SNP Links for Nucleotide (Select 336020348) - SNP

Links from Nucleotide

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Select item 14915869981.

rs1491586998 has merged into rs1233162492 [Homo sapiens]

Variant type:: DELINS
Alleles:: GTGT>-,GT,GTGTGT,GTGTGTGT [Show Flanks]
Chromosome:: 18:12870439 (GRCh38)
18:12870438 (GRCh37)
Canonical SPDI:: NC_000018.10:12870437:TGTGT:T,NC_000018.10:12870437:TGTGT:TGT,NC_000018.10:12870437:TGTGT:TGTGTGT,NC_000018.10:12870437:TGTGT:TGTGTGTGT
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGT=0./0 (ALFA)
-=0.01131/5 (NorthernSweden)
HGVS:: NC_000018.10:g.12870439_12870442del, NC_000018.10:g.12870439GT[1], NC_000018.10:g.12870439GT[3], NC_000018.10:g.12870439GT[4], NC_000018.9:g.12870438_12870441del, NC_000018.9:g.12870438GT[1], NC_000018.9:g.12870438GT[3], NC_000018.9:g.12870438GT[4], NG_029116.1:g.18895_18898del, NG_029116.1:g.18895CA[1], NG_029116.1:g.18895CA[3], NG_029116.1:g.18895CA[4]

Select item 14915592372.

rs1491559237 [Homo sapiens]

Variant type:: INS
Alleles:: ->AC,ATAC [Show Flanks]
Chromosome:: 18:12870392 (GRCh38)
18:12870392 (GRCh37)
Canonical SPDI:: NC_000018.10:12870392::AC,NC_000018.10:12870392::ATAC
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: ATAC=0./0 (ALFA)
AC=0.02853/42 (Korea1K)
AC=0.04922/736 (TOMMO)
HGVS:: NC_000018.10:g.12870392_12870393insAC, NC_000018.10:g.12870392_12870393insATAC, NC_000018.9:g.12870391_12870392insAC, NC_000018.9:g.12870391_12870392insATAC, NG_029116.1:g.18943_18944insGT, NG_029116.1:g.18943_18944insGTAT

Select item 14915490403.

rs1491549040 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->GT [Show Flanks]
Chromosome:: 18:12870384 (GRCh38)
18:12870384 (GRCh37)
Canonical SPDI:: NC_000018.10:12870384:GT:GTGT
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GTGT=0./0 (ALFA)
GT=0.00147/49 (GnomAD)
HGVS:: NC_000018.10:g.12870385_12870386dup, NC_000018.9:g.12870384_12870385dup, NG_029116.1:g.18950_18951dup

Select item 14915432004.

rs1491543200 [Homo sapiens]

Variant type:: INS
Alleles:: ->T [Show Flanks]
Chromosome:: 18:12874534 (GRCh38)
18:12874534 (GRCh37)
Canonical SPDI:: NC_000018.10:12874534::T
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.00005/2 (GnomAD)
HGVS:: NC_000018.10:g.12874534_12874535insT, NC_000018.9:g.12874533_12874534insT, NG_029116.1:g.14801_14802insA

Select item 14915413555.

rs1491541355 [Homo sapiens]

Variant type:: INS
Alleles:: ->ATAC,ATATACAC [Show Flanks]
Chromosome:: 18:12870438 (GRCh38)
18:12870438 (GRCh37)
Canonical SPDI:: NC_000018.10:12870438::ATAC,NC_000018.10:12870438::ATATACAC
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: ATATACAC=0./0 (ALFA)
HGVS:: NC_000018.10:g.12870438_12870439insATAC, NC_000018.10:g.12870438_12870439insATATACAC, NC_000018.9:g.12870437_12870438insATAC, NC_000018.9:g.12870437_12870438insATATACAC, NG_029116.1:g.18897_18898insGTAT, NG_029116.1:g.18897_18898insGTGTATAT

Select item 14915275506.

rs1491527550 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->A [Show Flanks]
Chromosome:: 18:12819217 (GRCh38)
18:12819217 (GRCh37)
Canonical SPDI:: NC_000018.10:12819217:A:AA
Gene:: PTPN2 (Varview)
Functional Consequence:: frameshift_variant,intron_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AA=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000018.10:g.12819218dup, NC_000018.9:g.12819217dup, NG_029116.1:g.70118dup, NM_001207013.2:c.560dup, NM_001207013.1:c.560dup, XM_047437695.1:c.812dup, NP_001193942.1:p.Ser189fs, XP_047293651.1:p.Ser273fs

Select item 14915264807.

rs1491526480 [Homo sapiens]

Variant type:: INS
Alleles:: ->AA,AC,ATAC [Show Flanks]
Chromosome:: 18:12870318 (GRCh38)
18:12870318 (GRCh37)
Canonical SPDI:: NC_000018.10:12870318::AA,NC_000018.10:12870318::AC,NC_000018.10:12870318::ATAC
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: ATAC=0./0 (ALFA)
HGVS:: NC_000018.10:g.12870318_12870319insAA, NC_000018.10:g.12870318_12870319insAC, NC_000018.10:g.12870318_12870319insATAC, NC_000018.9:g.12870317_12870318insAA, NC_000018.9:g.12870317_12870318insAC, NC_000018.9:g.12870317_12870318insATAC, NG_029116.1:g.19017_19018insTT, NG_029116.1:g.19017_19018insGT, NG_029116.1:g.19017_19018insGTAT

Select item 14915188248.

rs1491518824 has merged into rs1002659485 [Homo sapiens]

Variant type:: DELINS
Alleles:: ATATATATAT>-,AT,ATATAT,ATATATAT,ATATATATATAT [Show Flanks]
Chromosome:: 18:12789880 (GRCh38)
18:12789879 (GRCh37)
Canonical SPDI:: NC_000018.10:12789878:TATATATATAT:T,NC_000018.10:12789878:TATATATATAT:TAT,NC_000018.10:12789878:TATATATATAT:TATATAT,NC_000018.10:12789878:TATATATATAT:TATATATAT,NC_000018.10:12789878:TATATATATAT:TATATATATATAT
Gene:: PTPN2 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TATATAT=0./0 (ALFA)
TA=0.000011/3 (TOPMED)
-=0.001239/21 (TOMMO)
-=0.013889/3 (Vietnamese)
-=0.101811/510 (1000Genomes)
-=0.128333/77 (NorthernSweden)
-=0.275/11 (GENOME_DK)
-=0.325636/1255 (ALSPAC)
-=0.328479/1218 (TWINSUK)
HGVS:: NC_000018.10:g.12789880_12789889del, NC_000018.10:g.12789880AT[1], NC_000018.10:g.12789880AT[3], NC_000018.10:g.12789880AT[4], NC_000018.10:g.12789880AT[6], NC_000018.9:g.12789879_12789888del, NC_000018.9:g.12789879AT[1], NC_000018.9:g.12789879AT[3], NC_000018.9:g.12789879AT[4], NC_000018.9:g.12789879AT[6], NG_029116.1:g.99448_99457del, NG_029116.1:g.99448TA[1], NG_029116.1:g.99448TA[3], NG_029116.1:g.99448TA[4], NG_029116.1:g.99448TA[6]

Select item 14915150149.

rs1491515014 [Homo sapiens]

Variant type:: DELINS
Alleles:: ATAT>-,AT,ATATAT [Show Flanks]
Chromosome:: 18:12870295 (GRCh38)
18:12870294 (GRCh37)
Canonical SPDI:: NC_000018.10:12870290:ATATATAT:ATAT,NC_000018.10:12870290:ATATATAT:ATATAT,NC_000018.10:12870290:ATATATAT:ATATATATAT
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: ATATATATAT=0./0 (ALFA)
HGVS:: NC_000018.10:g.12870291AT[2], NC_000018.10:g.12870291AT[3], NC_000018.10:g.12870291AT[5], NC_000018.9:g.12870290AT[2], NC_000018.9:g.12870290AT[3], NC_000018.9:g.12870290AT[5], NG_029116.1:g.19038AT[2], NG_029116.1:g.19038AT[3], NG_029116.1:g.19038AT[5]

Select item 149148865810.

rs1491488658 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->GTATATATAT [Show Flanks]
Chromosome:: 18:12870426 (GRCh38)
18:12870426 (GRCh37)
Canonical SPDI:: NC_000018.10:12870426:GTATATATAT:GTATATATATGTATATATAT
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: GTATATATATGTATATATAT=0./0 (ALFA)
HGVS:: NC_000018.10:g.12870427_12870436dup, NC_000018.9:g.12870426_12870435dup, NG_029116.1:g.18900_18909dup

Select item 149146315311.

rs1491463153 [Homo sapiens]

Variant type:: INS
Alleles:: ->AC [Show Flanks]
Chromosome:: 18:12870350 (GRCh38)
18:12870350 (GRCh37)
Canonical SPDI:: NC_000018.10:12870350::AC
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AC=0.00008/1 (ALFA)
AC=0.00076/30 (GnomAD)
AC=0.00115/18 (TOMMO)
HGVS:: NC_000018.10:g.12870350_12870351insAC, NC_000018.9:g.12870349_12870350insAC, NG_029116.1:g.18985_18986insGT

Select item 149145306412.

rs1491453064 [Homo sapiens]

Variant type:: INS
Alleles:: ->C [Show Flanks]
Chromosome:: 18:12788433 (GRCh38)
18:12788433 (GRCh37)
Canonical SPDI:: NC_000018.10:12788433::C
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.00138/4 (GnomAD)
HGVS:: NC_000018.10:g.12788433_12788434insC, NC_000018.9:g.12788432_12788433insC, NG_029116.1:g.100902_100903insG

Select item 149144657513.

rs1491446575 has merged into rs753828976 [Homo sapiens]

Variant type:: DELINS
Alleles:: TT>-,T,TTT [Show Flanks]
Chromosome:: 18:12825976 (GRCh38)
18:12825975 (GRCh37)
Canonical SPDI:: NC_000018.10:12825968:TTTTTTTTT:TTTTTTT,NC_000018.10:12825968:TTTTTTTTT:TTTTTTTT,NC_000018.10:12825968:TTTTTTTTT:TTTTTTTTTT
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTT=0.000825/19 (ALFA)
-=0.000005/1 (GnomAD_exomes)
HGVS:: NC_000018.10:g.12825976_12825977del, NC_000018.10:g.12825977del, NC_000018.10:g.12825977dup, NC_000018.9:g.12825975_12825976del, NC_000018.9:g.12825976del, NC_000018.9:g.12825976dup, NG_029116.1:g.63366_63367del, NG_029116.1:g.63367del, NG_029116.1:g.63367dup

Select item 149143867214.

rs1491438672 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->GTGT [Show Flanks]
Chromosome:: 18:12870291 (GRCh38)
18:12870291 (GRCh37)
Canonical SPDI:: NC_000018.10:12870291:T:TGTGT
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: TGTGT=0./0 (ALFA)
HGVS:: NC_000018.10:g.12870292_12870293insGTGT, NC_000018.9:g.12870291_12870292insGTGT, NG_029116.1:g.19044_19045insCACA

Select item 149142890015.

rs1491428900 [Homo sapiens]

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

Select item 149141676016.

rs1491416760 has merged into rs201222736 [Homo sapiens]

Variant type:: DELINS
Alleles:: ATAT>-,AT,ATATAT [Show Flanks]
Chromosome:: 18:12870435 (GRCh38)
18:12870434 (GRCh37)
Canonical SPDI:: NC_000018.10:12870427:TATATATATAT:TATATAT,NC_000018.10:12870427:TATATATATAT:TATATATAT,NC_000018.10:12870427:TATATATATAT:TATATATATATAT
Gene:: PTPN2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TATATATAT=0./0 (ALFA)
-=0.14334/170 (Korea1K)
HGVS:: NC_000018.10:g.12870429AT[3], NC_000018.10:g.12870429AT[4], NC_000018.10:g.12870429AT[6], NC_000018.9:g.12870428AT[3], NC_000018.9:g.12870428AT[4], NC_000018.9:g.12870428AT[6], NG_029116.1:g.18899TA[3], NG_029116.1:g.18899TA[4], NG_029116.1:g.18899TA[6]

Select item 149141514917.

rs1491415149 has merged into rs577107678 [Homo sapiens]

Variant type:: DELINS
Alleles:: TATATATATATATA>-,TA,TATA,TATATA,TATATATA,TATATATATA,TATATATATATA,TATATATATATATATA,TATATATATATATATATA,TATATATATATATATATATA,TATATATATATATATATATATA [Show Flanks]
Chromosome:: 18:12870450 (GRCh38)
18:12870449 (GRCh37)
Canonical SPDI:: NC_000018.10:12870441:TATATATATATATATATATATA:TATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATATATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATATATATATATATATA,NC_000018.10:12870441:TATATATATATATATATATATA:TATATATATATATATATATATATATATATA
Gene:: PTPN2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TATATATA=0./0 (ALFA)
HGVS:: NC_000018.10:g.12870442TA[4], NC_000018.10:g.12870442TA[5], NC_000018.10:g.12870442TA[6], NC_000018.10:g.12870442TA[7], NC_000018.10:g.12870442TA[8], NC_000018.10:g.12870442TA[9], NC_000018.10:g.12870442TA[10], NC_000018.10:g.12870442TA[12], NC_000018.10:g.12870442TA[13], NC_000018.10:g.12870442TA[14], NC_000018.10:g.12870442TA[15], NC_000018.9:g.12870441TA[4], NC_000018.9:g.12870441TA[5], NC_000018.9:g.12870441TA[6], NC_000018.9:g.12870441TA[7], NC_000018.9:g.12870441TA[8], NC_000018.9:g.12870441TA[9], NC_000018.9:g.12870441TA[10], NC_000018.9:g.12870441TA[12], NC_000018.9:g.12870441TA[13], NC_000018.9:g.12870441TA[14], NC_000018.9:g.12870441TA[15], NG_029116.1:g.18873TA[4], NG_029116.1:g.18873TA[5], NG_029116.1:g.18873TA[6], NG_029116.1:g.18873TA[7], NG_029116.1:g.18873TA[8], NG_029116.1:g.18873TA[9], NG_029116.1:g.18873TA[10], NG_029116.1:g.18873TA[12], NG_029116.1:g.18873TA[13], NG_029116.1:g.18873TA[14], NG_029116.1:g.18873TA[15]

Select item 149140454118.

rs1491404541 [Homo sapiens]

Variant type:: DELINS
Alleles:: GT>- [Show Flanks]
Chromosome:: 18:12870393 (GRCh38)
18:12870392 (GRCh37)
Canonical SPDI:: NC_000018.10:12870391:TGT:T
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.00008/1 (ALFA)
-=0.00052/8 (TOMMO)
-=0.00085/55 (GnomAD)
HGVS:: NC_000018.10:g.12870393_12870394del, NC_000018.9:g.12870392_12870393del, NG_029116.1:g.18943_18944del

Select item 149140002519.

rs1491400025 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->G [Show Flanks]
Chromosome:: 18:12870509 (GRCh38)
18:12870509 (GRCh37)
Canonical SPDI:: NC_000018.10:12870509:G:GG
Gene:: PTPN2 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: GG=0./0 (ALFA)
G=0.00002/1 (GnomAD)
HGVS:: NC_000018.10:g.12870510dup, NC_000018.9:g.12870509dup, NG_029116.1:g.18826dup

Select item 149139974520.

rs1491399745 has merged into rs34452712 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAAAAAA>-,AAA,AAAA,AAAAA,AAAAAA,AAAAAAA,AAAAAAAAA,AAAAAAAAAA,AAAAAAAAAAA,AAAAAAAAAAAA [Show Flanks]
Chromosome:: 18:12864206 (GRCh38)
18:12864205 (GRCh37)
Canonical SPDI:: NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA,NC_000018.10:12864195:AAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAA
Gene:: PTPN2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,upstream_transcript_variant,intron_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAAAAAAAAAAA=0./0 (ALFA)
-=0.11/424 (ALSPAC)
A=0.1921/962 (1000Genomes)
HGVS:: NC_000018.10:g.12864206_12864213del, NC_000018.10:g.12864209_12864213del, NC_000018.10:g.12864210_12864213del, NC_000018.10:g.12864211_12864213del, NC_000018.10:g.12864212_12864213del, NC_000018.10:g.12864213del, NC_000018.10:g.12864213dup, NC_000018.10:g.12864212_12864213dup, NC_000018.10:g.12864211_12864213dup, NC_000018.10:g.12864210_12864213dup, NC_000018.9:g.12864205_12864212del, NC_000018.9:g.12864208_12864212del, NC_000018.9:g.12864209_12864212del, NC_000018.9:g.12864210_12864212del, NC_000018.9:g.12864211_12864212del, NC_000018.9:g.12864212del, NC_000018.9:g.12864212dup, NC_000018.9:g.12864211_12864212dup, NC_000018.9:g.12864210_12864212dup, NC_000018.9:g.12864209_12864212dup, NG_029116.1:g.25133_25140del, NG_029116.1:g.25136_25140del, NG_029116.1:g.25137_25140del, NG_029116.1:g.25138_25140del, NG_029116.1:g.25139_25140del, NG_029116.1:g.25140del, NG_029116.1:g.25140dup, NG_029116.1:g.25139_25140dup, NG_029116.1:g.25138_25140dup, NG_029116.1:g.25137_25140dup, XM_024451229.2:c.-791_-784del, XM_024451229.2:c.-788_-784del, XM_024451229.2:c.-787_-784del, XM_024451229.2:c.-786_-784del, XM_024451229.2:c.-785_-784del, XM_024451229.2:c.-784del, XM_024451229.2:c.-784dup, XM_024451229.2:c.-785_-784dup, XM_024451229.2:c.-786_-784dup, XM_024451229.2:c.-787_-784dup

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