SNP Links for Gene (Select 51599) - SNP

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Select item 14915729691.

rs1491572969 [Homo sapiens]

Variant type:: DELINS
Alleles:: A>-,AA [Show Flanks]
Chromosome:: 19:35259338 (GRCh38)
19:35750241 (GRCh37)
Canonical SPDI:: NC_000019.10:35259337:AAAAAAAA:AAAAAAA,NC_000019.10:35259337:AAAAAAAA:AAAAAAAAA
Gene:: LSR (Varview), LOC105372380 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAA=0.000108/2 (ALFA)
-=0.000023/6 (TOPMED)
-=0.000036/5 (GnomAD)
-=0.000342/4 (GnomAD_exomes)
-=0.000446/2 (Estonian)
HGVS:: NC_000019.10:g.35259345del, NC_000019.10:g.35259345dup, NC_000019.9:g.35750248del, NC_000019.9:g.35750248dup, XR_935939.3:n.275del, XR_935939.3:n.275dup, XR_935939.1:n.275del, XR_935939.1:n.275dup

Select item 14915110612.

rs1491511061 [Homo sapiens]

Variant type:: DEL
Alleles:: AT>- [Show Flanks]
Chromosome:: 19:35267018 (GRCh38)
19:35757921 (GRCh37)
Canonical SPDI:: NC_000019.10:35267017:AT:
Gene:: USF2 (Varview), LSR (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000005/1 (GnomAD_exomes)
-=0.000009/1 (ExAC)
HGVS:: NC_000019.10:g.35267018_35267019del, NC_000019.9:g.35757921_35757922del, NG_029241.1:g.3026_3027del

Select item 14914334313.

rs1491433431 [Homo sapiens]

Variant type:: DEL
Alleles:: TA>- [Show Flanks]
Chromosome:: 19:35259337 (GRCh38)
19:35750240 (GRCh37)
Canonical SPDI:: NC_000019.10:35259336:TA:
Gene:: LSR (Varview), LOC105372380 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.000043/6 (GnomAD)
-=0.00008/1 (GnomAD_exomes)
-=0.000091/24 (TOPMED)
-=0.000312/2 (1000Genomes)
HGVS:: NC_000019.10:g.35259337_35259338del, NC_000019.9:g.35750240_35750241del, XR_935939.3:n.267_268del, XR_935939.1:n.267_268del

Select item 14914188194.

rs1491418819 [Homo sapiens]

Variant type:: DEL
Alleles:: CA>- [Show Flanks]
Chromosome:: 19:35252648 (GRCh38)
19:35743551 (GRCh37)
Canonical SPDI:: NC_000019.10:35252647:CA:
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: -=0.00674/80 (ALFA)
HGVS:: NC_000019.10:g.35252648_35252649del, NC_000019.9:g.35743551_35743552del

Select item 14911669305.

rs1491166930 [Homo sapiens]

Variant type:: INS
Alleles:: ->AT [Show Flanks]
Chromosome:: 19:35260855 (GRCh38)
19:35751759 (GRCh37)
Canonical SPDI:: NC_000019.10:35260855::AT
Gene:: LSR (Varview), LOC105372380 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: AT=0./0 (ALFA)
AT=0.000014/2 (GnomAD)
HGVS:: NC_000019.10:g.35260855_35260856insAT, NC_000019.9:g.35751758_35751759insAT

Select item 14910672476.

rs1491067247 [Homo sapiens]

Variant type:: DEL
Alleles:: TG>- [Show Flanks]
Chromosome:: 19:35256725 (GRCh38)
19:35747628 (GRCh37)
Canonical SPDI:: NC_000019.10:35256724:TG:
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency
MAF:: -=0.000035/4 (GnomAD)
HGVS:: NC_000019.10:g.35256725_35256726del, NC_000019.9:g.35747628_35747629del

Select item 14908222297.

rs1490822229 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:35268397 (GRCh38)
19:35759300 (GRCh37)
Canonical SPDI:: NC_000019.10:35268396:C:T
Gene:: USF2 (Varview), LSR (Varview)
Functional Consequence:: 2KB_upstream_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000199/26 (GnomAD)
HGVS:: NC_000019.10:g.35268397C>T, NC_000019.9:g.35759300C>T, NG_029241.1:g.4405C>T

Select item 14907102768.

rs1490710276 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 19:35252285 (GRCh38)
19:35743188 (GRCh37)
Canonical SPDI:: NC_000019.10:35252284:T:C
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000023/6 (TOPMED)
HGVS:: NC_000019.10:g.35252285T>C, NC_000019.9:g.35743188T>C

Select item 14905489009.

rs1490548900 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 19:35251974 (GRCh38)
19:35742877 (GRCh37)
Canonical SPDI:: NC_000019.10:35251973:A:G
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000007/1 (GnomAD)
HGVS:: NC_000019.10:g.35251974A>G, NC_000019.9:g.35742877A>G

Select item 149052872410.

rs1490528724 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 19:35252405 (GRCh38)
19:35743308 (GRCh37)
Canonical SPDI:: NC_000019.10:35252404:T:C
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000019.10:g.35252405T>C, NC_000019.9:g.35743308T>C

Select item 149050492211.

rs1490504922 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->T [Show Flanks]
Chromosome:: 19:35265849 (GRCh38)
19:35756753 (GRCh37)
Canonical SPDI:: NC_000019.10:35265849:TTTTTT:TTTTTTT
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTT=0./0 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000015/4 (TOPMED)
T=0.005874/98 (TOMMO)
HGVS:: NC_000019.10:g.35265855dup, NC_000019.9:g.35756758dup, NG_029241.1:g.1863dup

Select item 149049261412.

rs1490492614 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 19:35252749 (GRCh38)
19:35743652 (GRCh37)
Canonical SPDI:: NC_000019.10:35252748:T:C
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
HGVS:: NC_000019.10:g.35252749T>C, NC_000019.9:g.35743652T>C

Select item 149015823813.

rs1490158238 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 19:35267557 (GRCh38)
19:35758460 (GRCh37)
Canonical SPDI:: NC_000019.10:35267556:C:G,NC_000019.10:35267556:C:T
Gene:: USF2 (Varview), LSR (Varview)
Functional Consequence:: 2KB_upstream_variant,synonymous_variant,upstream_transcript_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000028/1 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000019.10:g.35267557C>G, NC_000019.10:g.35267557C>T, NC_000019.9:g.35758460C>G, NC_000019.9:g.35758460C>T, NG_029241.1:g.3565C>G, NG_029241.1:g.3565C>T, NM_015925.7:c.1536C>G, NM_015925.7:c.1536C>T, NM_015925.6:c.1680C>G, NM_015925.6:c.1680C>T, NM_205834.4:c.1593C>G, NM_205834.4:c.1593C>T, NM_205834.3:c.1737C>G, NM_205834.3:c.1737C>T, NM_205835.4:c.1389C>G, NM_205835.4:c.1389C>T, NM_205835.3:c.1533C>G, NM_205835.3:c.1533C>T, XM_005258980.3:c.1590C>G, XM_005258980.3:c.1590C>T, XM_005258980.2:c.1734C>G, XM_005258980.2:c.1734C>T, XM_005258980.1:c.1734C>G, XM_005258980.1:c.1734C>T, XM_011527026.3:c.1446C>G, XM_011527026.3:c.1446C>T, XM_011527026.2:c.1590C>G, XM_011527026.2:c.1590C>T, XM_011527026.1:c.1590C>G, XM_011527026.1:c.1590C>T, NM_001260489.2:c.1533C>G, NM_001260489.2:c.1533C>T, NM_001260489.1:c.1677C>G, NM_001260489.1:c.1677C>T, NM_001260490.2:c.1269C>G, NM_001260490.2:c.1269C>T, NM_001260490.1:c.1413C>G, NM_001260490.1:c.1413C>T, XM_047438920.1:c.1443C>G, XM_047438920.1:c.1443C>T, NM_001385215.1:c.1386C>G, NM_001385215.1:c.1386C>T, XM_047438921.1:c.1266C>G, XM_047438921.1:c.1266C>T

Select item 149015771414.

rs1490157714 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:35253473 (GRCh38)
19:35744376 (GRCh37)
Canonical SPDI:: NC_000019.10:35253472:C:T
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000023/6 (TOPMED)
T=0.000036/5 (GnomAD)
T=0.000546/1 (Korea1K)
HGVS:: NC_000019.10:g.35253473C>T, NC_000019.9:g.35744376C>T

Select item 149010605815.

rs1490106058 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->CAAAAG [Show Flanks]
Chromosome:: 19:35254406 (GRCh38)
19:35745310 (GRCh37)
Canonical SPDI:: NC_000019.10:35254406:CAAAAG:CAAAAGCAAAAG
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CAAAAGCAAAAG=0./0 (ALFA)
CAAAAG=0.000014/2 (GnomAD)
CAAAAG=0.000038/10 (TOPMED)
HGVS:: NC_000019.10:g.35254407_35254412dup, NC_000019.9:g.35745310_35745315dup

Select item 149000130016.

rs1490001300 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 19:35253114 (GRCh38)
19:35744017 (GRCh37)
Canonical SPDI:: NC_000019.10:35253113:G:A
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0.000071/1 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000019.10:g.35253114G>A, NC_000019.9:g.35744017G>A

Select item 148980437517.

rs1489804375 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 19:35259656 (GRCh38)
19:35750559 (GRCh37)
Canonical SPDI:: NC_000019.10:35259655:A:G
Gene:: LSR (Varview), LOC105372380 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000071/1 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000015/4 (TOPMED)
HGVS:: NC_000019.10:g.35259656A>G, NC_000019.9:g.35750559A>G, XR_935939.3:n.586A>G, XR_935939.2:n.67A>G, XR_935939.1:n.586A>G

Select item 148979617418.

rs1489796174 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:35246701 (GRCh38)
19:35737604 (GRCh37)
Canonical SPDI:: NC_000019.10:35246700:C:T
Validated:: by frequency,by alfa
MAF:: T=0.000071/1 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000019.10:g.35246701C>T, NC_000019.9:g.35737604C>T

Select item 148970781919.

rs1489707819 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 19:35264920 (GRCh38)
19:35755823 (GRCh37)
Canonical SPDI:: NC_000019.10:35264919:G:A
Gene:: LSR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency
MAF:: A=0.000007/1 (GnomAD)
HGVS:: NC_000019.10:g.35264920G>A, NC_000019.9:g.35755823G>A, NG_029241.1:g.928G>A

Select item 148961486720.

rs1489614867 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 19:35247107 (GRCh38)
19:35738010 (GRCh37)
Canonical SPDI:: NC_000019.10:35247106:A:G
Gene:: LSR (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000108/2 (ALFA)
G=0.000034/9 (TOPMED)
G=0.000043/6 (GnomAD)
G=0.000223/1 (Estonian)
HGVS:: NC_000019.10:g.35247107A>G, NC_000019.9:g.35738010A>G

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