SNP Links for Gene (Select 58986) - SNP

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Select item 14915264131.

rs1491526413 [Homo sapiens]

Variant type:: DEL
Alleles:: CC>- [Show Flanks]
Chromosome:: 16:373828 (GRCh38)
16:423828 (GRCh37)
Canonical SPDI:: NC_000016.10:373827:CC:
Gene:: PGAP6 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000035/1 (TOMMO)
HGVS:: NC_000016.10:g.373828_373829del, NC_000016.9:g.423828_423829del, NG_052909.1:g.1741_1742del

Select item 14914715882.

rs1491471588 [Homo sapiens]

Variant type:: DEL
Alleles:: AG>- [Show Flanks]
Chromosome:: 16:382091 (GRCh38)
16:432091 (GRCh37)
Canonical SPDI:: NC_000016.10:382090:AG:
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,genic_upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: -=0.00008/1 (ALFA)
HGVS:: NC_000016.10:g.382091_382092del, NC_000016.9:g.432091_432092del

Select item 14914319453.

rs1491431945 [Homo sapiens]

Variant type:: DEL
Alleles:: AG>- [Show Flanks]
Chromosome:: 16:381890 (GRCh38)
16:431890 (GRCh37)
Canonical SPDI:: NC_000016.10:381889:AG:
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: 2KB_upstream_variant,5_prime_UTR_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency
MAF:: -=0.000038/5 (GnomAD)
HGVS:: NC_000016.10:g.381890_381891del, NC_000016.9:g.431890_431891del, NM_021259.3:c.-70_-69del, NM_021259.2:c.-70_-69del

Select item 14912739834.

rs1491273983 has merged into rs3041094 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAAA>-,AAA,AAAA,AAAAAA,AAAAAAA,AAAAAAAA,AAAAAAAAA [Show Flanks]
Chromosome:: 16:383209 (GRCh38)
16:433209 (GRCh37)
Canonical SPDI:: NC_000016.10:383199:AAAAAAAAAAAAAA:AAAAAAAAA,NC_000016.10:383199:AAAAAAAAAAAAAA:AAAAAAAAAAAA,NC_000016.10:383199:AAAAAAAAAAAAAA:AAAAAAAAAAAAA,NC_000016.10:383199:AAAAAAAAAAAAAA:AAAAAAAAAAAAAAA,NC_000016.10:383199:AAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA,NC_000016.10:383199:AAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA,NC_000016.10:383199:AAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAAA=0./0 (ALFA)
HGVS:: NC_000016.10:g.383209_383213del, NC_000016.10:g.383212_383213del, NC_000016.10:g.383213del, NC_000016.10:g.383213dup, NC_000016.10:g.383212_383213dup, NC_000016.10:g.383211_383213dup, NC_000016.10:g.383210_383213dup, NC_000016.9:g.433209_433213del, NC_000016.9:g.433212_433213del, NC_000016.9:g.433213del, NC_000016.9:g.433213dup, NC_000016.9:g.433212_433213dup, NC_000016.9:g.433211_433213dup, NC_000016.9:g.433210_433213dup

Select item 14911823685.

rs1491182368 has merged into rs909116095 [Homo sapiens]

Variant type:: DELINS
Alleles:: G>-,GG,GGG,GGGG,GGGGG,GGGGGG [Show Flanks]
Chromosome:: 16:382092 (GRCh38)
16:432092 (GRCh37)
Canonical SPDI:: NC_000016.10:382091:GGGGGG:GGGGG,NC_000016.10:382091:GGGGGG:GGGGGGG,NC_000016.10:382091:GGGGGG:GGGGGGGG,NC_000016.10:382091:GGGGGG:GGGGGGGGG,NC_000016.10:382091:GGGGGG:GGGGGGGGGG,NC_000016.10:382091:GGGGGG:GGGGGGGGGGG
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: 2KB_upstream_variant,intron_variant,upstream_transcript_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGGGGGG=0./0 (ALFA)
-=0.000004/1 (TOPMED)
GGG=0.03367/20 (NorthernSweden)
HGVS:: NC_000016.10:g.382097del, NC_000016.10:g.382097dup, NC_000016.10:g.382096_382097dup, NC_000016.10:g.382095_382097dup, NC_000016.10:g.382094_382097dup, NC_000016.10:g.382093_382097dup, NC_000016.9:g.432097del, NC_000016.9:g.432097dup, NC_000016.9:g.432096_432097dup, NC_000016.9:g.432095_432097dup, NC_000016.9:g.432094_432097dup, NC_000016.9:g.432093_432097dup

Select item 14911600736.

rs1491160073 [Homo sapiens]

Variant type:: INS
Alleles:: ->G [Show Flanks]
Chromosome:: 16:383200 (GRCh38)
16:433201 (GRCh37)
Canonical SPDI:: NC_000016.10:383200::G
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0.00007/1 (ALFA)
G=0.00001/1 (GnomAD)
HGVS:: NC_000016.10:g.383200_383201insG, NC_000016.9:g.433200_433201insG

Select item 14910066447.

rs1491006644 has merged into rs541482913 [Homo sapiens]

Variant type:: DELINS
Alleles:: GG>-,G,GGG,GGGG,GGGGG,GGGGGG [Show Flanks]
Chromosome:: 16:382051 (GRCh38)
16:432051 (GRCh37)
Canonical SPDI:: NC_000016.10:382044:GGGGGGGG:GGGGGG,NC_000016.10:382044:GGGGGGGG:GGGGGGG,NC_000016.10:382044:GGGGGGGG:GGGGGGGGG,NC_000016.10:382044:GGGGGGGG:GGGGGGGGGG,NC_000016.10:382044:GGGGGGGG:GGGGGGGGGGG,NC_000016.10:382044:GGGGGGGG:GGGGGGGGGGGG
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGGGGGGGGG=0./0 (ALFA)
-=0.2903/1428 (1000Genomes)
HGVS:: NC_000016.10:g.382051_382052del, NC_000016.10:g.382052del, NC_000016.10:g.382052dup, NC_000016.10:g.382051_382052dup, NC_000016.10:g.382050_382052dup, NC_000016.10:g.382049_382052dup, NC_000016.9:g.432051_432052del, NC_000016.9:g.432052del, NC_000016.9:g.432052dup, NC_000016.9:g.432051_432052dup, NC_000016.9:g.432050_432052dup, NC_000016.9:g.432049_432052dup

Select item 14909955368.

rs1490995536 has merged into rs373943287 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTT>-,T,TT,TTT,TTTTT,TTTTTT,TTTTTTT,TTTTTTTT [Show Flanks]
Chromosome:: 16:375545 (GRCh38)
16:425545 (GRCh37)
Canonical SPDI:: NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTT,NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT,NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT,NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTT,NC_000016.10:375533:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTT
Gene:: PGAP6 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTTTT=0./0 (ALFA)
HGVS:: NC_000016.10:g.375545_375548del, NC_000016.10:g.375546_375548del, NC_000016.10:g.375547_375548del, NC_000016.10:g.375548del, NC_000016.10:g.375548dup, NC_000016.10:g.375547_375548dup, NC_000016.10:g.375546_375548dup, NC_000016.10:g.375545_375548dup, NC_000016.9:g.425545_425548del, NC_000016.9:g.425546_425548del, NC_000016.9:g.425547_425548del, NC_000016.9:g.425548del, NC_000016.9:g.425548dup, NC_000016.9:g.425547_425548dup, NC_000016.9:g.425546_425548dup, NC_000016.9:g.425545_425548dup, NG_052909.1:g.33_36del, NG_052909.1:g.34_36del, NG_052909.1:g.35_36del, NG_052909.1:g.36del, NG_052909.1:g.36dup, NG_052909.1:g.35_36dup, NG_052909.1:g.34_36dup, NG_052909.1:g.33_36dup

Select item 14908204479.

rs1490820447 [Homo sapiens]

Variant type:: DEL
Alleles:: CACC>- [Show Flanks]
Chromosome:: 16:383253 (GRCh38)
16:433253 (GRCh37)
Canonical SPDI:: NC_000016.10:383252:CACC:
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: -=0.0002/1 (ALFA)
-=0.0002/1 (Estonian)
HGVS:: NC_000016.10:g.383253_383256del, NC_000016.9:g.433253_433256del

Select item 149073454610.

rs1490734546 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:380513 (GRCh38)
16:430513 (GRCh37)
Canonical SPDI:: NC_000016.10:380512:T:C
Gene:: PGAP6 (Varview), LOC100134368 (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)
HGVS:: NC_000016.10:g.380513T>C, NC_000016.9:g.430513T>C

Select item 149071184911.

rs1490711849 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->TCCCCTTCTGCCCCGGCGCCCC [Show Flanks]
Chromosome:: 16:370445 (GRCh38)
16:420446 (GRCh37)
Canonical SPDI:: NC_000016.10:370445:GCCCCTCCCCTTCTGCCCCGGCGCCCC:GCCCCTCCCCTTCTGCCCCGGCGCCCCTCCCCTTCTGCCCCGGCGCCCC
Gene:: MRPL28 (Varview), PGAP6 (Varview)
Functional Consequence:: downstream_transcript_variant,500B_downstream_variant,5_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: GCCCCTCCCCTTCTGCCCCGGCGCCCCTCCCCTTCTGCCCCGGCGCCCC=0./0 (ALFA)
HGVS:: NC_000016.10:g.370451_370472dup, NC_000016.9:g.420451_420472dup, NG_052909.1:g.5103_5124dup, XM_005255041.3:c.-31_-10dup, XM_005255041.2:c.-31_-10dup, XM_005255041.1:c.-31_-10dup

Select item 149062308512.

rs1490623085 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:372477 (GRCh38)
16:422477 (GRCh37)
Canonical SPDI:: NC_000016.10:372476:T:C
Gene:: MRPL28 (Varview), PGAP6 (Varview)
Functional Consequence:: 2KB_upstream_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.372477T>C, NC_000016.9:g.422477T>C, NG_052909.1:g.3093A>G

Select item 149050610413.

rs1490506104 [Homo sapiens]

Variant type:: DELINS
Alleles:: TT>- [Show Flanks]
Chromosome:: 16:370789 (GRCh38)
16:420789 (GRCh37)
Canonical SPDI:: NC_000016.10:370787:TTT:T
Gene:: MRPL28 (Varview), PGAP6 (Varview)
Functional Consequence:: 2KB_upstream_variant,3_prime_UTR_variant,upstream_transcript_variant
HGVS:: NC_000016.10:g.370789_370790del, NC_000016.9:g.420789_420790del, NG_052909.1:g.4781_4782del, NM_021259.3:c.*1198_*1199del, NM_021259.2:c.*1198_*1199del, XM_047434413.1:c.*1198_*1199del

Select item 149004148914.

rs1490041489 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,T [Show Flanks]
Chromosome:: 16:376181 (GRCh38)
16:426181 (GRCh37)
Canonical SPDI:: NC_000016.10:376180:G:A,NC_000016.10:376180:G:T
Gene:: PGAP6 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
T=0.000004/1 (GnomAD_exomes)
A=0.000004/1 (TOPMED)
A=0.000014/2 (GnomAD)
HGVS:: NC_000016.10:g.376181G>A, NC_000016.10:g.376181G>T, NC_000016.9:g.426181G>A, NC_000016.9:g.426181G>T, NM_021259.3:c.1179C>T, NM_021259.3:c.1179C>A, NM_021259.2:c.1179C>T, NM_021259.2:c.1179C>A, XM_047434413.1:c.600C>T, XM_047434413.1:c.600C>A

Select item 148993188315.

rs1489931883 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 16:379478 (GRCh38)
16:429478 (GRCh37)
Canonical SPDI:: NC_000016.10:379477:G:A
Gene:: PGAP6 (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_000016.10:g.379478G>A, NC_000016.9:g.429478G>A

Select item 148978421316.

rs1489784213 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 16:378468 (GRCh38)
16:428468 (GRCh37)
Canonical SPDI:: NC_000016.10:378467:C:G,NC_000016.10:378467:C:T
Gene:: PGAP6 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
G=0.00276/8 (KOREAN)
HGVS:: NC_000016.10:g.378468C>G, NC_000016.10:g.378468C>T, NC_000016.9:g.428468C>G, NC_000016.9:g.428468C>T

Select item 148975238117.

rs1489752381 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 16:379118 (GRCh38)
16:429118 (GRCh37)
Canonical SPDI:: NC_000016.10:379117:A:G
Gene:: PGAP6 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
G=0.000015/4 (TOPMED)
HGVS:: NC_000016.10:g.379118A>G, NC_000016.9:g.429118A>G

Select item 148939043618.

rs1489390436 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:379753 (GRCh38)
16:429753 (GRCh37)
Canonical SPDI:: NC_000016.10:379752:C:T
Gene:: PGAP6 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.379753C>T, NC_000016.9:g.429753C>T

Select item 148934410219.

rs1489344102 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 16:381138 (GRCh38)
16:431138 (GRCh37)
Canonical SPDI:: NC_000016.10:381137:G:A
Gene:: PGAP6 (Varview), LOC100134368 (Varview)
Functional Consequence:: 2KB_upstream_variant,intron_variant,upstream_transcript_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_000016.10:g.381138G>A, NC_000016.9:g.431138G>A

Select item 148932644520.

rs1489326445 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 16:378899 (GRCh38)
16:428899 (GRCh37)
Canonical SPDI:: NC_000016.10:378898:G:A
Gene:: PGAP6 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000008/2 (TOPMED)
A=0.125/1 (KOREAN)
HGVS:: NC_000016.10:g.378899G>A, NC_000016.9:g.428899G>A

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