAAAAAAACA,AAAAAAACA [Show Flanks]
Chromosome:: 15:78613786 (GRCh38)
15:78906129 (GRCh37)
Canonical SPDI:: NC_000015.10:78613786:CA:CAAAAAAAAACA,NC_000015.10:78613786:CA:CAAAAAAAACA
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CAAAAAAAACA=0.00008/1 (ALFA)
HGVS:: NC_000015.10:g.78613788_78613789insAAAAAAAACA, NC_000015.10:g.78613788_78613789insAAAAAAACA, NC_000015.9:g.78906130_78906131insAAAAAAAACA, NC_000015.9:g.78906130_78906131insAAAAAAACA, NG_016143.1:g.12509_12510insTTTTTTTTTG, NG_016143.1:g.12509_12510insTTTTTTTTG

Select item 149081932714.

rs1490819327 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 15:78612013 (GRCh38)
15:78904355 (GRCh37)
Canonical SPDI:: NC_000015.10:78612012:T:A
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0.000071/1 (ALFA)
A=0.000008/2 (TOPMED)
HGVS:: NC_000015.10:g.78612013T>A, NC_000015.9:g.78904355T>A, NG_016143.1:g.14283A>T

Select item 149079328915.

rs1490793289 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 15:78599575 (GRCh38)
15:78891917 (GRCh37)
Canonical SPDI:: NC_000015.10:78599574:G:A
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000011/3 (TOPMED)
HGVS:: NC_000015.10:g.78599575G>A, NC_000015.9:g.78891917G>A, NG_016143.1:g.26721C>T

Select item 149076817916.

rs1490768179 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 15:78611281 (GRCh38)
15:78903623 (GRCh37)
Canonical SPDI:: NC_000015.10:78611280:A:T
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000015.10:g.78611281A>T, NC_000015.9:g.78903623A>T, NG_016143.1:g.15015T>A

Select item 149068972617.

rs1490689726 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 15:78605826 (GRCh38)
15:78898168 (GRCh37)
Canonical SPDI:: NC_000015.10:78605825:C:T
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000014/2 (GnomAD)
T=0.000026/7 (TOPMED)
T=0.000035/1 (TOMMO)
HGVS:: NC_000015.10:g.78605826C>T, NC_000015.9:g.78898168C>T, NG_016143.1:g.20470G>A

Select item 149067346618.

rs1490673466 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 15:78602584 (GRCh38)
15:78894926 (GRCh37)
Canonical SPDI:: NC_000015.10:78602583:A:T
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000042/11 (TOPMED)
T=0.00005/7 (GnomAD)
HGVS:: NC_000015.10:g.78602584A>T, NC_000015.9:g.78894926A>T, NG_016143.1:g.23712T>A

Select item 149062320619.

rs1490623206 [Homo sapiens]

Variant type:: DELINS
Alleles:: TCCAC>- [Show Flanks]
Chromosome:: 15:78600544 (GRCh38)
15:78892886 (GRCh37)
Canonical SPDI:: NC_000015.10:78600541:ACTCCAC:AC
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency
MAF:: -=0.000008/1 (GnomAD)
HGVS:: NC_000015.10:g.78600544_78600548del, NC_000015.9:g.78892886_78892890del, NG_016143.1:g.25750_25754del

Select item 149023841020.

rs1490238410 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 15:78613858 (GRCh38)
15:78906200 (GRCh37)
Canonical SPDI:: NC_000015.10:78613857:A:C
Gene:: CHRNA3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000042/11 (TOPMED)
C=0.000043/6 (GnomAD)
HGVS:: NC_000015.10:g.78613858A>C, NC_000015.9:g.78906200A>C, NG_016143.1:g.12438T>G

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