SNP Links for Gene (Select 579) - SNP

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Select item 14913864581.

rs1491386458 [Homo sapiens]

Variant type:: DEL
Alleles:: CT>- [Show Flanks]
Chromosome:: 4:13545454 (GRCh38)
4:13547078 (GRCh37)
Canonical SPDI:: NC_000004.12:13545453:CT:
Gene:: NKX3-2 (Varview)
Functional Consequence:: upstream_transcript_variant,genic_upstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000007/1 (GnomAD)
HGVS:: NC_000004.12:g.13545454_13545455del, NC_000004.11:g.13547078_13547079del, NG_023192.1:g.4036_4037del, XM_047416049.1:c.-1041_-1040del, XM_047416050.1:c.-1041_-1040del

Select item 14912998332.

rs1491299833 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->T [Show Flanks]
Chromosome:: 4:13545454 (GRCh38)
4:13547079 (GRCh37)
Canonical SPDI:: NC_000004.12:13545454:TTTTTTTT:TTTTTTTTT
Gene:: NKX3-2 (Varview)
Functional Consequence:: upstream_transcript_variant,genic_upstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTT=0.000071/1 (ALFA)
T=0.000011/3 (TOPMED)
T=0.000029/4 (GnomAD)
HGVS:: NC_000004.12:g.13545462dup, NC_000004.11:g.13547086dup, NG_023192.1:g.4036dup, XM_047416049.1:c.-1041dup, XM_047416050.1:c.-1041dup

Select item 14909024083.

rs1490902408 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 4:13544603 (GRCh38)
4:13546227 (GRCh37)
Canonical SPDI:: NC_000004.12:13544602:A:C
Gene:: NKX3-2 (Varview)
Functional Consequence:: upstream_transcript_variant,genic_upstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: C=0.00066/7 (ALFA)
C=0.03132/89 (KOREAN)
HGVS:: NC_000004.12:g.13544603A>C, NC_000004.11:g.13546227A>C, NG_023192.1:g.4888T>G, XM_047416049.1:c.-189T>G, XM_047416050.1:c.-189T>G

Select item 14904573224.

rs1490457322 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 4:13544232 (GRCh38)
4:13545856 (GRCh37)
Canonical SPDI:: NC_000004.12:13544231:G:A,NC_000004.12:13544231:G:C
Gene:: NKX3-2 (Varview)
Functional Consequence:: synonymous_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000005/1 (GnomAD_exomes)
A=0.000156/1 (1000Genomes)
HGVS:: NC_000004.12:g.13544232G>A, NC_000004.12:g.13544232G>C, NC_000004.11:g.13545856G>A, NC_000004.11:g.13545856G>C, NG_023192.1:g.5259C>T, NG_023192.1:g.5259C>G, NM_001189.4:c.183C>T, NM_001189.4:c.183C>G, NM_001189.3:c.183C>T, NM_001189.3:c.183C>G, XM_047416049.1:c.183C>T, XM_047416049.1:c.183C>G, XM_047416050.1:c.183C>T, XM_047416050.1:c.183C>G

Select item 14899611545.

rs1489961154 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 4:13544088 (GRCh38)
4:13545712 (GRCh37)
Canonical SPDI:: NC_000004.12:13544087:G:T
Gene:: NKX3-2 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000015/4 (TOPMED)
T=0.000021/3 (GnomAD)
HGVS:: NC_000004.12:g.13544088G>T, NC_000004.11:g.13545712G>T, NG_023192.1:g.5403C>A, NM_001189.4:c.327C>A, NM_001189.3:c.327C>A, XM_047416049.1:c.327C>A, XM_047416050.1:c.327C>A, NP_001180.1:p.Asp109Glu, XP_047272005.1:p.Asp109Glu, XP_047272006.1:p.Asp109Glu

Select item 14887726936.

rs1488772693 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:13541958 (GRCh38)
4:13543582 (GRCh37)
Canonical SPDI:: NC_000004.12:13541957:C:T
Gene:: NKX3-2 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000014/2 (GnomAD)
T=0.000026/7 (TOPMED)
HGVS:: NC_000004.12:g.13541958C>T, NC_000004.11:g.13543582C>T, NG_023192.1:g.7533G>A, NM_001189.4:c.*35G>A, NM_001189.3:c.*35G>A, XM_047416049.1:c.*35G>A, XM_047416050.1:c.*35G>A

Select item 14883908107.

rs1488390810 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 4:13542760 (GRCh38)
4:13544384 (GRCh37)
Canonical SPDI:: NC_000004.12:13542759:T:G
Gene:: NKX3-2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000011/3 (TOPMED)
G=0.000014/2 (GnomAD)
HGVS:: NC_000004.12:g.13542760T>G, NC_000004.11:g.13544384T>G, NG_023192.1:g.6731A>C

Select item 14882590298.

rs1488259029 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C,T [Show Flanks]
Chromosome:: 4:13543818 (GRCh38)
4:13545442 (GRCh37)
Canonical SPDI:: NC_000004.12:13543817:G:C,NC_000004.12:13543817:G:T
Gene:: NKX3-2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
HGVS:: NC_000004.12:g.13543818G>C, NC_000004.12:g.13543818G>T, NC_000004.11:g.13545442G>C, NC_000004.11:g.13545442G>T, NG_023192.1:g.5673C>G, NG_023192.1:g.5673C>A

Select item 14882056689.

rs1488205668 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 4:13545588 (GRCh38)
4:13547212 (GRCh37)
Canonical SPDI:: NC_000004.12:13545587:A:G
Gene:: NKX3-2 (Varview), LINC01096 (Varview)
Functional Consequence:: 5_prime_UTR_variant,upstream_transcript_variant,downstream_transcript_variant,500B_downstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
HGVS:: NC_000004.12:g.13545588A>G, NC_000004.11:g.13547212A>G, NG_023192.1:g.3903T>C, XM_047416049.1:c.-1174T>C, XM_047416050.1:c.-1174T>C

Select item 148801690110.

rs1488016901 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 4:13545877 (GRCh38)
4:13547501 (GRCh37)
Canonical SPDI:: NC_000004.12:13545876:T:C
Gene:: NKX3-2 (Varview), LINC01096 (Varview)
Functional Consequence:: 5_prime_UTR_variant,upstream_transcript_variant,downstream_transcript_variant,500B_downstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
HGVS:: NC_000004.12:g.13545877T>C, NC_000004.11:g.13547501T>C, NG_023192.1:g.3614A>G, XM_047416049.1:c.-1463A>G, XM_047416050.1:c.-1463A>G

Select item 148686089411.

rs1486860894 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:13544397 (GRCh38)
4:13546021 (GRCh37)
Canonical SPDI:: NC_000004.12:13544396:G:A
Gene:: NKX3-2 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000008/2 (TOPMED)
HGVS:: NC_000004.12:g.13544397G>A, NC_000004.11:g.13546021G>A, NG_023192.1:g.5094C>T, NM_001189.4:c.18C>T, NM_001189.3:c.18C>T, XM_047416049.1:c.18C>T, XM_047416050.1:c.18C>T

Select item 148682890012.

rs1486828900 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 4:13544290 (GRCh38)
4:13545914 (GRCh37)
Canonical SPDI:: NC_000004.12:13544289:G:C
Gene:: NKX3-2 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant
HGVS:: NC_000004.12:g.13544290G>C, NC_000004.11:g.13545914G>C, NG_023192.1:g.5201C>G, NM_001189.4:c.125C>G, NM_001189.3:c.125C>G, XM_047416049.1:c.125C>G, XM_047416050.1:c.125C>G, NP_001180.1:p.Ser42Trp, XP_047272005.1:p.Ser42Trp, XP_047272006.1:p.Ser42Trp

Select item 148671077413.

rs1486710774 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G [Show Flanks]
Chromosome:: 4:13544602 (GRCh38)
4:13546226 (GRCh37)
Canonical SPDI:: NC_000004.12:13544601:C:A,NC_000004.12:13544601:C:G
Gene:: NKX3-2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,5_prime_UTR_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000004.12:g.13544602C>A, NC_000004.12:g.13544602C>G, NC_000004.11:g.13546226C>A, NC_000004.11:g.13546226C>G, NG_023192.1:g.4889G>T, NG_023192.1:g.4889G>C, XM_047416049.1:c.-188G>T, XM_047416049.1:c.-188G>C, XM_047416050.1:c.-188G>T, XM_047416050.1:c.-188G>C

Select item 148594473814.

rs1485944738 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 4:13545062 (GRCh38)
4:13546686 (GRCh37)
Canonical SPDI:: NC_000004.12:13545061:T:G
Gene:: NKX3-2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,5_prime_UTR_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
HGVS:: NC_000004.12:g.13545062T>G, NC_000004.11:g.13546686T>G, NG_023192.1:g.4429A>C, XM_047416049.1:c.-648A>C, XM_047416050.1:c.-648A>C

Select item 148512467115.

rs1485124671 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G,T [Show Flanks]
Chromosome:: 4:13541939 (GRCh38)
4:13543563 (GRCh37)
Canonical SPDI:: NC_000004.12:13541938:C:A,NC_000004.12:13541938:C:G,NC_000004.12:13541938:C:T
Gene:: NKX3-2 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
HGVS:: NC_000004.12:g.13541939C>A, NC_000004.12:g.13541939C>G, NC_000004.12:g.13541939C>T, NC_000004.11:g.13543563C>A, NC_000004.11:g.13543563C>G, NC_000004.11:g.13543563C>T, NG_023192.1:g.7552G>T, NG_023192.1:g.7552G>C, NG_023192.1:g.7552G>A, NM_001189.4:c.*54G>T, NM_001189.4:c.*54G>C, NM_001189.4:c.*54G>A, NM_001189.3:c.*54G>T, NM_001189.3:c.*54G>C, NM_001189.3:c.*54G>A, XM_047416049.1:c.*54G>T, XM_047416049.1:c.*54G>C, XM_047416049.1:c.*54G>A, XM_047416050.1:c.*54G>T, XM_047416050.1:c.*54G>C, XM_047416050.1:c.*54G>A

Select item 148493585616.

rs1484935856 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 4:13544911 (GRCh38)
4:13546535 (GRCh37)
Canonical SPDI:: NC_000004.12:13544910:C:G,NC_000004.12:13544910:C:T
Gene:: NKX3-2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,5_prime_UTR_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000312/2 (1000Genomes)
T=0.000557/1 (Korea1K)
T=0.000685/2 (KOREAN)
HGVS:: NC_000004.12:g.13544911C>G, NC_000004.12:g.13544911C>T, NC_000004.11:g.13546535C>G, NC_000004.11:g.13546535C>T, NG_023192.1:g.4580G>C, NG_023192.1:g.4580G>A, XM_047416049.1:c.-497G>C, XM_047416049.1:c.-497G>A, XM_047416050.1:c.-497G>C, XM_047416050.1:c.-497G>A

Select item 148377413117.

rs1483774131 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:13541852 (GRCh38)
4:13543476 (GRCh37)
Canonical SPDI:: NC_000004.12:13541851:C:T
Gene:: NKX3-2 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000011/3 (TOPMED)
HGVS:: NC_000004.12:g.13541852C>T, NC_000004.11:g.13543476C>T, NG_023192.1:g.7639G>A, NM_001189.4:c.*141G>A, NM_001189.3:c.*141G>A, XM_047416049.1:c.*141G>A, XM_047416050.1:c.*141G>A

Select item 148362131218.

rs1483621312 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 4:13543697 (GRCh38)
4:13545321 (GRCh37)
Canonical SPDI:: NC_000004.12:13543696:C:A
Gene:: NKX3-2 (Varview)
Functional Consequence:: intron_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_000004.12:g.13543697C>A, NC_000004.11:g.13545321C>A, NG_023192.1:g.5794G>T

Select item 148239770419.

rs1482397704 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 4:13541550 (GRCh38)
4:13543174 (GRCh37)
Canonical SPDI:: NC_000004.12:13541549:T:C
Gene:: NKX3-2 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000224/1 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000223/1 (Estonian)
HGVS:: NC_000004.12:g.13541550T>C, NC_000004.11:g.13543174T>C, NG_023192.1:g.7941A>G, NM_001189.4:c.*443A>G, NM_001189.3:c.*443A>G, XM_047416049.1:c.*443A>G, XM_047416050.1:c.*443A>G

Select item 148153074420.

rs1481530744 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:13544467 (GRCh38)
4:13546091 (GRCh37)
Canonical SPDI:: NC_000004.12:13544466:G:A
Gene:: NKX3-2 (Varview)
Functional Consequence:: 5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
HGVS:: NC_000004.12:g.13544467G>A, NC_000004.11:g.13546091G>A, NG_023192.1:g.5024C>T, NM_001189.4:c.-53C>T, NM_001189.3:c.-53C>T, XM_047416049.1:c.-53C>T, XM_047416050.1:c.-53C>T

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