SNP Links for Gene (Select 100132774) - SNP

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Select item 14915787711.

rs1491578771 [Homo sapiens]

Variant type:: DEL
Alleles:: CT>- [Show Flanks]
Chromosome:: 1:43706603 (GRCh38)
1:44172274 (GRCh37)
Canonical SPDI:: NC_000001.11:43706602:CT:
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: -=0.000071/1 (ALFA)
-=0.000007/1 (GnomAD)
HGVS:: NC_000001.11:g.43706603_43706604del, NC_000001.10:g.44172274_44172275del, NG_028196.1:g.4057_4058del

Select item 14908982882.

rs1490898288 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 1:43706000 (GRCh38)
1:44171671 (GRCh37)
Canonical SPDI:: NC_000001.11:43705999:A:G
Gene:: ST3GAL3 (Varview), KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: 500B_downstream_variant,intron_variant,upstream_transcript_variant,downstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000008/2 (TOPMED)
HGVS:: NC_000001.11:g.43706000A>G, NC_000001.10:g.44171671A>G, NG_028196.1:g.3454A>G

Select item 14905600063.

rs1490560006 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 1:43707958 (GRCh38)
1:44173629 (GRCh37)
Canonical SPDI:: NC_000001.11:43707957:C:T
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,5_prime_UTR_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000019/5 (TOPMED)
HGVS:: NC_000001.11:g.43707958C>T, NC_000001.10:g.44173629C>T, NG_028196.1:g.5412C>T, XM_017002113.2:c.-159C>T, XM_017002113.1:c.-159C>T, XM_047428185.1:c.-205C>T, XM_047428200.1:c.-205C>T, XM_047428199.1:c.-159C>T, XM_047428221.1:c.-205C>T, XM_047428232.1:c.-205C>T, XM_047428273.1:c.-205C>T

Select item 14904099624.

rs1490409962 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 1:43704871 (GRCh38)
1:44170542 (GRCh37)
Canonical SPDI:: NC_000001.11:43704870:C:T
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000034/9 (TOPMED)
T=0.000043/6 (GnomAD)
HGVS:: NC_000001.11:g.43704871C>T, NC_000001.10:g.44170542C>T, NG_028196.1:g.2325C>T, NM_014663.3:c.*501C>T, NM_014663.2:c.*501C>T

Select item 14900795205.

rs1490079520 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 1:43707016 (GRCh38)
1:44172687 (GRCh37)
Canonical SPDI:: NC_000001.11:43707015:T:C
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000021/3 (GnomAD)
C=0.00003/8 (TOPMED)
C=0.001092/2 (Korea1K)
C=0.001345/23 (TOMMO)
C=0.001711/5 (KOREAN)
HGVS:: NC_000001.11:g.43707016T>C, NC_000001.10:g.44172687T>C, NG_028196.1:g.4470T>C

Select item 14899856646.

rs1489985664 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 1:43700474 (GRCh38)
1:44166145 (GRCh37)
Canonical SPDI:: NC_000001.11:43700473:C:T
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_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_000001.11:g.43700474C>T, NC_000001.10:g.44166145C>T, NR_033827.1:n.824G>A

Select item 14899470017.

rs1489947001 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 1:43704842 (GRCh38)
1:44170513 (GRCh37)
Canonical SPDI:: NC_000001.11:43704841:C:A
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000015/4 (TOPMED)
HGVS:: NC_000001.11:g.43704842C>A, NC_000001.10:g.44170513C>A, NG_028196.1:g.2296C>A, NM_014663.3:c.*472C>A, NM_014663.2:c.*472C>A

Select item 14897273528.

rs1489727352 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 1:43707116 (GRCh38)
1:44172787 (GRCh37)
Canonical SPDI:: NC_000001.11:43707115:G:A
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
HGVS:: NC_000001.11:g.43707116G>A, NC_000001.10:g.44172787G>A, NG_028196.1:g.4570G>A, NR_033827.1:n.226C>T

Select item 14894677749.

rs1489467774 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->GAAGGCGGGGTCGGGGCACGG [Show Flanks]
Chromosome:: 1:43707824 (GRCh38)
1:44173496 (GRCh37)
Canonical SPDI:: NC_000001.11:43707824:CGGGAAGGCGGGGTCGGGGCACGG:CGGGAAGGCGGGGTCGGGGCACGGGAAGGCGGGGTCGGGGCACGG
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,5_prime_UTR_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CGGGAAGGCGGGGTCGGGGCACGGGAAGGCGGGGTCGGGGCACGG=0./0 (ALFA)
CGGGAAGGCGGGGTCGGGGCA=0.000029/4 (GnomAD)
CGGGAAGGCGGGGTCGGGGCA=0.000156/1 (1000Genomes)
HGVS:: NC_000001.11:g.43707828_43707848dup, NC_000001.10:g.44173499_44173519dup, NG_028196.1:g.5282_5302dup, XM_017002113.2:c.-289_-269dup, XM_017002113.1:c.-269_-268insGAAGGCGGGGTCGGGGCACGG, XM_017002113.1:c.-269_-268insGAAGGCGGGGTCGGGGCACGGGAAGGCGGGGTCGGGGCACGG, XM_047428185.1:c.-335_-315dup, XM_047428200.1:c.-335_-315dup, XM_047428199.1:c.-289_-269dup, XM_047428221.1:c.-335_-315dup, XM_047428232.1:c.-335_-315dup, XM_047428273.1:c.-335_-315dup

Select item 148887762510.

rs1488877625 [Homo sapiens]

Variant type:: DEL
Alleles:: G>- [Show Flanks]
Chromosome:: 1:43702227 (GRCh38)
1:44167898 (GRCh37)
Canonical SPDI:: NC_000001.11:43702226:G:
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
-=0.000004/1 (TOPMED)
HGVS:: NC_000001.11:g.43702227del, NC_000001.10:g.44167898del

Select item 148856534511.

rs1488565345 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 1:43699567 (GRCh38)
1:44165238 (GRCh37)
Canonical SPDI:: NC_000001.11:43699566:T:C
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant,downstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000023/6 (TOPMED)
HGVS:: NC_000001.11:g.43699567T>C, NC_000001.10:g.44165238T>C

Select item 148851413312.

rs1488514133 [Homo sapiens]

Variant type:: DELINS
Alleles:: GT>- [Show Flanks]
Chromosome:: 1:43700462 (GRCh38)
1:44166133 (GRCh37)
Canonical SPDI:: NC_000001.11:43700458:TGTGT:TGT
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGT=0.000071/1 (ALFA)
-=0.000007/1 (GnomAD)
-=0.000011/3 (TOPMED)
HGVS:: NC_000001.11:g.43700460GT[1], NC_000001.10:g.44166131GT[1], NR_033827.1:n.836CA[1]

Select item 148839712613.

rs1488397126 [Homo sapiens]

Variant type:: DELINS
Alleles:: CA>- [Show Flanks]
Chromosome:: 1:43705778 (GRCh38)
1:44171449 (GRCh37)
Canonical SPDI:: NC_000001.11:43705776:ACA:A
Gene:: ST3GAL3 (Varview), KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: 500B_downstream_variant,intron_variant,upstream_transcript_variant,downstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
-=0.000014/2 (GnomAD)
-=0.000023/6 (TOPMED)
HGVS:: NC_000001.11:g.43705778_43705779del, NC_000001.10:g.44171449_44171450del, NG_028196.1:g.3232_3233del

Select item 148834713114.

rs1488347131 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 1:43709102 (GRCh38)
1:44174773 (GRCh37)
Canonical SPDI:: NC_000001.11:43709101:G:A
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview), ST3GAL3-AS1 (Varview)
Functional Consequence:: intron_variant,500B_downstream_variant,upstream_transcript_variant,downstream_transcript_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_000001.11:g.43709102G>A, NC_000001.10:g.44174773G>A, NG_028196.1:g.6556G>A

Select item 148816700715.

rs1488167007 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 1:43702355 (GRCh38)
1:44168026 (GRCh37)
Canonical SPDI:: NC_000001.11:43702354:A:G
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
G=0.000015/4 (TOPMED)
HGVS:: NC_000001.11:g.43702355A>G, NC_000001.10:g.44168026A>G

Select item 148808561916.

rs1488085619 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 1:43708855 (GRCh38)
1:44174526 (GRCh37)
Canonical SPDI:: NC_000001.11:43708854:A:G
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000008/2 (TOPMED)
G=0.000014/2 (GnomAD)
HGVS:: NC_000001.11:g.43708855A>G, NC_000001.10:g.44174526A>G, NG_028196.1:g.6309A>G

Select item 148773122017.

rs1487731220 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 1:43708319 (GRCh38)
1:44173990 (GRCh37)
Canonical SPDI:: NC_000001.11:43708318:A:G
Gene:: ST3GAL3 (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000014/2 (GnomAD)
HGVS:: NC_000001.11:g.43708319A>G, NC_000001.10:g.44173990A>G, NG_028196.1:g.5773A>G

Select item 148747898518.

rs1487478985 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 1:43705324 (GRCh38)
1:44170995 (GRCh37)
Canonical SPDI:: NC_000001.11:43705323:A:G
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: 3_prime_UTR_variant,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_000001.11:g.43705324A>G, NC_000001.10:g.44170995A>G, NG_028196.1:g.2778A>G, NM_014663.3:c.*954A>G, NM_014663.2:c.*954A>G

Select item 148738678419.

rs1487386784 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 1:43703626 (GRCh38)
1:44169297 (GRCh37)
Canonical SPDI:: NC_000001.11:43703625:T:C
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,missense_variant,coding_sequence_variant
Validated:: by frequency
MAF:: C=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000001.11:g.43703626T>C, NC_000001.10:g.44169297T>C, NG_028196.1:g.1080T>C, NM_014663.3:c.2851T>C, NM_014663.2:c.2851T>C, NR_033827.1:n.410A>G, NP_055478.2:p.Cys951Arg

Select item 148727027320.

rs1487270273 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 1:43702776 (GRCh38)
1:44168447 (GRCh37)
Canonical SPDI:: NC_000001.11:43702775:A:G
Gene:: KDM4A (Varview), KDM4A-AS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000008/2 (TOPMED)
HGVS:: NC_000001.11:g.43702776A>G, NC_000001.10:g.44168447A>G, NG_028196.1:g.230A>G

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