SNP Links for Gene (Select 100130587) - SNP

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Select item 14915872701.

rs1491587270 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->GT,GTGT,GTGTAT,GTGTATGT,GTGTGT,GTGTGTGT [Show Flanks]
Chromosome:: 20:63359867 (GRCh38)
20:61991220 (GRCh37)
Canonical SPDI:: NC_000020.11:63359867:T:TGT,NC_000020.11:63359867:T:TGTGT,NC_000020.11:63359867:T:TGTGTAT,NC_000020.11:63359867:T:TGTGTATGT,NC_000020.11:63359867:T:TGTGTGT,NC_000020.11:63359867:T:TGTGTGTGT
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGTGT=0./0 (ALFA)
TG=0.0001/0 (TOMMO)
HGVS:: NC_000020.11:g.63359868_63359869insGT, NC_000020.11:g.63359868_63359869insGTGT, NC_000020.11:g.63359868TG[2]TAT[1], NC_000020.11:g.63359868TG[2]TATGT[1], NC_000020.11:g.63359869GT[3], NC_000020.11:g.63359869GT[4], NC_000020.10:g.61991220_61991221insGT, NC_000020.10:g.61991220_61991221insGTGT, NC_000020.10:g.61991220TG[2]TAT[1], NC_000020.10:g.61991220TG[2]TATGT[1], NC_000020.10:g.61991221GT[3], NC_000020.10:g.61991221GT[4], NG_011931.1:g.6476_6477insCA, NG_011931.1:g.6476_6477insCACA, NG_011931.1:g.6476_6477insTACACA, NG_011931.1:g.6476_6477insCATACACA, NG_011931.1:g.6477CA[3], NG_011931.1:g.6477CA[4]

Select item 14913995002.

rs1491399500 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->TCTGTCCGCCTGCAGCCCCCGCCTTC [Show Flanks]
Chromosome:: 20:63361832 (GRCh38)
20:61993185 (GRCh37)
Canonical SPDI:: NC_000020.11:63361832:TCTCTGTCCGCCTGCAGCCCCCGCCTTC:TCTCTGTCCGCCTGCAGCCCCCGCCTTCTCTGTCCGCCTGCAGCCCCCGCCTTC
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TCTCTGTCCGCCTGCAGCCCCCGCCTTCTCTGTCCGCCTGCAGCCCCCGCCTTC=0./0 (ALFA)
TCTCTGTCCGCCTGCAGCCCCCGCCT=0.000011/3 (TOPMED)
TCTCTGTCCGCCTGCAGCCCCCGCCT=0.000029/4 (GnomAD)
HGVS:: NC_000020.11:g.63361835_63361860dup, NC_000020.10:g.61993187_61993212dup, NG_011931.1:g.4486_4511dup, NR_110634.1:n.200_225dup

Select item 14913411213.

rs1491341121 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->TGGGGCCTGGGGTCCCGGTCAATGT [Show Flanks]
Chromosome:: 20:63366797 (GRCh38)
20:61998150 (GRCh37)
Canonical SPDI:: NC_000020.11:63366797:GT:GTTGGGGCCTGGGGTCCCGGTCAATGT
Gene:: LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant
Validated:: by frequency
MAF:: GTTGGGGCCTGGGGTCCCGGTCAAT=0.000029/4 (GnomAD)
HGVS:: NC_000020.11:g.63366799_63366800insTGGGGCCTGGGGTCCCGGTCAATGT, NC_000020.10:g.61998151_61998152insTGGGGCCTGGGGTCCCGGTCAATGT, NR_110634.1:n.686_687insTGGGGCCTGGGGTCCCGGTCAATGT

Select item 14913249504.

rs1491324950 [Homo sapiens]

Variant type:: DEL
Alleles:: GG>- [Show Flanks]
Chromosome:: 20:63366797 (GRCh38)
20:61998149 (GRCh37)
Canonical SPDI:: NC_000020.11:63366796:GG:
Gene:: LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant
HGVS:: NC_000020.11:g.63366797_63366798del, NC_000020.10:g.61998149_61998150del, NR_110634.1:n.684_685del

Select item 14912506775.

rs1491250677 [Homo sapiens]

Variant type:: INS
Alleles:: ->A,G,T [Show Flanks]
Chromosome:: 20:63362415 (GRCh38)
20:61993768 (GRCh37)
Canonical SPDI:: NC_000020.11:63362415::A,NC_000020.11:63362415::G,NC_000020.11:63362415::T
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
HGVS:: NC_000020.11:g.63362415_63362416insA, NC_000020.11:g.63362415_63362416insG, NC_000020.11:g.63362415_63362416insT, NC_000020.10:g.61993767_61993768insA, NC_000020.10:g.61993767_61993768insG, NC_000020.10:g.61993767_61993768insT, NG_011931.1:g.3928_3929insT, NG_011931.1:g.3928_3929insC, NG_011931.1:g.3928_3929insA

Select item 14911707816.

rs1491170781 [Homo sapiens]

Variant type:: DELINS
Alleles:: CT>- [Show Flanks]
Chromosome:: 20:63361836 (GRCh38)
20:61993188 (GRCh37)
Canonical SPDI:: NC_000020.11:63361831:CTCTCT:CTCT
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CTCT=0.000214/3 (ALFA)
-=0.000036/5 (GnomAD)
-=0.000087/23 (TOPMED)
HGVS:: NC_000020.11:g.63361832CT[2], NC_000020.10:g.61993184CT[2], NG_011931.1:g.4507AG[2], NR_110634.1:n.197CT[2]

Select item 14910762957.

rs1491076295 has merged into rs1296560500 [Homo sapiens]

Variant type:: DELINS
Alleles:: TGTG>-,TG,TGTGTG [Show Flanks]
Chromosome:: 20:63359882 (GRCh38)
20:61991234 (GRCh37)
Canonical SPDI:: NC_000020.11:63359869:TGTGTGTGTGTGTGTG:TGTGTGTGTGTG,NC_000020.11:63359869:TGTGTGTGTGTGTGTG:TGTGTGTGTGTGTG,NC_000020.11:63359869:TGTGTGTGTGTGTGTG:TGTGTGTGTGTGTGTGTG
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: TGTGTGTGTGTGTG=0./0 (ALFA)
HGVS:: NC_000020.11:g.63359870TG[6], NC_000020.11:g.63359870TG[7], NC_000020.11:g.63359870TG[9], NC_000020.10:g.61991222TG[6], NC_000020.10:g.61991222TG[7], NC_000020.10:g.61991222TG[9], NG_011931.1:g.6459CA[6], NG_011931.1:g.6459CA[7], NG_011931.1:g.6459CA[9]

Select item 14910245708.

rs1491024570 [Homo sapiens]

Variant type:: INS
Alleles:: ->GT [Show Flanks]
Chromosome:: 20:63369379 (GRCh38)
20:62000732 (GRCh37)
Canonical SPDI:: NC_000020.11:63369379::GT
Gene:: LOC100130587 (Varview)
Functional Consequence:: intron_variant
HGVS:: NC_000020.11:g.63369379_63369380insGT, NC_000020.10:g.62000731_62000732insGT

Select item 14908300949.

rs1490830094 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 20:63367663 (GRCh38)
20:61999015 (GRCh37)
Canonical SPDI:: NC_000020.11:63367662:G:A
Gene:: LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000020.11:g.63367663G>A, NC_000020.10:g.61999015G>A, NR_110634.1:n.1550G>A

Select item 149023044210.

rs1490230442 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 20:63360627 (GRCh38)
20:61991979 (GRCh37)
Canonical SPDI:: NC_000020.11:63360626:C:A
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: intron_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_000020.11:g.63360627C>A, NC_000020.10:g.61991979C>A, NG_011931.1:g.5717G>T

Select item 149020414811.

rs1490204148 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 20:63361290 (GRCh38)
20:61992642 (GRCh37)
Canonical SPDI:: NC_000020.11:63361289:C:G,NC_000020.11:63361289:C:T
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant,5_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
G=0.000011/3 (TOPMED)
T=0.000156/1 (1000Genomes)
HGVS:: NC_000020.11:g.63361290C>G, NC_000020.11:g.63361290C>T, NC_000020.10:g.61992642C>G, NC_000020.10:g.61992642C>T, NG_011931.1:g.5054G>C, NG_011931.1:g.5054G>A, NM_000744.7:c.-125G>C, NM_000744.7:c.-125G>A, NM_000744.6:c.-125G>C, NM_000744.6:c.-125G>A, NR_046317.2:n.60G>C, NR_046317.2:n.60G>A, NR_046317.1:n.107G>C, NR_046317.1:n.107G>A, NM_001256573.2:c.-584G>C, NM_001256573.2:c.-584G>A, NM_001256573.1:c.-584G>C, NM_001256573.1:c.-584G>A

Select item 149007406912.

rs1490074069 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 20:63361891 (GRCh38)
20:61993243 (GRCh37)
Canonical SPDI:: NC_000020.11:63361890:T:C
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
HGVS:: NC_000020.11:g.63361891T>C, NC_000020.10:g.61993243T>C, NG_011931.1:g.4453A>G, NR_110634.1:n.256T>C

Select item 149003779913.

rs1490037799 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 20:63363592 (GRCh38)
20:61994944 (GRCh37)
Canonical SPDI:: NC_000020.11:63363591:C:T
Gene:: LOC100130587 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
T=0.000029/4 (GnomAD)
HGVS:: NC_000020.11:g.63363592C>T, NC_000020.10:g.61994944C>T, NG_011931.1:g.2752G>A

Select item 148996244114.

rs1489962441 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 20:63366641 (GRCh38)
20:61997993 (GRCh37)
Canonical SPDI:: NC_000020.11:63366640:G:A
Gene:: LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000071/1 (ALFA)
A=0.000021/3 (GnomAD)
A=0.000026/7 (TOPMED)
A=0.000495/8 (TOMMO)
A=0.001092/2 (Korea1K)
A=0.002738/8 (KOREAN)
HGVS:: NC_000020.11:g.63366641G>A, NC_000020.10:g.61997993G>A, NR_110634.1:n.528G>A

Select item 148987373715.

rs1489873737 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 20:63362777 (GRCh38)
20:61994129 (GRCh37)
Canonical SPDI:: NC_000020.11:63362776:C:T
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000008/2 (TOPMED)
HGVS:: NC_000020.11:g.63362777C>T, NC_000020.10:g.61994129C>T, NG_011931.1:g.3567G>A

Select item 148985104616.

rs1489851046 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 20:63361412 (GRCh38)
20:61992764 (GRCh37)
Canonical SPDI:: NC_000020.11:63361411:G:T
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.00045/7 (TOMMO)
T=0.00109/7 (1000Genomes)
T=0.00417/11 (KOREAN)
G=0.5/1 (SGDP_PRJ)
HGVS:: NC_000020.11:g.63361412G>T, NC_000020.10:g.61992764G>T, NG_011931.1:g.4932C>A

Select item 148935224517.

rs1489352245 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 20:63367585 (GRCh38)
20:61998937 (GRCh37)
Canonical SPDI:: NC_000020.11:63367584:G:C
Gene:: LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_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_000020.11:g.63367585G>C, NC_000020.10:g.61998937G>C, NR_110634.1:n.1472G>C

Select item 148913238718.

rs1489132387 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 20:63365357 (GRCh38)
20:61996709 (GRCh37)
Canonical SPDI:: NC_000020.11:63365356:C:A,NC_000020.11:63365356:C:T
Gene:: LOC100130587 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000014/2 (GnomAD)
A=0.000026/7 (TOPMED)
T=0.000035/1 (TOMMO)
HGVS:: NC_000020.11:g.63365357C>A, NC_000020.11:g.63365357C>T, NC_000020.10:g.61996709C>A, NC_000020.10:g.61996709C>T, NG_011931.1:g.987G>T, NG_011931.1:g.987G>A

Select item 148902078619.

rs1489020786 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G [Show Flanks]
Chromosome:: 20:63360295 (GRCh38)
20:61991647 (GRCh37)
Canonical SPDI:: NC_000020.11:63360294:A:C,NC_000020.11:63360294:A:G
Gene:: CHRNA4 (Varview), LOC100130587 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
C=0.000004/1 (TOPMED)
G=0.000007/1 (GnomAD)
HGVS:: NC_000020.11:g.63360295A>C, NC_000020.11:g.63360295A>G, NC_000020.10:g.61991647A>C, NC_000020.10:g.61991647A>G, NG_011931.1:g.6049T>G, NG_011931.1:g.6049T>C

Select item 148900001420.

rs1489000014 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 20:63366686 (GRCh38)
20:61998038 (GRCh37)
Canonical SPDI:: NC_000020.11:63366685:G:T
Gene:: LOC100130587 (Varview)
Functional Consequence:: non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000049/13 (TOPMED)
HGVS:: NC_000020.11:g.63366686G>T, NC_000020.10:g.61998038G>T, NR_110634.1:n.573G>T

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