SNP Links for Gene (Select 3169) - SNP

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Select item 14911595911.

rs1491159591 [Homo sapiens]

Variant type:: DEL
Alleles:: AT>- [Show Flanks]
Chromosome:: 14:37589736 (GRCh38)
14:38058941 (GRCh37)
Canonical SPDI:: NC_000014.9:37589735:AT:
Gene:: FOXA1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency
MAF:: -=0.000014/2 (GnomAD)
HGVS:: NC_000014.9:g.37589736_37589737del, NC_000014.8:g.38058941_38058942del, NG_033028.1:g.10384_10385del, NM_004496.5:c.*1628_*1629del, NM_004496.4:c.*1628_*1629del, NM_004496.3:c.*1628_*1629del

Select item 14910551442.

rs1491055144 [Homo sapiens]

Variant type:: DEL
Alleles:: GG>- [Show Flanks]
Chromosome:: 14:37595145 (GRCh38)
14:38064350 (GRCh37)
Canonical SPDI:: NC_000014.9:37595144:GG:
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,5_prime_UTR_variant
Validated:: by frequency,by cluster
MAF:: -=0.0055/61 (GnomAD)
HGVS:: NC_000014.9:g.37595145_37595146del, NC_000014.8:g.38064350_38064351del, NG_033028.1:g.4975_4976del, NM_004496.5:c.-174_-173del

Select item 14910220853.

rs1491022085 has merged into rs144611453 [Homo sapiens]

Variant type:: DELINS
Alleles:: TT>-,T,TTT,TTTT [Show Flanks]
Chromosome:: 14:37596056 (GRCh38)
14:38065261 (GRCh37)
Canonical SPDI:: NC_000014.9:37596046:TTTTTTTTTTT:TTTTTTTTT,NC_000014.9:37596046:TTTTTTTTTTT:TTTTTTTTTT,NC_000014.9:37596046:TTTTTTTTTTT:TTTTTTTTTTTT,NC_000014.9:37596046:TTTTTTTTTTT:TTTTTTTTTTTTT
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,2KB_upstream_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTT=0./0 (ALFA)
-=0.325635/1551 (1000Genomes)
-=0.338309/89547 (TOPMED)
-=0.375/15 (GENOME_DK)
T=0.3881/711 (Korea1K)
T=0.399781/6700 (TOMMO)
-=0.4/240 (NorthernSweden)
-=0.419364/1555 (TWINSUK)
-=0.423975/1634 (ALSPAC)
-=0.433868/433 (GoNL)
HGVS:: NC_000014.9:g.37596056_37596057del, NC_000014.9:g.37596057del, NC_000014.9:g.37596057dup, NC_000014.9:g.37596056_37596057dup, NC_000014.8:g.38065261_38065262del, NC_000014.8:g.38065262del, NC_000014.8:g.38065262dup, NC_000014.8:g.38065261_38065262dup, NG_033028.1:g.4073_4074del, NG_033028.1:g.4074del, NG_033028.1:g.4074dup, NG_033028.1:g.4073_4074dup

Select item 14908977104.

rs1490897710 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 14:37591325 (GRCh38)
14:38060530 (GRCh37)
Canonical SPDI:: NC_000014.9:37591324:C:A,NC_000014.9:37591324:C:T
Gene:: FOXA1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by cluster
HGVS:: NC_000014.9:g.37591325C>A, NC_000014.9:g.37591325C>T, NC_000014.8:g.38060530C>A, NC_000014.8:g.38060530C>T, NG_033028.1:g.8796G>T, NG_033028.1:g.8796G>A, NM_004496.5:c.*40G>T, NM_004496.5:c.*40G>A, NM_004496.4:c.*40G>T, NM_004496.4:c.*40G>A, NM_004496.3:c.*40G>T, NM_004496.3:c.*40G>A

Select item 14905615535.

rs1490561553 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->G [Show Flanks]
Chromosome:: 14:37593069 (GRCh38)
14:38062275 (GRCh37)
Canonical SPDI:: NC_000014.9:37593069:GG:GGG
Gene:: FOXA1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGG=0.000142/2 (ALFA)
G=0.000157/22 (GnomAD)
G=0.00017/45 (TOPMED)
HGVS:: NC_000014.9:g.37593071dup, NC_000014.8:g.38062276dup, NG_033028.1:g.7051dup

Select item 14905324496.

rs1490532449 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 14:37594246 (GRCh38)
14:38063451 (GRCh37)
Canonical SPDI:: NC_000014.9:37594245:G:A
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000036/5 (GnomAD)
HGVS:: NC_000014.9:g.37594246G>A, NC_000014.8:g.38063451G>A, NG_033028.1:g.5875C>T

Select item 14896331187.

rs1489633118 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 14:37594699 (GRCh38)
14:38063904 (GRCh37)
Canonical SPDI:: NC_000014.9:37594698:G:A,NC_000014.9:37594698:G:C
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
HGVS:: NC_000014.9:g.37594699G>A, NC_000014.9:g.37594699G>C, NC_000014.8:g.38063904G>A, NC_000014.8:g.38063904G>C, NG_033028.1:g.5422C>T, NG_033028.1:g.5422C>G

Select item 14895818728.

rs1489581872 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 14:37595627 (GRCh38)
14:38064832 (GRCh37)
Canonical SPDI:: NC_000014.9:37595626:C:T
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000007/1 (GnomAD)
HGVS:: NC_000014.9:g.37595627C>T, NC_000014.8:g.38064832C>T, NG_033028.1:g.4494G>A, NM_001310135.1:c.-429C>T

Select item 14895143419.

rs1489514341 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G,T [Show Flanks]
Chromosome:: 14:37592586 (GRCh38)
14:38061791 (GRCh37)
Canonical SPDI:: NC_000014.9:37592585:C:A,NC_000014.9:37592585:C:G,NC_000014.9:37592585:C:T
Gene:: FOXA1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Validated:: by frequency,by cluster
MAF:: T=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000014.9:g.37592586C>A, NC_000014.9:g.37592586C>G, NC_000014.9:g.37592586C>T, NC_000014.8:g.38061791C>A, NC_000014.8:g.38061791C>G, NC_000014.8:g.38061791C>T, NG_033028.1:g.7535G>T, NG_033028.1:g.7535G>C, NG_033028.1:g.7535G>A, NM_004496.5:c.198G>T, NM_004496.5:c.198G>C, NM_004496.5:c.198G>A, NM_004496.4:c.198G>T, NM_004496.4:c.198G>C, NM_004496.4:c.198G>A, NM_004496.3:c.198G>T, NM_004496.3:c.198G>C, NM_004496.3:c.198G>A, NP_004487.2:p.Met66Ile, NP_004487.2:p.Met66Ile, NP_004487.2:p.Met66Ile

Select item 148946689110.

rs1489466891 [Homo sapiens]

Variant type:: DELINS
Alleles:: C>- [Show Flanks]
Chromosome:: 14:37591964 (GRCh38)
14:38061169 (GRCh37)
Canonical SPDI:: NC_000014.9:37591963:CCCCC:CCCC
Gene:: FOXA1 (Varview)
Functional Consequence:: coding_sequence_variant,frameshift_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CCCC=0./0 (ALFA)
-=0.000008/2 (TOPMED)
-=0.000014/2 (GnomAD)
HGVS:: NC_000014.9:g.37591968del, NC_000014.8:g.38061173del, NG_033028.1:g.8157del, NM_004496.5:c.820del, NM_004496.4:c.820del, NM_004496.3:c.820del, NP_004487.2:p.Ala274fs

Select item 148935759511.

rs1489357595 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 14:37596856 (GRCh38)
14:38066061 (GRCh37)
Canonical SPDI:: NC_000014.9:37596855:T:G
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000142/2 (ALFA)
G=0.000015/4 (TOPMED)
G=0.000029/4 (GnomAD)
HGVS:: NC_000014.9:g.37596856T>G, NC_000014.8:g.38066061T>G, NG_033028.1:g.3265A>C

Select item 148930467112.

rs1489304671 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 14:37595057 (GRCh38)
14:38064262 (GRCh37)
Canonical SPDI:: NC_000014.9:37595056:T:G
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
HGVS:: NC_000014.9:g.37595057T>G, NC_000014.8:g.38064262T>G, NG_033028.1:g.5064A>C, NM_004496.5:c.-85A>C, NM_004496.4:c.-85A>C, NM_004496.3:c.-85A>C

Select item 148876275313.

rs1488762753 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 14:37594210 (GRCh38)
14:38063415 (GRCh37)
Canonical SPDI:: NC_000014.9:37594209:G:A
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: A=0.000223/2 (ALFA)
A=0.000016/2 (GnomAD_exomes)
HGVS:: NC_000014.9:g.37594210G>A, NC_000014.8:g.38063415G>A, NG_033028.1:g.5911C>T

Select item 148766816814.

rs1487668168 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->A [Show Flanks]
Chromosome:: 14:37595283 (GRCh38)
14:38064489 (GRCh37)
Canonical SPDI:: NC_000014.9:37595283:A:AA
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: AA=0./0 (ALFA)
A=0.000008/2 (TOPMED)
HGVS:: NC_000014.9:g.37595284dup, NC_000014.8:g.38064489dup, NG_033028.1:g.4837dup, NM_001310135.1:c.-772dup

Select item 148756620115.

rs1487566201 [Homo sapiens]

Variant type:: DELINS
Alleles:: G>- [Show Flanks]
Chromosome:: 14:37596308 (GRCh38)
14:38065513 (GRCh37)
Canonical SPDI:: NC_000014.9:37596307:GGG:GG
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GG=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000007/1 (GnomAD)
HGVS:: NC_000014.9:g.37596310del, NC_000014.8:g.38065515del, NG_033028.1:g.3813del

Select item 148754505616.

rs1487545056 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 14:37595152 (GRCh38)
14:38064357 (GRCh37)
Canonical SPDI:: NC_000014.9:37595151:G:A
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
HGVS:: NC_000014.9:g.37595152G>A, NC_000014.8:g.38064357G>A, NG_033028.1:g.4969C>T, NM_004496.5:c.-180C>T

Select item 148727550017.

rs1487275500 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 14:37593505 (GRCh38)
14:38062710 (GRCh37)
Canonical SPDI:: NC_000014.9:37593504:C:T
Gene:: FOXA1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0.00037/6 (ALFA)
HGVS:: NC_000014.9:g.37593505C>T, NC_000014.8:g.38062710C>T, NG_033028.1:g.6616G>A

Select item 148679085018.

rs1486790850 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 14:37590487 (GRCh38)
14:38059692 (GRCh37)
Canonical SPDI:: NC_000014.9:37590486:G:C
Gene:: FOXA1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000071/1 (ALFA)
C=0.000014/2 (GnomAD)
C=0.000015/4 (TOPMED)
HGVS:: NC_000014.9:g.37590487G>C, NC_000014.8:g.38059692G>C, NG_033028.1:g.9634C>G, NM_004496.5:c.*878C>G, NM_004496.4:c.*878C>G, NM_004496.3:c.*878C>G

Select item 148672232419.

rs1486722324 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 14:37593048 (GRCh38)
14:38062253 (GRCh37)
Canonical SPDI:: NC_000014.9:37593047:A:C
Gene:: FOXA1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000071/1 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000008/2 (TOPMED)
HGVS:: NC_000014.9:g.37593048A>C, NC_000014.8:g.38062253A>C, NG_033028.1:g.7073T>G

Select item 148656030220.

rs1486560302 [Homo sapiens]

Variant type:: DEL
Alleles:: ACATAAATCTAAATAAG>- [Show Flanks]
Chromosome:: 14:37593993 (GRCh38)
14:38063198 (GRCh37)
Canonical SPDI:: NC_000014.9:37593992:ACATAAATCTAAATAAG:
Gene:: FOXA1 (Varview), TTC6 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
-=0.000014/2 (GnomAD)
HGVS:: NC_000014.9:g.37593993_37594009del, NC_000014.8:g.38063198_38063214del, NG_033028.1:g.6112_6128del