SNP Links for Gene (Select 135932) - SNP

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Select item 14909370031.

rs1490937003 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 7:143286686 (GRCh38)
7:142983779 (GRCh37)
Canonical SPDI:: NC_000007.14:143286685:G:A
Gene:: CASP2 (Varview), TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,2KB_upstream_variant,coding_sequence_variant,upstream_transcript_variant,missense_variant
Validated:: by frequency
MAF:: A=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000007.14:g.143286686G>A, NC_000007.13:g.142983779G>A, NG_029248.1:g.3472G>A, NR_040003.3:n.751G>A, NR_040003.2:n.759G>A, NR_040003.1:n.762G>A, NM_001242774.3:c.508G>A, NM_001242774.2:c.508G>A, NM_001242774.1:c.508G>A, NM_001242775.3:c.508G>A, NM_001242775.2:c.508G>A, NM_001242775.1:c.508G>A, NM_153345.3:c.508G>A, NM_153345.2:c.508G>A, NM_001282876.2:c.508G>A, NM_001282876.1:c.508G>A, NM_001242773.2:c.508G>A, NM_001242773.1:c.508G>A, NR_104254.2:n.402G>A, NR_104254.1:n.461G>A, NR_104253.2:n.304G>A, NR_104253.1:n.363G>A, NM_001282877.1:c.508G>A, NR_104250.1:n.440G>A, NR_104252.1:n.437G>A, NM_001242776.1:c.79G>A, NR_104251.1:n.339G>A, NM_001242777.1:c.79G>A, NP_001229703.1:p.Ala170Thr, NP_001229704.1:p.Ala170Thr, NP_699176.1:p.Ala170Thr, NP_001269805.1:p.Ala170Thr, NP_001229702.1:p.Ala170Thr, NP_001269806.1:p.Ala170Thr

Select item 14905299212.

rs1490529921 has merged into rs965415147 [Homo sapiens]

Variant type:: DELINS
Alleles:: T>-,TT [Show Flanks]
Chromosome:: 7:143283239 (GRCh38)
7:142980332 (GRCh37)
Canonical SPDI:: NC_000007.14:143283238:TTTTTTTTT:TTTTTTTT,NC_000007.14:143283238:TTTTTTTTT:TTTTTTTTTT
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTT=0./0 (ALFA)
-=0.00125/8 (1000Genomes)
-=0.00491/9 (Korea1K)
HGVS:: NC_000007.14:g.143283247del, NC_000007.14:g.143283247dup, NC_000007.13:g.142980340del, NC_000007.13:g.142980340dup, NG_029248.1:g.33del, NG_029248.1:g.33dup

Select item 14900395323.

rs1490039532 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 7:143283774 (GRCh38)
7:142980867 (GRCh37)
Canonical SPDI:: NC_000007.14:143283773:T:C
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: 2KB_upstream_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000008/2 (TOPMED)
C=0.000035/1 (TOMMO)
HGVS:: NC_000007.14:g.143283774T>C, NC_000007.13:g.142980867T>C, NG_029248.1:g.560T>C

Select item 14886694094.

rs1488669409 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 7:143285166 (GRCh38)
7:142982259 (GRCh37)
Canonical SPDI:: NC_000007.14:143285165:C:T
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,5_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000007/1 (GnomAD)
HGVS:: NC_000007.14:g.143285166C>T, NC_000007.13:g.142982259C>T, NG_029248.1:g.1952C>T, NR_040003.3:n.209C>T, NR_040003.2:n.217C>T, NR_040003.1:n.220C>T, NM_001282876.2:c.-297C>T, NM_001282876.1:c.-297C>T

Select item 14879162065.

rs1487916206 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 7:143284656 (GRCh38)
7:142981749 (GRCh37)
Canonical SPDI:: NC_000007.14:143284655:C:G
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: 2KB_upstream_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000007.14:g.143284656C>G, NC_000007.13:g.142981749C>G, NG_029248.1:g.1442C>G

Select item 14862513776.

rs1486251377 [Homo sapiens]

Variant type:: DELINS
Alleles:: C>- [Show Flanks]
Chromosome:: 7:143285944 (GRCh38)
7:142983037 (GRCh37)
Canonical SPDI:: NC_000007.14:143285943:CC:C
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: intron_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: CC=0./0 (ALFA)
-=0.000011/3 (TOPMED)
-=0.000014/2 (GnomAD)
HGVS:: NC_000007.14:g.143285945del, NC_000007.13:g.142983038del, NG_029248.1:g.2731del, NM_001242774.3:c.-13del, NM_001242774.2:c.-13del, NM_001242774.1:c.-13del, NM_001242775.3:c.-13del, NM_001242775.2:c.-13del, NM_001242775.1:c.-13del, NM_153345.3:c.-13del, NM_153345.2:c.-13del, NM_001282876.2:c.-13del, NM_001282876.1:c.-13del, NM_001242773.2:c.-13del, NM_001242773.1:c.-13del, NM_001282877.1:c.-13del

Select item 14858587297.

rs1485858729 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 7:143285822 (GRCh38)
7:142982915 (GRCh37)
Canonical SPDI:: NC_000007.14:143285821:A:C
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000071/1 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000007/1 (GnomAD)
HGVS:: NC_000007.14:g.143285822A>C, NC_000007.13:g.142982915A>C, NG_029248.1:g.2608A>C, NR_133932.1:n.375T>G

Select item 14853807508.

rs1485380750 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 7:143287434 (GRCh38)
7:142984527 (GRCh37)
Canonical SPDI:: NC_000007.14:143287433:T:C
Gene:: CASP2 (Varview), TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,3_prime_UTR_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000008/2 (TOPMED)
C=0.000014/2 (GnomAD)
HGVS:: NC_000007.14:g.143287434T>C, NC_000007.13:g.142984527T>C, NG_029248.1:g.4220T>C, NR_040003.3:n.1499T>C, NR_040003.2:n.1507T>C, NR_040003.1:n.1510T>C, NM_001242774.3:c.*605T>C, NM_001242774.2:c.*605T>C, NM_001242774.1:c.*605T>C, NM_001242775.3:c.*605T>C, NM_001242775.2:c.*605T>C, NM_001242775.1:c.*605T>C, NM_153345.3:c.*605T>C, NM_153345.2:c.*605T>C, NM_001282876.2:c.*605T>C, NM_001282876.1:c.*605T>C, NM_001242773.2:c.*605T>C, NM_001242773.1:c.*605T>C, NR_104254.2:n.1150T>C, NR_104254.1:n.1209T>C, NR_104253.2:n.1052T>C, NR_104253.1:n.1111T>C, NM_001282877.1:c.*605T>C, NR_104250.1:n.1188T>C, NR_104252.1:n.1185T>C, NM_001242776.1:c.*605T>C, NR_104251.1:n.1087T>C, NM_001242777.1:c.*605T>C

Select item 14852261619.

rs1485226161 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->TGGGTATGCCAC [Show Flanks]
Chromosome:: 7:143286980 (GRCh38)
7:142984074 (GRCh37)
Canonical SPDI:: NC_000007.14:143286980:C:CTGGGTATGCCAC
Gene:: CASP2 (Varview), TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,3_prime_UTR_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: CTGGGTATGCCAC=0./0 (ALFA)
CTGGGTATGCCA=0.000011/3 (TOPMED)
HGVS:: NC_000007.14:g.143286981_143286982insTGGGTATGCCAC, NC_000007.13:g.142984074_142984075insTGGGTATGCCAC, NG_029248.1:g.3767_3768insTGGGTATGCCAC, NR_040003.3:n.1046_1047insTGGGTATGCCAC, NR_040003.2:n.1054_1055insTGGGTATGCCAC, NR_040003.1:n.1057_1058insTGGGTATGCCAC, NM_001242774.3:c.*152_*153insTGGGTATGCCAC, NM_001242774.2:c.*152_*153insTGGGTATGCCAC, NM_001242774.1:c.*152_*153insTGGGTATGCCAC, NM_001242775.3:c.*152_*153insTGGGTATGCCAC, NM_001242775.2:c.*152_*153insTGGGTATGCCAC, NM_001242775.1:c.*152_*153insTGGGTATGCCAC, NM_153345.3:c.*152_*153insTGGGTATGCCAC, NM_153345.2:c.*152_*153insTGGGTATGCCAC, NM_001282876.2:c.*152_*153insTGGGTATGCCAC, NM_001282876.1:c.*152_*153insTGGGTATGCCAC, NM_001242773.2:c.*152_*153insTGGGTATGCCAC, NM_001242773.1:c.*152_*153insTGGGTATGCCAC, NR_104254.2:n.697_698insTGGGTATGCCAC, NR_104254.1:n.756_757insTGGGTATGCCAC, NR_104253.2:n.599_600insTGGGTATGCCAC, NR_104253.1:n.658_659insTGGGTATGCCAC, NM_001282877.1:c.*152_*153insTGGGTATGCCAC, NR_104250.1:n.735_736insTGGGTATGCCAC, NR_104252.1:n.732_733insTGGGTATGCCAC, NM_001242776.1:c.*152_*153insTGGGTATGCCAC, NR_104251.1:n.634_635insTGGGTATGCCAC, NM_001242777.1:c.*152_*153insTGGGTATGCCAC

Select item 148519518710.

rs1485195187 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 7:143288053 (GRCh38)
7:142985146 (GRCh37)
Canonical SPDI:: NC_000007.14:143288052:C:A,NC_000007.14:143288052:C:T
Gene:: CASP2 (Varview), TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: downstream_transcript_variant,500B_downstream_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
A=0.00004/1 (TOMMO)
HGVS:: NC_000007.14:g.143288053C>A, NC_000007.14:g.143288053C>T, NC_000007.13:g.142985146C>A, NC_000007.13:g.142985146C>T, NG_029248.1:g.4839C>A, NG_029248.1:g.4839C>T

Select item 148430021711.

rs1484300217 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 7:143287828 (GRCh38)
7:142984921 (GRCh37)
Canonical SPDI:: NC_000007.14:143287827:T:C
Gene:: CASP2 (Varview), TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,3_prime_UTR_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000071/1 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000007/1 (GnomAD)
HGVS:: NC_000007.14:g.143287828T>C, NC_000007.13:g.142984921T>C, NG_029248.1:g.4614T>C, NR_040003.3:n.1893T>C, NR_040003.2:n.1901T>C, NR_040003.1:n.1904T>C, NM_001242774.3:c.*999T>C, NM_001242774.2:c.*999T>C, NM_001242774.1:c.*999T>C, NM_001242775.3:c.*999T>C, NM_001242775.2:c.*999T>C, NM_001242775.1:c.*999T>C, NM_153345.3:c.*999T>C, NM_153345.2:c.*999T>C, NM_001282876.2:c.*999T>C, NM_001282876.1:c.*999T>C, NM_001242773.2:c.*999T>C, NM_001242773.1:c.*999T>C, NR_104254.2:n.1544T>C, NR_104254.1:n.1603T>C, NR_104253.2:n.1446T>C, NR_104253.1:n.1505T>C, NM_001282877.1:c.*999T>C, NR_104250.1:n.1582T>C, NR_104252.1:n.1579T>C, NM_001242776.1:c.*999T>C, NR_104251.1:n.1481T>C, NM_001242777.1:c.*999T>C

Select item 148410539812.

rs1484105398 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 7:143283111 (GRCh38)
7:142980204 (GRCh37)
Canonical SPDI:: NC_000007.14:143283110:A:G
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,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_000007.14:g.143283111A>G, NC_000007.13:g.142980204A>G

Select item 148407670313.

rs1484076703 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 7:143284045 (GRCh38)
7:142981138 (GRCh37)
Canonical SPDI:: NC_000007.14:143284044:G:A
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000008/2 (TOPMED)
HGVS:: NC_000007.14:g.143284045G>A, NC_000007.13:g.142981138G>A, NG_029248.1:g.831G>A

Select item 148082580714.

rs1480825807 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 7:143283330 (GRCh38)
7:142980423 (GRCh37)
Canonical SPDI:: NC_000007.14:143283329:A:G
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_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_000007.14:g.143283330A>G, NC_000007.13:g.142980423A>G, NG_029248.1:g.116A>G

Select item 148007064215.

rs1480070642 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 7:143285153 (GRCh38)
7:142982246 (GRCh37)
Canonical SPDI:: NC_000007.14:143285152:G:A
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
HGVS:: NC_000007.14:g.143285153G>A, NC_000007.13:g.142982246G>A, NG_029248.1:g.1939G>A, NR_040003.3:n.196G>A, NR_040003.2:n.204G>A, NR_040003.1:n.207G>A, NM_001282876.2:c.-310G>A, NM_001282876.1:c.-310G>A

Select item 147992030716.

rs1479920307 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 7:143282976 (GRCh38)
7:142980069 (GRCh37)
Canonical SPDI:: NC_000007.14:143282975:A:G
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_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_000007.14:g.143282976A>G, NC_000007.13:g.142980069A>G

Select item 147972636117.

rs1479726361 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 7:143283969 (GRCh38)
7:142981062 (GRCh37)
Canonical SPDI:: NC_000007.14:143283968:C:A
Gene:: TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000008/2 (TOPMED)
A=0.000021/3 (GnomAD)
HGVS:: NC_000007.14:g.143283969C>A, NC_000007.13:g.142981062C>A, NG_029248.1:g.755C>A

Select item 147952381118.

rs1479523811 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 7:143287115 (GRCh38)
7:142984208 (GRCh37)
Canonical SPDI:: NC_000007.14:143287114:G:T
Gene:: CASP2 (Varview), TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,3_prime_UTR_variant,2KB_upstream_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_000007.14:g.143287115G>T, NC_000007.13:g.142984208G>T, NG_029248.1:g.3901G>T, NR_040003.3:n.1180G>T, NR_040003.2:n.1188G>T, NR_040003.1:n.1191G>T, NM_001242774.3:c.*286G>T, NM_001242774.2:c.*286G>T, NM_001242774.1:c.*286G>T, NM_001242775.3:c.*286G>T, NM_001242775.2:c.*286G>T, NM_001242775.1:c.*286G>T, NM_153345.3:c.*286G>T, NM_153345.2:c.*286G>T, NM_001282876.2:c.*286G>T, NM_001282876.1:c.*286G>T, NM_001242773.2:c.*286G>T, NM_001242773.1:c.*286G>T, NR_104254.2:n.831G>T, NR_104254.1:n.890G>T, NR_104253.2:n.733G>T, NR_104253.1:n.792G>T, NM_001282877.1:c.*286G>T, NR_104250.1:n.869G>T, NR_104252.1:n.866G>T, NM_001242776.1:c.*286G>T, NR_104251.1:n.768G>T, NM_001242777.1:c.*286G>T

Select item 147932547019.

rs1479325470 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 7:143286433 (GRCh38)
7:142983526 (GRCh37)
Canonical SPDI:: NC_000007.14:143286432:A:T
Gene:: CASP2 (Varview), TMEM139 (Varview), TMEM139-AS1 (Varview)
Functional Consequence:: non_coding_transcript_variant,2KB_upstream_variant,upstream_transcript_variant,missense_variant,coding_sequence_variant
HGVS:: NC_000007.14:g.143286433A>T, NC_000007.13:g.142983526A>T, NG_029248.1:g.3219A>T, NR_040003.3:n.498A>T, NR_040003.2:n.506A>T, NR_040003.1:n.509A>T, NM_001242774.3:c.255A>T, NM_001242774.2:c.255A>T, NM_001242774.1:c.255A>T, NM_001242775.3:c.255A>T, NM_001242775.2:c.255A>T, NM_001242775.1:c.255A>T, NM_153345.3:c.255A>T, NM_153345.2:c.255A>T, NM_001282876.2:c.255A>T, NM_001282876.1:c.255A>T, NM_001242773.2:c.255A>T, NM_001242773.1:c.255A>T, NR_104254.2:n.149A>T, NR_104254.1:n.208A>T, NR_104253.2:n.51A>T, NR_104253.1:n.110A>T, NM_001282877.1:c.255A>T, NR_104250.1:n.187A>T, NR_104252.1:n.184A>T, NM_001242776.1:c.-175A>T, NR_104251.1:n.86A>T, NM_001242777.1:c.-175A>T, NP_001229703.1:p.Glu85Asp, NP_001229704.1:p.Glu85Asp, NP_699176.1:p.Glu85Asp, NP_001269805.1:p.Glu85Asp, NP_001229702.1:p.Glu85Asp, NP_001269806.1:p.Glu85Asp

Select item 147903139020.

rs1479031390 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 7:143288344 (GRCh38)
7:142985437 (GRCh37)
Canonical SPDI:: NC_000007.14:143288343:C:A
Gene:: CASP2 (Varview), TMEM139 (Varview)
Functional Consequence:: downstream_transcript_variant,500B_downstream_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000224/1 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000223/1 (Estonian)
HGVS:: NC_000007.14:g.143288344C>A, NC_000007.13:g.142985437C>A, NG_029248.1:g.5130C>A, NM_032982.3:c.-112C>A, NM_032983.3:c.-112C>A

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