SNP Links for Gene (Select 65110) - SNP

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Select item 14915660851.

rs1491566085 has merged into rs35035838 [Homo sapiens]

Variant type:: DELINS
Alleles:: GTGTGT>-,GT,GTGT,GTGTGTGT,GTGTGTGTGT,GTGTGTGTGTGT [Show Flanks]
Chromosome:: 13:114284393 (GRCh38)
13:115049868 (GRCh37)
Canonical SPDI:: NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGT
Gene:: UPF3A (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGTGTGTGTGT=0./0 (ALFA)
-=0.08395/316 (1000Genomes)
HGVS:: NC_000013.11:g.114284385GT[4], NC_000013.11:g.114284385GT[5], NC_000013.11:g.114284385GT[6], NC_000013.11:g.114284385GT[8], NC_000013.11:g.114284385GT[9], NC_000013.11:g.114284385GT[10], NC_000013.10:g.115049860GT[4], NC_000013.10:g.115049860GT[5], NC_000013.10:g.115049860GT[6], NC_000013.10:g.115049860GT[8], NC_000013.10:g.115049860GT[9], NC_000013.10:g.115049860GT[10], NG_029528.1:g.7802GT[4], NG_029528.1:g.7802GT[5], NG_029528.1:g.7802GT[6], NG_029528.1:g.7802GT[8], NG_029528.1:g.7802GT[9], NG_029528.1:g.7802GT[10]

Select item 14914203132.

rs1491420313 has merged into rs35035838 [Homo sapiens]

Variant type:: DELINS
Alleles:: GTGTGT>-,GT,GTGT,GTGTGTGT,GTGTGTGTGT,GTGTGTGTGTGT [Show Flanks]
Chromosome:: 13:114284393 (GRCh38)
13:115049868 (GRCh37)
Canonical SPDI:: NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGT,NC_000013.11:114284383:TGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGT
Gene:: UPF3A (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGTGTGTGTGT=0./0 (ALFA)
-=0.08395/316 (1000Genomes)
HGVS:: NC_000013.11:g.114284385GT[4], NC_000013.11:g.114284385GT[5], NC_000013.11:g.114284385GT[6], NC_000013.11:g.114284385GT[8], NC_000013.11:g.114284385GT[9], NC_000013.11:g.114284385GT[10], NC_000013.10:g.115049860GT[4], NC_000013.10:g.115049860GT[5], NC_000013.10:g.115049860GT[6], NC_000013.10:g.115049860GT[8], NC_000013.10:g.115049860GT[9], NC_000013.10:g.115049860GT[10], NG_029528.1:g.7802GT[4], NG_029528.1:g.7802GT[5], NG_029528.1:g.7802GT[6], NG_029528.1:g.7802GT[8], NG_029528.1:g.7802GT[9], NG_029528.1:g.7802GT[10]

Select item 14912288723.

rs1491228872 has merged into rs1181794334 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTT>-,T,TT,TTTT,TTTTT,TTTTTT [Show Flanks]
Chromosome:: 13:114297234 (GRCh38)
13:115062709 (GRCh37)
Canonical SPDI:: NC_000013.11:114297222:TTTTTTTTTTTTTT:TTTTTTTTTTT,NC_000013.11:114297222:TTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000013.11:114297222:TTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000013.11:114297222:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000013.11:114297222:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT,NC_000013.11:114297222:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT
Gene:: UPF3A (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTTT=0./0 (ALFA)
-=0.000045/12 (TOPMED)
T=0.036913/22 (NorthernSweden)
HGVS:: NC_000013.11:g.114297234_114297236del, NC_000013.11:g.114297235_114297236del, NC_000013.11:g.114297236del, NC_000013.11:g.114297236dup, NC_000013.11:g.114297235_114297236dup, NC_000013.11:g.114297234_114297236dup, NC_000013.10:g.115062709_115062711del, NC_000013.10:g.115062710_115062711del, NC_000013.10:g.115062711del, NC_000013.10:g.115062711dup, NC_000013.10:g.115062710_115062711dup, NC_000013.10:g.115062709_115062711dup, NG_029528.1:g.20651_20653del, NG_029528.1:g.20652_20653del, NG_029528.1:g.20653del, NG_029528.1:g.20653dup, NG_029528.1:g.20652_20653dup, NG_029528.1:g.20651_20653dup

Select item 14911668604.

rs1491166860 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->G [Show Flanks]
Chromosome:: 13:114291744 (GRCh38)
13:115057220 (GRCh37)
Canonical SPDI:: NC_000013.11:114291744:G:GG
Gene:: UPF3A (Varview), LOC124903222 (Varview)
Functional Consequence:: frameshift_variant,intron_variant,3_prime_UTR_variant,coding_sequence_variant,upstream_transcript_variant,genic_downstream_transcript_variant,2KB_upstream_variant,non_coding_transcript_variant
HGVS:: NC_000013.11:g.114291745dup, NC_000013.10:g.115057220dup, NG_029528.1:g.15162dup, NM_023011.4:c.799dup, NM_023011.3:c.799dup, NM_080687.3:c.700dup, NM_080687.2:c.700dup, NM_001353648.2:c.196dup, NM_001353648.1:c.196dup, NM_001353644.2:c.196dup, NM_001353644.1:c.196dup, NR_148482.2:n.782dup, NR_148482.1:n.799dup, NR_148485.2:n.632dup, NR_148485.1:n.649dup, NM_001353645.1:c.196dup, NM_001353650.1:c.196dup, NM_001353647.1:c.196dup, NR_148491.1:n.646dup, NM_001353646.1:c.196dup, NM_001353649.1:c.196dup, NR_148486.1:n.580dup, NR_148487.1:n.702dup, NR_148492.1:n.679dup, NR_148489.1:n.603dup, NR_148493.1:n.440dup, NR_148496.1:n.580dup, NR_148490.1:n.473dup, NR_148494.1:n.547dup, XM_011534845.3:c.409dup, XM_011534845.2:c.409dup, XM_011534845.1:c.409dup, XM_011534844.2:c.589dup, XM_011534844.1:c.589dup, XM_024449401.2:c.196dup, XM_024449401.1:c.196dup, XM_011534846.2:c.799dup, XM_011534846.1:c.799dup, XM_024449402.2:c.776dup, XM_024449402.1:c.776dup, XM_024449403.2:c.*112dup, XM_047430548.1:c.196dup, XM_047430546.1:c.799dup, XM_047430549.1:c.700dup, NP_075387.1:p.Glu267fs, NP_542418.1:p.Glu234fs, NP_001340577.1:p.Glu66fs, NP_001340573.1:p.Glu66fs, NP_001340574.1:p.Glu66fs, NP_001340579.1:p.Glu66fs, NP_001340576.1:p.Glu66fs, NP_001340575.1:p.Glu66fs, NP_001340578.1:p.Glu66fs, XP_011533147.1:p.Glu137fs, XP_011533146.1:p.Glu197fs, XP_024305169.1:p.Glu66fs, XP_011533148.1:p.Glu267fs, XP_024305170.1:p.Asp260fs, XP_047286504.1:p.Glu66fs, XP_047286502.1:p.Glu267fs, XP_047286505.1:p.Glu234fs

Select item 14910397145.

rs1491039714 has merged into rs762648432 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->TA [Show Flanks]
Chromosome:: 13:114284397 (GRCh38)
13:115049873 (GRCh37)
Canonical SPDI:: NC_000013.11:114284397:TA:TATA
Gene:: UPF3A (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TATA=0./0 (ALFA)
TA=0.0005/69 (GnomAD)
TA=0.124805/481 (ALSPAC)
TA=0.134844/500 (TWINSUK)
HGVS:: NC_000013.11:g.114284398_114284399dup, NC_000013.10:g.115049873_115049874dup, NG_029528.1:g.7815_7816dup

Select item 14907063496.

rs1490706349 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 13:114299571 (GRCh38)
13:115065046 (GRCh37)
Canonical SPDI:: NC_000013.11:114299570:T:C
Gene:: UPF3A (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: C=0.000071/1 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000013.11:g.114299571T>C, NC_000013.10:g.115065046T>C, NG_029528.1:g.22988T>C

Select item 14906365727.

rs1490636572 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 13:114285739 (GRCh38)
13:115051214 (GRCh37)
Canonical SPDI:: NC_000013.11:114285738:C:G
Gene:: UPF3A (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000008/2 (TOPMED)
G=0.000342/1 (KOREAN)
HGVS:: NC_000013.11:g.114285739C>G, NC_000013.10:g.115051214C>G, NG_029528.1:g.9156C>G

Select item 14906031388.

rs1490603138 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 13:114291734 (GRCh38)
13:115057209 (GRCh37)
Canonical SPDI:: NC_000013.11:114291733:G:A
Gene:: UPF3A (Varview), LOC124903222 (Varview)
Functional Consequence:: intron_variant,3_prime_UTR_variant,coding_sequence_variant,upstream_transcript_variant,genic_downstream_transcript_variant,missense_variant,2KB_upstream_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.0011/10 (ALFA)
HGVS:: NC_000013.11:g.114291734G>A, NC_000013.10:g.115057209G>A, NG_029528.1:g.15151G>A, NM_023011.4:c.788G>A, NM_023011.3:c.788G>A, NM_080687.3:c.689G>A, NM_080687.2:c.689G>A, NM_001353648.2:c.185G>A, NM_001353648.1:c.185G>A, NM_001353644.2:c.185G>A, NM_001353644.1:c.185G>A, NR_148482.2:n.771G>A, NR_148482.1:n.788G>A, NR_148485.2:n.621G>A, NR_148485.1:n.638G>A, NM_001353645.1:c.185G>A, NM_001353650.1:c.185G>A, NM_001353647.1:c.185G>A, NR_148491.1:n.635G>A, NM_001353646.1:c.185G>A, NM_001353649.1:c.185G>A, NR_148486.1:n.569G>A, NR_148487.1:n.691G>A, NR_148492.1:n.668G>A, NR_148489.1:n.592G>A, NR_148493.1:n.429G>A, NR_148496.1:n.569G>A, NR_148490.1:n.462G>A, NR_148494.1:n.536G>A, XM_011534845.3:c.398G>A, XM_011534845.2:c.398G>A, XM_011534845.1:c.398G>A, XM_011534844.2:c.578G>A, XM_011534844.1:c.578G>A, XM_024449401.2:c.185G>A, XM_024449401.1:c.185G>A, XM_011534846.2:c.788G>A, XM_011534846.1:c.788G>A, XM_024449402.2:c.765G>A, XM_024449402.1:c.765G>A, XM_024449403.2:c.*101G>A, XM_047430548.1:c.185G>A, XM_047430546.1:c.788G>A, XM_047430549.1:c.689G>A, NP_075387.1:p.Cys263Tyr, NP_542418.1:p.Cys230Tyr, NP_001340577.1:p.Cys62Tyr, NP_001340573.1:p.Cys62Tyr, NP_001340574.1:p.Cys62Tyr, NP_001340579.1:p.Cys62Tyr, NP_001340576.1:p.Cys62Tyr, NP_001340575.1:p.Cys62Tyr, NP_001340578.1:p.Cys62Tyr, XP_011533147.1:p.Cys133Tyr, XP_011533146.1:p.Cys193Tyr, XP_024305169.1:p.Cys62Tyr, XP_011533148.1:p.Cys263Tyr, XP_024305170.1:p.Met255Ile, XP_047286504.1:p.Cys62Tyr, XP_047286502.1:p.Cys263Tyr, XP_047286505.1:p.Cys230Tyr

Select item 14904944289.

rs1490494428 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 13:114292550 (GRCh38)
13:115058025 (GRCh37)
Canonical SPDI:: NC_000013.11:114292549:C:T
Gene:: UPF3A (Varview), LOC124903222 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000022/3 (GnomAD)
HGVS:: NC_000013.11:g.114292550C>T, NC_000013.10:g.115058025C>T, NG_029528.1:g.15967C>T, XR_007063884.1:n.752C>T

Select item 149046485310.

rs1490464853 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 13:114290330 (GRCh38)
13:115055805 (GRCh37)
Canonical SPDI:: NC_000013.11:114290329:A:G
Gene:: UPF3A (Varview), LOC124903222 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
HGVS:: NC_000013.11:g.114290330A>G, NC_000013.10:g.115055805A>G, NG_029528.1:g.13747A>G

Select item 149042517011.

rs1490425170 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 13:114280230 (GRCh38)
13:115045705 (GRCh37)
Canonical SPDI:: NC_000013.11:114280229:C:G,NC_000013.11:114280229:C:T
Gene:: UPF3A (Varview), LOC105370384 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,non_coding_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
G=0.000014/2 (GnomAD)
G=0.000015/4 (TOPMED)
HGVS:: NC_000013.11:g.114280230C>G, NC_000013.11:g.114280230C>T, NC_000013.10:g.115045705C>G, NC_000013.10:g.115045705C>T, NG_029528.1:g.3647C>G, NG_029528.1:g.3647C>T, XR_001750058.2:n.840G>C, XR_001750058.2:n.840G>A, XR_001750058.1:n.840G>C, XR_001750058.1:n.840G>A, XR_001750056.2:n.840G>C, XR_001750056.2:n.840G>A, XR_001750056.1:n.840G>C, XR_001750056.1:n.840G>A, XR_001750057.2:n.840G>C, XR_001750057.2:n.840G>A, XR_001750057.1:n.840G>C, XR_001750057.1:n.840G>A, XR_001750059.2:n.840G>C, XR_001750059.2:n.840G>A, XR_001750059.1:n.840G>C, XR_001750059.1:n.840G>A, XR_007063887.1:n.840G>C, XR_007063887.1:n.840G>A, XR_007063889.1:n.702G>C, XR_007063889.1:n.702G>A, XR_007063886.1:n.708G>C, XR_007063886.1:n.708G>A, XR_007063885.1:n.546G>C, XR_007063885.1:n.546G>A

Select item 149039404212.

rs1490394042 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 13:114303093 (GRCh38)
13:115068568 (GRCh37)
Canonical SPDI:: NC_000013.11:114303092:T:G
Gene:: UPF3A (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000013.11:g.114303093T>G, NC_000013.10:g.115068568T>G, NG_029528.1:g.26510T>G

Select item 149037389413.

rs1490373894 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 13:114281009 (GRCh38)
13:115046484 (GRCh37)
Canonical SPDI:: NC_000013.11:114281008:T:C
Gene:: UPF3A (Varview), LOC105370384 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,non_coding_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
HGVS:: NC_000013.11:g.114281009T>C, NC_000013.10:g.115046484T>C, NG_029528.1:g.4426T>C, XR_001750058.2:n.61A>G, XR_001750058.1:n.61A>G, XR_001750056.2:n.61A>G, XR_001750056.1:n.61A>G, XR_001750057.2:n.61A>G, XR_001750057.1:n.61A>G, XR_001750059.2:n.61A>G, XR_001750059.1:n.61A>G, XR_007063887.1:n.61A>G, XR_007063885.1:n.61A>G, XR_007063888.1:n.61A>G

Select item 149035557414.

rs1490355574 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 13:114292087 (GRCh38)
13:115057562 (GRCh37)
Canonical SPDI:: NC_000013.11:114292086:G:A
Gene:: UPF3A (Varview), LOC124903222 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant,non_coding_transcript_variant,downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000022/3 (GnomAD)
HGVS:: NC_000013.11:g.114292087G>A, NC_000013.10:g.115057562G>A, NG_029528.1:g.15504G>A, XR_007063884.1:n.289G>A

Select item 149031302415.

rs1490313024 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 13:114289162 (GRCh38)
13:115054637 (GRCh37)
Canonical SPDI:: NC_000013.11:114289161:C:T
Gene:: UPF3A (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000054/1 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000008/2 (TOPMED)
T=0.000223/1 (Estonian)
HGVS:: NC_000013.11:g.114289162C>T, NC_000013.10:g.115054637C>T, NG_029528.1:g.12579C>T

Select item 149024955316.

rs1490249553 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 13:114304552 (GRCh38)
13:115070027 (GRCh37)
Canonical SPDI:: NC_000013.11:114304551:A:G
Gene:: UPF3A (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000013.11:g.114304552A>G, NC_000013.10:g.115070027A>G, NG_029528.1:g.27969A>G

Select item 149010824517.

rs1490108245 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 13:114296724 (GRCh38)
13:115062199 (GRCh37)
Canonical SPDI:: NC_000013.11:114296723:T:C
Gene:: UPF3A (Varview)
Functional Consequence:: genic_downstream_transcript_variant,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_000013.11:g.114296724T>C, NC_000013.10:g.115062199T>C, NG_029528.1:g.20141T>C

Select item 149002310118.

rs1490023101 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 13:114303403 (GRCh38)
13:115068878 (GRCh37)
Canonical SPDI:: NC_000013.11:114303402:C:G
Gene:: UPF3A (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
HGVS:: NC_000013.11:g.114303403C>G, NC_000013.10:g.115068878C>G, NG_029528.1:g.26820C>G

Select item 148979298619.

rs1489792986 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->T [Show Flanks]
Chromosome:: 13:114287267 (GRCh38)
13:115052743 (GRCh37)
Canonical SPDI:: NC_000013.11:114287267:TTT:TTTT
Gene:: UPF3A (Varview)
Functional Consequence:: intron_variant,non_coding_transcript_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: TTTT=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000013.11:g.114287270dup, NC_000013.10:g.115052745dup, NG_029528.1:g.10687dup, NM_001353652.2:c.*515dup, NM_001353652.1:c.*515dup, NR_148483.2:n.996dup, NR_148483.1:n.1013dup

Select item 148957067920.

rs1489570679 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 13:114284563 (GRCh38)
13:115050038 (GRCh37)
Canonical SPDI:: NC_000013.11:114284562:A:G
Gene:: UPF3A (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000022/3 (GnomAD)
G=0.000035/1 (TOMMO)
HGVS:: NC_000013.11:g.114284563A>G, NC_000013.10:g.115050038A>G, NG_029528.1:g.7980A>G

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