SNP Links for Gene (Select 133383) - SNP

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Select item 14910766051.

rs1491076605 has merged into rs1554041077 [Homo sapiens]

Variant type:: DELINS
Alleles:: CTCTCTCT>-,CT,CTCT,CTCTCT,CTCTCTCTCT,CTCTCTCTCTCT [Show Flanks]
Chromosome:: 5:56929020 (GRCh38)
5:56224847 (GRCh37)
Canonical SPDI:: NC_000005.10:56929005:CTCTCTCTCTCTCTCTCTCTCT:CTCTCTCTCTCTCT,NC_000005.10:56929005:CTCTCTCTCTCTCTCTCTCTCT:CTCTCTCTCTCTCTCT,NC_000005.10:56929005:CTCTCTCTCTCTCTCTCTCTCT:CTCTCTCTCTCTCTCTCT,NC_000005.10:56929005:CTCTCTCTCTCTCTCTCTCTCT:CTCTCTCTCTCTCTCTCTCT,NC_000005.10:56929005:CTCTCTCTCTCTCTCTCTCTCT:CTCTCTCTCTCTCTCTCTCTCTCT,NC_000005.10:56929005:CTCTCTCTCTCTCTCTCTCTCT:CTCTCTCTCTCTCTCTCTCTCTCTCT
Gene:: SETD9 (Varview), MIER3 (Varview)
Functional Consequence:: 500B_downstream_variant,intron_variant,downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CTCTCTCTCTCTCTCT=0./0 (ALFA)
CT=0.00667/4 (NorthernSweden)
HGVS:: NC_000005.10:g.56929006CT[7], NC_000005.10:g.56929006CT[8], NC_000005.10:g.56929006CT[9], NC_000005.10:g.56929006CT[10], NC_000005.10:g.56929006CT[12], NC_000005.10:g.56929006CT[13], NC_000005.9:g.56224833CT[7], NC_000005.9:g.56224833CT[8], NC_000005.9:g.56224833CT[9], NC_000005.9:g.56224833CT[10], NC_000005.9:g.56224833CT[12], NC_000005.9:g.56224833CT[13]

Select item 14910068612.

rs1491006861 has merged into rs74270761 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTTTT>-,T,TT,TTT,TTTT,TTTTT,TTTTTTT,TTTTTTTT,TTTTTTTTT,TTTTTTTTTT [Show Flanks]
Chromosome:: 5:56913774 (GRCh38)
5:56209601 (GRCh37)
Canonical SPDI:: NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTT,NC_000005.10:56913763:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTT
Gene:: SETD9 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTT=0./0 (ALFA)
-=0.000008/2 (TOPMED)
T=0.038462/23 (NorthernSweden)
HGVS:: NC_000005.10:g.56913774_56913779del, NC_000005.10:g.56913775_56913779del, NC_000005.10:g.56913776_56913779del, NC_000005.10:g.56913777_56913779del, NC_000005.10:g.56913778_56913779del, NC_000005.10:g.56913779del, NC_000005.10:g.56913779dup, NC_000005.10:g.56913778_56913779dup, NC_000005.10:g.56913777_56913779dup, NC_000005.10:g.56913776_56913779dup, NC_000005.9:g.56209601_56209606del, NC_000005.9:g.56209602_56209606del, NC_000005.9:g.56209603_56209606del, NC_000005.9:g.56209604_56209606del, NC_000005.9:g.56209605_56209606del, NC_000005.9:g.56209606del, NC_000005.9:g.56209606dup, NC_000005.9:g.56209605_56209606dup, NC_000005.9:g.56209604_56209606dup, NC_000005.9:g.56209603_56209606dup

Select item 14908238633.

rs1490823863 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 5:56918562 (GRCh38)
5:56214389 (GRCh37)
Canonical SPDI:: NC_000005.10:56918561:A:C
Gene:: SETD9 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000019/5 (TOPMED)
HGVS:: NC_000005.10:g.56918562A>C, NC_000005.9:g.56214389A>C

Select item 14906575134.

rs1490657513 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 5:56923252 (GRCh38)
5:56219079 (GRCh37)
Canonical SPDI:: NC_000005.10:56923251:T:G
Gene:: SETD9 (Varview), MIER3 (Varview)
Functional Consequence:: intron_variant,missense_variant,genic_downstream_transcript_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000012/3 (GnomAD_exomes)
G=0.000014/2 (GnomAD)
HGVS:: NC_000005.10:g.56923252T>G, NC_000005.9:g.56219079T>G, NM_152622.5:c.1526A>C, NM_152622.4:c.1526A>C, NM_152622.3:c.1526A>C, XM_011543216.3:c.1577A>C, XM_011543216.2:c.1577A>C, XM_011543216.1:c.1577A>C, XM_011543217.3:c.1574A>C, XM_011543217.2:c.1574A>C, XM_011543217.1:c.1574A>C, NM_001297598.2:c.1544A>C, NM_001297598.1:c.1544A>C, NM_001297599.2:c.1529A>C, NM_001297599.1:c.1529A>C, XM_047416840.1:c.1448A>C, XM_047416839.1:c.1448A>C, NP_689835.3:p.His509Pro, XP_011541518.1:p.His526Pro, XP_011541519.1:p.His525Pro, NP_001284527.1:p.His515Pro, NP_001284528.1:p.His510Pro, XP_047272796.1:p.His483Pro, XP_047272795.1:p.His483Pro

Select item 14906440485.

rs1490644048 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 5:56908942 (GRCh38)
5:56204769 (GRCh37)
Canonical SPDI:: NC_000005.10:56908941:T:A
Gene:: SETD9 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000011/3 (TOPMED)
A=0.000014/2 (GnomAD)
HGVS:: NC_000005.10:g.56908942T>A, NC_000005.9:g.56204769T>A

Select item 14905958286.

rs1490595828 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:56926074 (GRCh38)
5:56221901 (GRCh37)
Canonical SPDI:: NC_000005.10:56926073:A:G
Gene:: SETD9 (Varview), MIER3 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant,non_coding_transcript_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000005.10:g.56926074A>G, NC_000005.9:g.56221901A>G, NM_001171990.3:c.*738A>G, NM_001171990.2:c.*738A>G, NR_136555.2:n.1236A>G, NR_136555.1:n.1572A>G

Select item 14904776827.

rs1490477682 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->GAG [Show Flanks]
Chromosome:: 5:56918727 (GRCh38)
5:56214555 (GRCh37)
Canonical SPDI:: NC_000005.10:56918727:GAGGAG:GAGGAGGAG
Gene:: SETD9 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GAGGAGGAG=0.000071/1 (ALFA)
GAG=0.000143/20 (GnomAD)
GAG=0.000147/39 (TOPMED)
HGVS:: NC_000005.10:g.56918728GAG[3], NC_000005.9:g.56214555GAG[3]

Select item 14904019658.

rs1490401965 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C,G [Show Flanks]
Chromosome:: 5:56913883 (GRCh38)
5:56209710 (GRCh37)
Canonical SPDI:: NC_000005.10:56913882:T:C,NC_000005.10:56913882:T:G
Gene:: SETD9 (Varview)
Functional Consequence:: synonymous_variant,non_coding_transcript_variant,missense_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
G=0.000004/1 (GnomAD_exomes)
C=0.000007/1 (GnomAD)
C=0.000008/2 (TOPMED)
HGVS:: NC_000005.10:g.56913883T>C, NC_000005.10:g.56913883T>G, NC_000005.9:g.56209710T>C, NC_000005.9:g.56209710T>G, XM_005248426.5:c.168T>C, XM_005248426.5:c.168T>G, XM_005248426.4:c.168T>C, XM_005248426.4:c.168T>G, XM_005248426.3:c.168T>C, XM_005248426.3:c.168T>G, XM_005248426.2:c.168T>C, XM_005248426.2:c.168T>G, XM_005248426.1:c.168T>C, XM_005248426.1:c.168T>G, NM_153706.4:c.600T>C, NM_153706.4:c.600T>G, NM_153706.3:c.600T>C, NM_153706.3:c.600T>G, XM_011543140.4:c.372T>C, XM_011543140.4:c.372T>G, XM_011543140.3:c.372T>C, XM_011543140.3:c.372T>G, XM_011543140.2:c.372T>C, XM_011543140.2:c.372T>G, XM_011543140.1:c.372T>C, XM_011543140.1:c.372T>G, NM_001171990.3:c.600T>C, NM_001171990.3:c.600T>G, NM_001171990.2:c.600T>C, NM_001171990.2:c.600T>G, NM_001171990.1:c.600T>C, NM_001171990.1:c.600T>G, XM_011543139.3:c.504T>C, XM_011543139.3:c.504T>G, XM_011543139.2:c.504T>C, XM_011543139.2:c.504T>G, XM_011543139.1:c.504T>C, XM_011543139.1:c.504T>G, NR_136555.2:n.282T>C, NR_136555.2:n.282T>G, NR_136555.1:n.618T>C, NR_136555.1:n.618T>G, NM_001323020.2:c.522T>C, NM_001323020.2:c.522T>G, NM_001323020.1:c.522T>C, NM_001323020.1:c.522T>G, NM_001323018.2:c.522T>C, NM_001323018.2:c.522T>G, NM_001323018.1:c.522T>C, NM_001323018.1:c.522T>G, NM_001323019.2:c.600T>C, NM_001323019.2:c.600T>G, NM_001323019.1:c.600T>C, NM_001323019.1:c.600T>G, NR_136556.2:n.282T>C, NR_136556.2:n.282T>G, NR_136556.1:n.618T>C, NR_136556.1:n.618T>G, NR_136558.2:n.282T>C, NR_136558.2:n.282T>G, NR_136558.1:n.618T>C, NR_136558.1:n.618T>G, NM_001323022.1:c.144T>C, NM_001323022.1:c.144T>G, NR_136557.1:n.467T>C, NR_136557.1:n.467T>G, XP_005248483.1:p.Asn56Lys, NP_714917.2:p.Asn200Lys, XP_011541442.1:p.Asn124Lys, NP_001165461.1:p.Asn200Lys, XP_011541441.1:p.Asn168Lys, NP_001309949.1:p.Asn174Lys, NP_001309947.1:p.Asn174Lys, NP_001309948.1:p.Asn200Lys, NP_001309951.1:p.Asn48Lys

Select item 14903101689.

rs1490310168 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:56908027 (GRCh38)
5:56203854 (GRCh37)
Canonical SPDI:: NC_000005.10:56908026:G:A
Gene:: SETD9 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
HGVS:: NC_000005.10:g.56908027G>A, NC_000005.9:g.56203854G>A

Select item 149027140310.

rs1490271403 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 5:56925127 (GRCh38)
5:56220954 (GRCh37)
Canonical SPDI:: NC_000005.10:56925126:T:C
Gene:: SETD9 (Varview), MIER3 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000014/2 (GnomAD)
C=0.000015/4 (TOPMED)
HGVS:: NC_000005.10:g.56925127T>C, NC_000005.9:g.56220954T>C

Select item 149024571611.

rs1490245716 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:56910867 (GRCh38)
5:56206694 (GRCh37)
Canonical SPDI:: NC_000005.10:56910866:A:G
Gene:: SETD9 (Varview)
Functional Consequence:: 5_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
HGVS:: NC_000005.10:g.56910867A>G, NC_000005.9:g.56206694A>G, XM_011543139.3:c.-54A>G, XM_011543139.2:c.-54A>G, XM_011543139.1:c.-54A>G

Select item 149021587612.

rs1490215876 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 5:56913571 (GRCh38)
5:56209398 (GRCh37)
Canonical SPDI:: NC_000005.10:56913570:T:A
Gene:: SETD9 (Varview)
Functional Consequence:: intron_variant
HGVS:: NC_000005.10:g.56913571T>A, NC_000005.9:g.56209398T>A

Select item 149010338513.

rs1490103385 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 5:56915892 (GRCh38)
5:56211719 (GRCh37)
Canonical SPDI:: NC_000005.10:56915891:G:T
Gene:: SETD9 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000014/2 (GnomAD)
T=0.000019/5 (TOPMED)
HGVS:: NC_000005.10:g.56915892G>T, NC_000005.9:g.56211719G>T

Select item 149003156214.

rs1490031562 has merged into rs758154357 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTT>-,TTTTT [Show Flanks]
Chromosome:: 5:56916957 (GRCh38)
5:56212784 (GRCh37)
Canonical SPDI:: NC_000005.10:56916954:TTTTTT:TT,NC_000005.10:56916954:TTTTTT:TTTTTTT
Gene:: SETD9 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,3_prime_UTR_variant,non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTT=0./0 (ALFA)
T=0.000004/1 (TOPMED)
-=0.000005/1 (GnomAD_exomes)
-=0.000009/1 (ExAC)
HGVS:: NC_000005.10:g.56916957_56916960del, NC_000005.10:g.56916960dup, NC_000005.9:g.56212784_56212787del, NC_000005.9:g.56212787dup, XM_005248426.5:c.*55_*58del, XM_005248426.5:c.*58dup, XM_005248426.4:c.*55_*58del, XM_005248426.4:c.*58dup, XM_005248426.3:c.*55_*58del, XM_005248426.3:c.*58dup, XM_005248426.2:c.*55_*58del, XM_005248426.2:c.*58dup, XM_005248426.1:c.*55_*58del, XM_005248426.1:c.*58dup, NM_153706.4:c.*55_*58del, NM_153706.4:c.*58dup, NM_153706.3:c.*55_*58del, NM_153706.3:c.*58dup, XM_011543140.4:c.*55_*58del, XM_011543140.4:c.*58dup, XM_011543140.3:c.*55_*58del, XM_011543140.3:c.*58dup, XM_011543140.2:c.*55_*58del, XM_011543140.2:c.*58dup, XM_011543140.1:c.*55_*58del, XM_011543140.1:c.*58dup, XM_011543139.3:c.*55_*58del, XM_011543139.3:c.*58dup, XM_011543139.2:c.*55_*58del, XM_011543139.2:c.*58dup, XM_011543139.1:c.*55_*58del, XM_011543139.1:c.*58dup, NM_001323018.2:c.*55_*58del, NM_001323018.2:c.*58dup, NM_001323018.1:c.*55_*58del, NM_001323018.1:c.*58dup, NR_136556.2:n.637_640del, NR_136556.2:n.640dup, NR_136556.1:n.973_976del, NR_136556.1:n.976dup, NM_001323022.1:c.*55_*58del, NM_001323022.1:c.*58dup, NR_136557.1:n.822_825del, NR_136557.1:n.825dup

Select item 148977085115.

rs1489770851 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A,C,G [Show Flanks]
Chromosome:: 5:56925627 (GRCh38)
5:56221454 (GRCh37)
Canonical SPDI:: NC_000005.10:56925626:T:A,NC_000005.10:56925626:T:C,NC_000005.10:56925626:T:G
Gene:: SETD9 (Varview), MIER3 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant,non_coding_transcript_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000071/1 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000005.10:g.56925627T>A, NC_000005.10:g.56925627T>C, NC_000005.10:g.56925627T>G, NC_000005.9:g.56221454T>A, NC_000005.9:g.56221454T>C, NC_000005.9:g.56221454T>G, NM_001171990.3:c.*291T>A, NM_001171990.3:c.*291T>C, NM_001171990.3:c.*291T>G, NM_001171990.2:c.*291T>A, NM_001171990.2:c.*291T>C, NM_001171990.2:c.*291T>G, NR_136555.2:n.789T>A, NR_136555.2:n.789T>C, NR_136555.2:n.789T>G, NR_136555.1:n.1125T>A, NR_136555.1:n.1125T>C, NR_136555.1:n.1125T>G

Select item 148966768116.

rs1489667681 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:56926621 (GRCh38)
5:56222448 (GRCh37)
Canonical SPDI:: NC_000005.10:56926620:A:G
Gene:: SETD9 (Varview), MIER3 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant,non_coding_transcript_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
HGVS:: NC_000005.10:g.56926621A>G, NC_000005.9:g.56222448A>G, NM_001171990.3:c.*1285A>G, NM_001171990.2:c.*1285A>G, NR_136555.2:n.1783A>G, NR_136555.1:n.2119A>G

Select item 148965641817.

rs1489656418 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 5:56914715 (GRCh38)
5:56210542 (GRCh37)
Canonical SPDI:: NC_000005.10:56914714:T:G
Gene:: SETD9 (Varview)
Functional Consequence:: downstream_transcript_variant,intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0.000071/1 (ALFA)
G=0.000007/1 (GnomAD)
HGVS:: NC_000005.10:g.56914715T>G, NC_000005.9:g.56210542T>G

Select item 148952717518.

rs1489527175 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->A [Show Flanks]
Chromosome:: 5:56909735 (GRCh38)
5:56205563 (GRCh37)
Canonical SPDI:: NC_000005.10:56909735:AA:AAA
Gene:: SETD9 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,coding_sequence_variant,non_coding_transcript_variant,genic_upstream_transcript_variant,frameshift_variant
Validated:: by frequency,by alfa
MAF:: AAA=0./0 (ALFA)
HGVS:: NC_000005.10:g.56909737dup, NC_000005.9:g.56205564dup, NM_153706.4:c.92dup, NM_153706.3:c.92dup, NM_001171990.3:c.92dup, NM_001171990.2:c.92dup, NM_001171990.1:c.92dup, NR_136555.2:n.142dup, NR_136555.1:n.478dup, NM_001323019.2:c.92dup, NM_001323019.1:c.92dup, NR_136556.2:n.142dup, NR_136556.1:n.478dup, NR_136558.2:n.142dup, NR_136558.1:n.478dup, NP_714917.2:p.Asn31fs, NP_001165461.1:p.Asn31fs, NP_001309948.1:p.Asn31fs

Select item 148946791519.

rs1489467915 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:56910405 (GRCh38)
5:56206232 (GRCh37)
Canonical SPDI:: NC_000005.10:56910404:C:T
Gene:: SETD9 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,intron_variant,upstream_transcript_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_000005.10:g.56910405C>T, NC_000005.9:g.56206232C>T

Select item 148939737320.

rs1489397373 [Homo sapiens]

Variant type:: SNV:
Alleles:: ->TAGTTATTATTATAT
Chromosome:: no mapping
Canonical SPDI:

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