SNP Links for Gene (Select 55627) - SNP

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Select item 14915420001.

rs1491542000 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->A [Show Flanks]
Chromosome:: 2:130163383 (GRCh38)
2:130920957 (GRCh37)
Canonical SPDI:: NC_000002.12:130163383:A:AA
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AA=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000015/4 (TOPMED)
HGVS:: NC_000002.12:g.130163384dup, NC_000002.11:g.130920957dup, NG_053070.1:g.24367dup, NW_025791762.1:g.339932dup

Select item 14913546392.

rs1491354639 [Homo sapiens]

Variant type:: DEL
Alleles:: CA>- [Show Flanks]
Chromosome:: 2:130166308 (GRCh38)
2:130923881 (GRCh37)
Canonical SPDI:: NC_000002.12:130166307:CA:
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: -=0.00067/8 (ALFA)
HGVS:: NC_000002.12:g.130166308_130166309del, NC_000002.11:g.130923881_130923882del, NG_053070.1:g.21442_21443del

Select item 14912342153.

rs1491234215 [Homo sapiens]

Variant type:: DEL
Alleles:: TG>- [Show Flanks]
Chromosome:: 2:130183989 (GRCh38)
2:130941562 (GRCh37)
Canonical SPDI:: NC_000002.12:130183988:TG:
Gene:: MZT2B (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.000071/1 (ALFA)
-=0.000014/2 (GnomAD)
-=0.000015/4 (TOPMED)
HGVS:: NC_000002.12:g.130183989_130183990del, NC_000002.11:g.130941562_130941563del, NG_053070.1:g.3761_3762del, NW_025791762.1:g.360541_360542del

Select item 14912007214.

rs1491200721 has merged into rs56226182 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAAAAAAAAAAAA>-,A,AA,AAA,AAAA,AAAAA,AAAAAA,AAAAAAA,AAAAAAAA,AAAAAAAAA,AAAAAAAAAA,AAAAAAAAAAA,AAAAAAAAAAAA,AAAAAAAAAAAAA,AAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAAAA [Show Flanks]
Chromosome:: 2:130166321 (GRCh38)
2:130923894 (GRCh37)
Canonical SPDI:: NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000002.12:130166308:AAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAAA=0./0 (ALFA)
AAAAAAAA=0./0 (GENOME_DK)
HGVS:: NC_000002.12:g.130166321_130166334del, NC_000002.12:g.130166322_130166334del, NC_000002.12:g.130166323_130166334del, NC_000002.12:g.130166324_130166334del, NC_000002.12:g.130166325_130166334del, NC_000002.12:g.130166326_130166334del, NC_000002.12:g.130166327_130166334del, NC_000002.12:g.130166328_130166334del, NC_000002.12:g.130166329_130166334del, NC_000002.12:g.130166330_130166334del, NC_000002.12:g.130166331_130166334del, NC_000002.12:g.130166332_130166334del, NC_000002.12:g.130166333_130166334del, NC_000002.12:g.130166334del, NC_000002.12:g.130166334dup, NC_000002.12:g.130166333_130166334dup, NC_000002.12:g.130166332_130166334dup, NC_000002.12:g.130166331_130166334dup, NC_000002.12:g.130166330_130166334dup, NC_000002.11:g.130923894_130923907del, NC_000002.11:g.130923895_130923907del, NC_000002.11:g.130923896_130923907del, NC_000002.11:g.130923897_130923907del, NC_000002.11:g.130923898_130923907del, NC_000002.11:g.130923899_130923907del, NC_000002.11:g.130923900_130923907del, NC_000002.11:g.130923901_130923907del, NC_000002.11:g.130923902_130923907del, NC_000002.11:g.130923903_130923907del, NC_000002.11:g.130923904_130923907del, NC_000002.11:g.130923905_130923907del, NC_000002.11:g.130923906_130923907del, NC_000002.11:g.130923907del, NC_000002.11:g.130923907dup, NC_000002.11:g.130923906_130923907dup, NC_000002.11:g.130923905_130923907dup, NC_000002.11:g.130923904_130923907dup, NC_000002.11:g.130923903_130923907dup, NG_053070.1:g.21429_21442del, NG_053070.1:g.21430_21442del, NG_053070.1:g.21431_21442del, NG_053070.1:g.21432_21442del, NG_053070.1:g.21433_21442del, NG_053070.1:g.21434_21442del, NG_053070.1:g.21435_21442del, NG_053070.1:g.21436_21442del, NG_053070.1:g.21437_21442del, NG_053070.1:g.21438_21442del, NG_053070.1:g.21439_21442del, NG_053070.1:g.21440_21442del, NG_053070.1:g.21441_21442del, NG_053070.1:g.21442del, NG_053070.1:g.21442dup, NG_053070.1:g.21441_21442dup, NG_053070.1:g.21440_21442dup, NG_053070.1:g.21439_21442dup, NG_053070.1:g.21438_21442dup, NW_025791762.1:g.342872_342885del, NW_025791762.1:g.342873_342885del, NW_025791762.1:g.342874_342885del, NW_025791762.1:g.342875_342885del, NW_025791762.1:g.342876_342885del, NW_025791762.1:g.342877_342885del, NW_025791762.1:g.342878_342885del, NW_025791762.1:g.342879_342885del, NW_025791762.1:g.342880_342885del, NW_025791762.1:g.342881_342885del, NW_025791762.1:g.342882_342885del, NW_025791762.1:g.342883_342885del, NW_025791762.1:g.342884_342885del, NW_025791762.1:g.342885del, NW_025791762.1:g.342885dup, NW_025791762.1:g.342884_342885dup, NW_025791762.1:g.342883_342885dup, NW_025791762.1:g.342882_342885dup, NW_025791762.1:g.342881_342885dup

Select item 14907981065.

rs1490798106 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 2:130181419 (GRCh38)
2:130938992 (GRCh37)
Canonical SPDI:: NC_000002.12:130181418:T:G
Gene:: SMPD4 (Varview), MZT2B (Varview)
Functional Consequence:: intron_variant,synonymous_variant,coding_sequence_variant,genic_upstream_transcript_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000011/3 (TOPMED)
HGVS:: NC_000002.12:g.130181419T>G, NC_000002.11:g.130938992T>G, NG_053070.1:g.6332A>C, NW_025791762.1:g.357971T>G, XM_011511444.4:c.183A>C, XM_011511444.3:c.183A>C, XM_011511444.2:c.183A>C, XM_011511444.1:c.183A>C, XM_011511443.3:c.183A>C, XM_011511443.2:c.183A>C, XM_011511443.1:c.183A>C

Select item 14907506646.

rs1490750664 [Homo sapiens]

Variant type:: DEL
Alleles:: TTAAAGA>- [Show Flanks]
Chromosome:: 2:130154059 (GRCh38)
2:130911632 (GRCh37)
Canonical SPDI:: NC_000002.12:130154058:TTAAAGA:
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.130154059_130154065del, NC_000002.11:g.130911632_130911638del, NG_053070.1:g.33686_33692del, NW_025791762.1:g.330607_330613del

Select item 14907291287.

rs1490729128 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 2:130166396 (GRCh38)
2:130923969 (GRCh37)
Canonical SPDI:: NC_000002.12:130166395:C:T
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000002.12:g.130166396C>T, NC_000002.11:g.130923969C>T, NG_053070.1:g.21355G>A, NW_025791762.1:g.342947C>T

Select item 14906644278.

rs1490664427 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 2:130180360 (GRCh38)
2:130937933 (GRCh37)
Canonical SPDI:: NC_000002.12:130180359:C:T
Gene:: SMPD4 (Varview), MZT2B (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000014/2 (GnomAD)
HGVS:: NC_000002.12:g.130180360C>T, NC_000002.11:g.130937933C>T, NG_053070.1:g.7391G>A, NW_025791762.1:g.356912C>T

Select item 14906332079.

rs1490633207 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:130181139 (GRCh38)
2:130938712 (GRCh37)
Canonical SPDI:: NC_000002.12:130181138:G:A
Gene:: SMPD4 (Varview), MZT2B (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant,genic_upstream_transcript_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_000002.12:g.130181139G>A, NC_000002.11:g.130938712G>A, NG_053070.1:g.6612C>T, NW_025791762.1:g.357691G>A

Select item 149058747410.

rs1490587474 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 2:130153649 (GRCh38)
2:130911222 (GRCh37)
Canonical SPDI:: NC_000002.12:130153648:T:G
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000008/2 (TOPMED)
HGVS:: NC_000002.12:g.130153649T>G, NC_000002.11:g.130911222T>G, NG_053070.1:g.34102A>C, NW_025791762.1:g.330197T>G

Select item 149056487011.

rs1490564870 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 2:130166108 (GRCh38)
2:130923681 (GRCh37)
Canonical SPDI:: NC_000002.12:130166107:T:C
Gene:: SMPD4 (Varview)
Functional Consequence:: 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.130166108T>C, NC_000002.11:g.130923681T>C, NG_053070.1:g.21643A>G, NW_025791762.1:g.342658T>C

Select item 149054940212.

rs1490549402 [Homo sapiens]

Variant type:: DEL
Alleles:: A>- [Show Flanks]
Chromosome:: 2:130166938 (GRCh38)
2:130924511 (GRCh37)
Canonical SPDI:: NC_000002.12:130166937:A:
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.130166938del, NC_000002.11:g.130924511del, NG_053070.1:g.20813del, NW_025791762.1:g.343489del

Select item 149051828513.

rs1490518285 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:130184126 (GRCh38)
2:130941699 (GRCh37)
Canonical SPDI:: NC_000002.12:130184125:G:A
Gene:: MZT2B (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000008/2 (TOPMED)
A=0.000017/2 (GnomAD_exomes)
HGVS:: NC_000002.12:g.130184126G>A, NC_000002.11:g.130941699G>A, NG_053070.1:g.3625C>T, NW_025791762.1:g.360678G>A

Select item 149044910914.

rs1490449109 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:130173334 (GRCh38)
2:130930907 (GRCh37)
Canonical SPDI:: NC_000002.12:130173333:A:G
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant,coding_sequence_variant,genic_upstream_transcript_variant,upstream_transcript_variant,missense_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000002.12:g.130173334A>G, NC_000002.11:g.130930907A>G, NG_053070.1:g.14417T>C, NM_017951.5:c.290T>C, NM_017951.4:c.407T>C, NM_017751.4:c.407T>C, NR_033231.3:n.265T>C, NR_033231.2:n.420T>C, NW_025791762.1:g.349886A>G, XM_011511444.4:c.641T>C, XM_011511444.3:c.641T>C, XM_011511444.2:c.641T>C, XM_011511444.1:c.641T>C, XM_011511443.3:c.641T>C, XM_011511443.2:c.641T>C, XM_011511443.1:c.641T>C, NR_033230.2:n.1556T>C, XM_047444938.1:c.14T>C, NP_060421.3:p.Val97Ala, NP_060221.2:p.Val136Ala, XP_011509746.1:p.Val214Ala, XP_011509745.1:p.Val214Ala, XP_047300894.1:p.Val5Ala

Select item 149040899615.

rs1490408996 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 2:130168145 (GRCh38)
2:130925718 (GRCh37)
Canonical SPDI:: NC_000002.12:130168144:T:C
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.130168145T>C, NC_000002.11:g.130925718T>C, NG_053070.1:g.19606A>G, NW_025791762.1:g.344696T>C

Select item 149039549516.

rs1490395495 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 2:130154695 (GRCh38)
2:130912268 (GRCh37)
Canonical SPDI:: NC_000002.12:130154694:T:C
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0./0 (GnomAD)
C=0.000014/1 (GnomAD_exomes)
T=0.5/1 (SGDP_PRJ)
HGVS:: NC_000002.12:g.130154695T>C, NC_000002.11:g.130912268T>C, NG_053070.1:g.33056A>G, NW_025791762.1:g.331243T>C

Select item 149037810617.

rs1490378106 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 2:130170303 (GRCh38)
2:130927876 (GRCh37)
Canonical SPDI:: NC_000002.12:130170302:A:T
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000011/3 (TOPMED)
T=0.000014/2 (GnomAD)
HGVS:: NC_000002.12:g.130170303A>T, NC_000002.11:g.130927876A>T, NG_053070.1:g.17448T>A, NW_025791762.1:g.346855A>T

Select item 149037006418.

rs1490370064 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:130159620 (GRCh38)
2:130917193 (GRCh37)
Canonical SPDI:: NC_000002.12:130159619:G:A
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000084/1 (ALFA)
A=0.000022/3 (GnomAD)
A=0.000343/1 (KOREAN)
HGVS:: NC_000002.12:g.130159620G>A, NC_000002.11:g.130917193G>A, NG_053070.1:g.28131C>T, NW_025791762.1:g.336168G>A

Select item 149029541519.

rs1490295415 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 2:130160008 (GRCh38)
2:130917581 (GRCh37)
Canonical SPDI:: NC_000002.12:130160007:C:A,NC_000002.12:130160007:C:T
Gene:: SMPD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
HGVS:: NC_000002.12:g.130160008C>A, NC_000002.12:g.130160008C>T, NC_000002.11:g.130917581C>A, NC_000002.11:g.130917581C>T, NG_053070.1:g.27743G>T, NG_053070.1:g.27743G>A, NW_025791762.1:g.336556C>A, NW_025791762.1:g.336556C>T

Select item 149024813820.

rs1490248138 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 2:130153389 (GRCh38)
2:130910962 (GRCh37)
Canonical SPDI:: NC_000002.12:130153388:C:G
Gene:: SMPD4 (Varview)
Functional Consequence:: non_coding_transcript_variant,missense_variant,coding_sequence_variant
Validated:: by frequency
MAF:: G=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000002.12:g.130153389C>G, NC_000002.11:g.130910962C>G, NG_053070.1:g.34362G>C, NM_017951.5:c.1955G>C, NM_017951.4:c.2072G>C, NM_017751.4:c.1985G>C, NR_033231.3:n.1930G>C, NR_033231.2:n.2085G>C, NR_033232.3:n.1910G>C, NR_033232.2:n.2065G>C, NM_001171083.2:c.1766G>C, NW_025791762.1:g.329937C>G, XM_011511444.4:c.2219G>C, XM_011511444.3:c.2219G>C, XM_011511444.2:c.2219G>C, XM_011511444.1:c.2219G>C, XM_011511443.3:c.2306G>C, XM_011511443.2:c.2306G>C, XM_011511443.1:c.2306G>C, XM_024452978.2:c.1295G>C, XM_024452978.1:c.1295G>C, NR_033230.2:n.3221G>C, NM_001171084.1:c.1319G>C, XM_047444938.1:c.1679G>C, NP_060421.3:p.Gly652Ala, NP_060221.2:p.Gly662Ala, NP_001164554.1:p.Gly589Ala, XP_011509746.1:p.Gly740Ala, XP_011509745.1:p.Gly769Ala, XP_024308746.1:p.Gly432Ala, XP_047300894.1:p.Gly560Ala

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