SNP Links for Gene (Select 149345) - SNP

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Select item 14913753591.

rs1491375359 has merged into rs35664943 [Homo sapiens]

Variant type:: DELINS
Alleles:: GG>-,G,GGG,GGGG [Show Flanks]
Chromosome:: 1:201892782 (GRCh38)
1:201861910 (GRCh37)
Canonical SPDI:: NC_000001.11:201892774:GGGGGGGGG:GGGGGGG,NC_000001.11:201892774:GGGGGGGGG:GGGGGGGG,NC_000001.11:201892774:GGGGGGGGG:GGGGGGGGGG,NC_000001.11:201892774:GGGGGGGGG:GGGGGGGGGGG
Gene:: SHISA4 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGGGGGGGGGG=0.000464/6 (ALFA)
-=0.178032/778 (Estonian)
-=0.198882/996 (1000Genomes)
-=0.199792/52883 (TOPMED)
-=0.206041/764 (TWINSUK)
-=0.21562/831 (ALSPAC)
HGVS:: NC_000001.11:g.201892782_201892783del, NC_000001.11:g.201892783del, NC_000001.11:g.201892783dup, NC_000001.11:g.201892782_201892783dup, NC_000001.10:g.201861910_201861911del, NC_000001.10:g.201861911del, NC_000001.10:g.201861911dup, NC_000001.10:g.201861910_201861911dup

Select item 14913250402.

rs1491325040 [Homo sapiens]

Variant type:: INS
Alleles:: ->T [Show Flanks]
Chromosome:: 1:201892775 (GRCh38)
1:201861904 (GRCh37)
Canonical SPDI:: NC_000001.11:201892775::T
Gene:: SHISA4 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000019/5 (TOPMED)
T=0.000024/2 (GnomAD)
HGVS:: NC_000001.11:g.201892775_201892776insT, NC_000001.10:g.201861903_201861904insT

Select item 14905737093.

rs1490573709 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 1:201895169 (GRCh38)
1:201864297 (GRCh37)
Canonical SPDI:: NC_000001.11:201895168:G:A
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000224/1 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000223/1 (Estonian)
HGVS:: NC_000001.11:g.201895169G>A, NC_000001.10:g.201864297G>A

Select item 14893584824.

rs1489358482 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 1:201887020 (GRCh38)
1:201856148 (GRCh37)
Canonical SPDI:: NC_000001.11:201887019:G:T
Gene:: SHISA4 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000001.11:g.201887020G>T, NC_000001.10:g.201856148G>T

Select item 14893032835.

rs1489303283 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 1:201893692 (GRCh38)
1:201862820 (GRCh37)
Canonical SPDI:: NC_000001.11:201893691:C:A
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000001.11:g.201893692C>A, NC_000001.10:g.201862820C>A

Select item 14889879476.

rs1488987947 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 1:201887359 (GRCh38)
1:201856487 (GRCh37)
Canonical SPDI:: NC_000001.11:201887358:T:A
Gene:: SHISA4 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000224/1 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000223/1 (Estonian)
HGVS:: NC_000001.11:g.201887359T>A, NC_000001.10:g.201856487T>A

Select item 14886293477.

rs1488629347 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 1:201889594 (GRCh38)
1:201858722 (GRCh37)
Canonical SPDI:: NC_000001.11:201889593:C:G
Gene:: SHISA4 (Varview)
Functional Consequence:: non_coding_transcript_variant,missense_variant,coding_sequence_variant
Validated:: by frequency
MAF:: G=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000001.11:g.201889594C>G, NC_000001.10:g.201858722C>G, NM_198149.3:c.223C>G, NM_198149.2:c.223C>G, NR_030775.2:n.255C>G, NR_030775.1:n.263C>G, NP_937792.2:p.Gln75Glu

Select item 14886254198.

rs1488625419 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 1:201894919 (GRCh38)
1:201864047 (GRCh37)
Canonical SPDI:: NC_000001.11:201894918:C:T
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000001.11:g.201894919C>T, NC_000001.10:g.201864047C>T

Select item 14885227989.

rs1488522798 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 1:201893812 (GRCh38)
1:201862940 (GRCh37)
Canonical SPDI:: NC_000001.11:201893811:C:A
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
HGVS:: NC_000001.11:g.201893812C>A, NC_000001.10:g.201862940C>A

Select item 148803824810.

rs1488038248 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 1:201891393 (GRCh38)
1:201860521 (GRCh37)
Canonical SPDI:: NC_000001.11:201891392:C:A
Gene:: SHISA4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0.000111/1 (ALFA)
A=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000001.11:g.201891393C>A, NC_000001.10:g.201860521C>A

Select item 148797193011.

rs1487971930 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 1:201888477 (GRCh38)
1:201857605 (GRCh37)
Canonical SPDI:: NC_000001.11:201888476:T:A
Gene:: SHISA4 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000008/2 (TOPMED)
A=0.000021/3 (GnomAD)
HGVS:: NC_000001.11:g.201888477T>A, NC_000001.10:g.201857605T>A

Select item 148754629012.

rs1487546290 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 1:201886863 (GRCh38)
1:201855991 (GRCh37)
Canonical SPDI:: NC_000001.11:201886862:C:A
Gene:: SHISA4 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000023/6 (TOPMED)
A=0.000029/4 (GnomAD)
HGVS:: NC_000001.11:g.201886863C>A, NC_000001.10:g.201855991C>A

Select item 148753846013.

rs1487538460 [Homo sapiens]

Variant type:: DEL
Alleles:: AC>- [Show Flanks]
Chromosome:: 1:201893239 (GRCh38)
1:201862367 (GRCh37)
Canonical SPDI:: NC_000001.11:201893238:AC:
Validated:: by frequency,by alfa
MAF:: -=0.000071/1 (ALFA)
-=0.000004/1 (TOPMED)
HGVS:: NC_000001.11:g.201893239_201893240del, NC_000001.10:g.201862367_201862368del

Select item 148739389314.

rs1487393893 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 1:201898619 (GRCh38)
1:201867747 (GRCh37)
Canonical SPDI:: NC_000001.11:201898618:T:C
Gene:: LMOD1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000008/2 (TOPMED)
HGVS:: NC_000001.11:g.201898619T>C, NC_000001.10:g.201867747T>C

Select item 148732284115.

rs1487322841 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 1:201899751 (GRCh38)
1:201868879 (GRCh37)
Canonical SPDI:: NC_000001.11:201899750:C:T
Gene:: LMOD1 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant
Clinical significance:: pathogenic
HGVS:: NC_000001.11:g.201899751C>T, NC_000001.10:g.201868879C>T, NM_012134.3:c.1262G>A, NM_012134.2:c.1262G>A, NP_036266.2:p.Arg421His

Select item 148732193216.

rs1487321932 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 1:201897398 (GRCh38)
1:201866526 (GRCh37)
Canonical SPDI:: NC_000001.11:201897397:C:A
Gene:: LMOD1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000001.11:g.201897398C>A, NC_000001.10:g.201866526C>A, NM_012134.3:c.*974G>T, NM_012134.2:c.*974G>T

Select item 148713775117.

rs1487137751 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 1:201891687 (GRCh38)
1:201860815 (GRCh37)
Canonical SPDI:: NC_000001.11:201891686:G:A
Gene:: SHISA4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000071/1 (ALFA)
A=0.000029/4 (GnomAD)
A=0.00003/8 (TOPMED)
A=0.000035/1 (TOMMO)
HGVS:: NC_000001.11:g.201891687G>A, NC_000001.10:g.201860815G>A

Select item 148710105918.

rs1487101059 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 1:201888836 (GRCh38)
1:201857964 (GRCh37)
Canonical SPDI:: NC_000001.11:201888835:G:T
Gene:: SHISA4 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0.000071/1 (ALFA)
T=0.000007/1 (GnomAD)
HGVS:: NC_000001.11:g.201888836G>T, NC_000001.10:g.201857964G>T, NG_060449.1:g.196G>T, NM_198149.2:c.-159G>T

Select item 148668519119.

rs1486685191 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 1:201894002 (GRCh38)
1:201863130 (GRCh37)
Canonical SPDI:: NC_000001.11:201894001:C:T
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000071/1 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000007/1 (GnomAD)
HGVS:: NC_000001.11:g.201894002C>T, NC_000001.10:g.201863130C>T

Select item 148630843020.

rs1486308430 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 1:201896990 (GRCh38)
1:201866118 (GRCh37)
Canonical SPDI:: NC_000001.11:201896989:C:A
Gene:: LMOD1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000011/3 (TOPMED)
HGVS:: NC_000001.11:g.201896990C>A, NC_000001.10:g.201866118C>A, NM_012134.3:c.*1382G>T, NM_012134.2:c.*1382G>T

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