SNP Links for Gene (Select 3059) - SNP

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Select item 14914826581.

rs1491482658 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->T,TTTT,TTTTT,TTTTTT,TTTTTTT [Show Flanks]
Chromosome:: 3:121655460 (GRCh38)
3:121374308 (GRCh37)
Canonical SPDI:: NC_000003.12:121655460:T:TT,NC_000003.12:121655460:T:TTTTT,NC_000003.12:121655460:T:TTTTTT,NC_000003.12:121655460:T:TTTTTTT,NC_000003.12:121655460:T:TTTTTTTT
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTT=0./0 (ALFA)
TTTTT=0.00056/1 (Korea1K)
HGVS:: NC_000003.12:g.121655461dup, NC_000003.12:g.121655461_121655462insTTTT, NC_000003.12:g.121655461_121655462insTTTTT, NC_000003.12:g.121655461_121655462insTTTTTT, NC_000003.12:g.121655461_121655462insTTTTTTT, NC_000003.11:g.121374308dup, NC_000003.11:g.121374308_121374309insTTTT, NC_000003.11:g.121374308_121374309insTTTTT, NC_000003.11:g.121374308_121374309insTTTTTT, NC_000003.11:g.121374308_121374309insTTTTTTT, NG_045952.1:g.244dup, NG_045952.1:g.244_245insAAAA, NG_045952.1:g.244_245insAAAAA, NG_045952.1:g.244_245insAAAAAA, NG_045952.1:g.244_245insAAAAAAA

Select item 14914621332.

rs1491462133 [Homo sapiens]

Variant type:: DELINS
Alleles:: CT>- [Show Flanks]
Chromosome:: 3:121655462 (GRCh38)
3:121374309 (GRCh37)
Canonical SPDI:: NC_000003.12:121655459:CTCT:CT
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: CTCT=0./0 (ALFA)
HGVS:: NC_000003.12:g.121655460CT[1], NC_000003.11:g.121374307CT[1], NG_045952.1:g.242AG[1]

Select item 14914118483.

rs1491411848 has merged into rs34223359 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAAAAAAAAA>-,AAAAAAAAA,AAAAAAAAAA,AAAAAAAAAAAA,AAAAAAAAAAAAA,AAAAAAAAAAAAAA,AAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAA [Show Flanks]
Chromosome:: 3:121642309 (GRCh38)
3:121361156 (GRCh37)
Canonical SPDI:: NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAA,NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA,NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA,NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA,NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA,NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAA,NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA,NC_000003.12:121642303:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAAAAAA=0./0 (ALFA)
A=0.3868/1937 (1000Genomes)
HGVS:: NC_000003.12:g.121642309_121642319del, NC_000003.12:g.121642318_121642319del, NC_000003.12:g.121642319del, NC_000003.12:g.121642319dup, NC_000003.12:g.121642318_121642319dup, NC_000003.12:g.121642317_121642319dup, NC_000003.12:g.121642316_121642319dup, NC_000003.12:g.121642315_121642319dup, NC_000003.11:g.121361156_121361166del, NC_000003.11:g.121361165_121361166del, NC_000003.11:g.121361166del, NC_000003.11:g.121361166dup, NC_000003.11:g.121361165_121361166dup, NC_000003.11:g.121361164_121361166dup, NC_000003.11:g.121361163_121361166dup, NC_000003.11:g.121361162_121361166dup

Select item 14913902194.

rs1491390219 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->CT,CTCT,CTCTCTCT,CTCTCTCTCTCT [Show Flanks]
Chromosome:: 3:121635235 (GRCh38)
3:121354083 (GRCh37)
Canonical SPDI:: NC_000003.12:121635235:T:TCT,NC_000003.12:121635235:T:TCTCT,NC_000003.12:121635235:T:TCTCTCTCT,NC_000003.12:121635235:T:TCTCTCTCTCTCT
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: TCTCT=0./0 (ALFA)
HGVS:: NC_000003.12:g.121635236_121635237insCT, NC_000003.12:g.121635236_121635237insCTCT, NC_000003.12:g.121635237CT[4], NC_000003.12:g.121635237CT[6], NC_000003.11:g.121354083_121354084insCT, NC_000003.11:g.121354083_121354084insCTCT, NC_000003.11:g.121354084CT[4], NC_000003.11:g.121354084CT[6]

Select item 14913773225.

rs1491377322 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->T,TATATTACATAGTATATTACATAGT [Show Flanks]
Chromosome:: 3:121646399 (GRCh38)
3:121365247 (GRCh37)
Canonical SPDI:: NC_000003.12:121646399:T:TT,NC_000003.12:121646399:T:TTATATTACATAGTATATTACATAGT
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTATATTACATAGTATATTACATAGT=0./0 (ALFA)
TTATATTACATAGTATATTACATAG=0.000004/1 (TOPMED)
TTATATTACATAGTATATTACATAG=0.000012/1 (GnomAD)
HGVS:: NC_000003.12:g.121646400dup, NC_000003.12:g.121646400_121646401insTATATTACATAGTATATTACATAGT, NC_000003.11:g.121365247dup, NC_000003.11:g.121365247_121365248insTATATTACATAGTATATTACATAGT

Select item 14913631246.

rs1491363124 has merged into rs1214658906 [Homo sapiens]

Variant type:: DELINS
Alleles:: ATAT>-,AT [Show Flanks]
Chromosome:: 3:121646401 (GRCh38)
3:121365248 (GRCh37)
Canonical SPDI:: NC_000003.12:121646398:ATATAT:AT,NC_000003.12:121646398:ATATAT:ATAT
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AT=0./0 (ALFA)
-=0.000008/2 (TOPMED)
HGVS:: NC_000003.12:g.121646399AT[1], NC_000003.12:g.121646399AT[2], NC_000003.11:g.121365246AT[1], NC_000003.11:g.121365246AT[2]

Select item 14912629747.

rs1491262974 has merged into rs56054727 [Homo sapiens]

Variant type:: DELINS
Alleles:: ACACAC>-,AC,ACAC,ACACACAC,ACACACACAC [Show Flanks]
Chromosome:: 3:121639019 (GRCh38)
3:121357866 (GRCh37)
Canonical SPDI:: NC_000003.12:121639010:ACACACACACACAC:ACACACAC,NC_000003.12:121639010:ACACACACACACAC:ACACACACAC,NC_000003.12:121639010:ACACACACACACAC:ACACACACACAC,NC_000003.12:121639010:ACACACACACACAC:ACACACACACACACAC,NC_000003.12:121639010:ACACACACACACAC:ACACACACACACACACAC
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: ACACACACAC=0./0 (ALFA)
-=0.16658/642 (ALSPAC)
AC=0.225/9 (GENOME_DK)
AC=0.26667/160 (NorthernSweden)
AC=0.36462/1826 (1000Genomes)
AC=0.40296/6754 (TOMMO)
HGVS:: NC_000003.12:g.121639011AC[4], NC_000003.12:g.121639011AC[5], NC_000003.12:g.121639011AC[6], NC_000003.12:g.121639011AC[8], NC_000003.12:g.121639011AC[9], NC_000003.11:g.121357858AC[4], NC_000003.11:g.121357858AC[5], NC_000003.11:g.121357858AC[6], NC_000003.11:g.121357858AC[8], NC_000003.11:g.121357858AC[9]

Select item 14912176558.

rs1491217655 [Homo sapiens]

Variant type:: DELINS
Alleles:: TT>- [Show Flanks]
Chromosome:: 3:121635237 (GRCh38)
3:121354084 (GRCh37)
Canonical SPDI:: NC_000003.12:121635234:TTTT:TT
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTT=0.00031/5 (ALFA)
-=0.00031/2 (1000Genomes)
-=0.00036/33 (GnomAD)
HGVS:: NC_000003.12:g.121635237_121635238del, NC_000003.11:g.121354084_121354085del

Select item 14910348969.

rs1491034896 has merged into rs546867872 [Homo sapiens]

Variant type:: DELINS
Alleles:: TATGTAATATATTACTATGTAATATATTAC>-,TATGTAATATATTAC,TATGTAATATATTACTATGTAATATATTACTATGTAATATATTAC [Show Flanks]
Chromosome:: 3:121646378 (GRCh38)
3:121365225 (GRCh37)
Canonical SPDI:: NC_000003.12:121646371:TATTACTATGTAATATATTACTATGTAATATATTAC:TATTAC,NC_000003.12:121646371:TATTACTATGTAATATATTACTATGTAATATATTAC:TATTACTATGTAATATATTAC,NC_000003.12:121646371:TATTACTATGTAATATATTACTATGTAATATATTAC:TATTACTATGTAATATATTACTATGTAATATATTACTATGTAATATATTAC
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TATTACTATGTAATATATTAC=0./0 (ALFA)
-=0.06635/569 (TOMMO)
-=0.08926/447 (1000Genomes)
-=0.09305/91 (Korea1K)
HGVS:: NC_000003.12:g.121646378_121646407del, NC_000003.12:g.121646378TATGTAATATATTAC[1], NC_000003.12:g.121646378TATGTAATATATTAC[3], NC_000003.11:g.121365225_121365254del, NC_000003.11:g.121365225TATGTAATATATTAC[1], NC_000003.11:g.121365225TATGTAATATATTAC[3]

Select item 149092642710.

rs1490926427 has merged into rs202153876 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTT>-,TTTTTT [Show Flanks]
Chromosome:: 3:121639530 (GRCh38)
3:121358377 (GRCh37)
Canonical SPDI:: NC_000003.12:121639526:TTTTTT:TTT,NC_000003.12:121639526:TTTTTT:TTTTTTTTT
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTT=0./0 (ALFA)
-=0.00055/1 (Korea1K)
HGVS:: NC_000003.12:g.121639530_121639532del, NC_000003.12:g.121639530_121639532dup, NC_000003.11:g.121358377_121358379del, NC_000003.11:g.121358377_121358379dup

Select item 149079915911.

rs1490799159 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 3:121645855 (GRCh38)
3:121364702 (GRCh37)
Canonical SPDI:: NC_000003.12:121645854:T:C
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000015/2 (GnomAD)
HGVS:: NC_000003.12:g.121645855T>C, NC_000003.11:g.121364702T>C

Select item 149063200412.

rs1490632004 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C,G [Show Flanks]
Chromosome:: 3:121646441 (GRCh38)
3:121365288 (GRCh37)
Canonical SPDI:: NC_000003.12:121646440:T:C,NC_000003.12:121646440:T:G
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
HGVS:: NC_000003.12:g.121646441T>C, NC_000003.12:g.121646441T>G, NC_000003.11:g.121365288T>C, NC_000003.11:g.121365288T>G

Select item 149060516113.

rs1490605161 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 3:121632195 (GRCh38)
3:121351042 (GRCh37)
Canonical SPDI:: NC_000003.12:121632194:A:G
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency
MAF:: G=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000003.12:g.121632195A>G, NC_000003.11:g.121351042A>G

Select item 149054148914.

rs1490541489 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 3:121655507 (GRCh38)
3:121374354 (GRCh37)
Canonical SPDI:: NC_000003.12:121655506:G:T
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.00051/6 (ALFA)
T=0.0005/14 (TOMMO)
T=0.03082/90 (KOREAN)
HGVS:: NC_000003.12:g.121655507G>T, NC_000003.11:g.121374354G>T, NG_045952.1:g.198C>A

Select item 149052576015.

rs1490525760 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 3:121654465 (GRCh38)
3:121373312 (GRCh37)
Canonical SPDI:: NC_000003.12:121654464:C:G,NC_000003.12:121654464:C:T
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
HGVS:: NC_000003.12:g.121654465C>G, NC_000003.12:g.121654465C>T, NC_000003.11:g.121373312C>G, NC_000003.11:g.121373312C>T

Select item 149049860216.

rs1490498602 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 3:121642961 (GRCh38)
3:121361808 (GRCh37)
Canonical SPDI:: NC_000003.12:121642960:A:G
Gene:: HCLS1 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
HGVS:: NC_000003.12:g.121642961A>G, NC_000003.11:g.121361808A>G, NM_005335.6:c.420T>C, NM_005335.5:c.420T>C, NM_005335.4:c.420T>C, NM_001292041.2:c.420T>C, NM_001292041.1:c.420T>C

Select item 149047303317.

rs1490473033 [Homo sapiens]

Variant type:: DELINS
Alleles:: CGGGA>- [Show Flanks]
Chromosome:: 3:121640834 (GRCh38)
3:121359681 (GRCh37)
Canonical SPDI:: NC_000003.12:121640829:GGGACGGGA:GGGA
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGGA=0./0 (ALFA)
-=0.0002/3 (TOMMO)
-=0.00113/2 (Korea1K)
HGVS:: NC_000003.12:g.121640834_121640838del, NC_000003.11:g.121359681_121359685del

Select item 149035910218.

rs1490359102 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 3:121631606 (GRCh38)
3:121350453 (GRCh37)
Canonical SPDI:: NC_000003.12:121631605:T:A
Gene:: HCLS1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000008/2 (TOPMED)
A=0.000014/2 (GnomAD)
HGVS:: NC_000003.12:g.121631606T>A, NC_000003.11:g.121350453T>A, NM_005335.6:c.*240A>T, NM_005335.5:c.*240A>T, NM_005335.4:c.*240A>T, NM_001292041.2:c.*240A>T, NM_001292041.1:c.*240A>T

Select item 149023015519.

rs1490230155 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A,C [Show Flanks]
Chromosome:: 3:121646290 (GRCh38)
3:121365137 (GRCh37)
Canonical SPDI:: NC_000003.12:121646289:T:A,NC_000003.12:121646289:T:C
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
A=0.00006/1 (TOMMO)
A=0.02896/19 (KOREAN)
HGVS:: NC_000003.12:g.121646290T>A, NC_000003.12:g.121646290T>C, NC_000003.11:g.121365137T>A, NC_000003.11:g.121365137T>C

Select item 149020794520.

rs1490207945 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 3:121632290 (GRCh38)
3:121351137 (GRCh37)
Canonical SPDI:: NC_000003.12:121632289:T:C
Gene:: HCLS1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000008/2 (TOPMED)
HGVS:: NC_000003.12:g.121632290T>C, NC_000003.11:g.121351137T>C

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