SNP Links for Gene (Select 3060) - SNP

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Select item 14915336861.

rs1491533686 has merged into rs71157609 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTTTT>-,T,TT,TTT,TTTT,TTTTT,TTTTTTT,TTTTTTTT,TTTTTTTTT,TTTTTTTTTT,TTTTTTTTTTT [Show Flanks]
Chromosome:: 17:42186834 (GRCh38)
17:40338852 (GRCh37)
Canonical SPDI:: NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTT,NC_000017.11:42186821:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTT
Gene:: HCRT (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTTT=0./0 (ALFA)
-=0.000004/1 (TOPMED)
HGVS:: NC_000017.11:g.42186834_42186839del, NC_000017.11:g.42186835_42186839del, NC_000017.11:g.42186836_42186839del, NC_000017.11:g.42186837_42186839del, NC_000017.11:g.42186838_42186839del, NC_000017.11:g.42186839del, NC_000017.11:g.42186839dup, NC_000017.11:g.42186838_42186839dup, NC_000017.11:g.42186837_42186839dup, NC_000017.11:g.42186836_42186839dup, NC_000017.11:g.42186835_42186839dup, NC_000017.10:g.40338852_40338857del, NC_000017.10:g.40338853_40338857del, NC_000017.10:g.40338854_40338857del, NC_000017.10:g.40338855_40338857del, NC_000017.10:g.40338856_40338857del, NC_000017.10:g.40338857del, NC_000017.10:g.40338857dup, NC_000017.10:g.40338856_40338857dup, NC_000017.10:g.40338855_40338857dup, NC_000017.10:g.40338854_40338857dup, NC_000017.10:g.40338853_40338857dup, NG_011448.1:g.3626_3631del, NG_011448.1:g.3627_3631del, NG_011448.1:g.3628_3631del, NG_011448.1:g.3629_3631del, NG_011448.1:g.3630_3631del, NG_011448.1:g.3631del, NG_011448.1:g.3631dup, NG_011448.1:g.3630_3631dup, NG_011448.1:g.3629_3631dup, NG_011448.1:g.3628_3631dup, NG_011448.1:g.3627_3631dup

Select item 14910547992.

rs1491054799 [Homo sapiens]

Variant type:: DELINS
Alleles:: CT>- [Show Flanks]
Chromosome:: 17:42186476 (GRCh38)
17:40338494 (GRCh37)
Canonical SPDI:: NC_000017.11:42186474:TCT:T
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
-=0.0002/5 (TOMMO)
HGVS:: NC_000017.11:g.42186476_42186477del, NC_000017.10:g.40338494_40338495del, NG_011448.1:g.3977_3978del

Select item 14901809813.

rs1490180981 [Homo sapiens]

Variant type:: DELINS
Alleles:: CT>- [Show Flanks]
Chromosome:: 17:42186429 (GRCh38)
17:40338447 (GRCh37)
Canonical SPDI:: NC_000017.11:42186427:TCT:T
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
-=0.000004/1 (TOPMED)
HGVS:: NC_000017.11:g.42186429_42186430del, NC_000017.10:g.40338447_40338448del, NG_011448.1:g.4024_4025del

Select item 14890378304.

rs1489037830 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 17:42187144 (GRCh38)
17:40339162 (GRCh37)
Canonical SPDI:: NC_000017.11:42187143:T:C
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by cluster
MAF:: C=0.000008/1 (GnomAD)
HGVS:: NC_000017.11:g.42187144T>C, NC_000017.10:g.40339162T>C, NG_011448.1:g.3309A>G

Select item 14887137655.

rs1488713765 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 17:42186339 (GRCh38)
17:40338357 (GRCh37)
Canonical SPDI:: NC_000017.11:42186338:G:A
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: A=0.000084/1 (ALFA)
A=0.000008/2 (TOPMED)
HGVS:: NC_000017.11:g.42186339G>A, NC_000017.10:g.40338357G>A, NG_011448.1:g.4114C>T

Select item 14884957306.

rs1488495730 [Homo sapiens]

Variant type:: DELINS
Alleles:: TCTC>-,TCTCTC [Show Flanks]
Chromosome:: 17:42186446 (GRCh38)
17:40338464 (GRCh37)
Canonical SPDI:: NC_000017.11:42186439:TCTCTCTCTC:TCTCTC,NC_000017.11:42186439:TCTCTCTCTC:TCTCTCTCTCTC
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: TCTCTCTCTCTC=0./0 (ALFA)
-=0.000022/3 (GnomAD)
HGVS:: NC_000017.11:g.42186440TC[3], NC_000017.11:g.42186440TC[6], NC_000017.10:g.40338458TC[3], NC_000017.10:g.40338458TC[6], NG_011448.1:g.4004GA[3], NG_011448.1:g.4004GA[6]

Select item 14882742997.

rs1488274299 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 17:42185202 (GRCh38)
17:40337220 (GRCh37)
Canonical SPDI:: NC_000017.11:42185201:C:G
Gene:: HCRT (Varview)
Functional Consequence:: intron_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_000017.11:g.42185202C>G, NC_000017.10:g.40337220C>G, NG_011448.1:g.5251G>C

Select item 14878925688.

rs1487892568 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 17:42185529 (GRCh38)
17:40337547 (GRCh37)
Canonical SPDI:: NC_000017.11:42185528:G:C
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
HGVS:: NC_000017.11:g.42185529G>C, NC_000017.10:g.40337547G>C, NG_011448.1:g.4924C>G

Select item 14875675419.

rs1487567541 [Homo sapiens]

Variant type:: DEL
Alleles:: G>- [Show Flanks]
Chromosome:: 17:42186840 (GRCh38)
17:40338858 (GRCh37)
Canonical SPDI:: NC_000017.11:42186839:G:
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.000566/73 (GnomAD)
-=0.003017/84 (TOMMO)
HGVS:: NC_000017.11:g.42186840del, NC_000017.10:g.40338858del, NG_011448.1:g.3613del

Select item 148707938810.

rs1487079388 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 17:42185433 (GRCh38)
17:40337451 (GRCh37)
Canonical SPDI:: NC_000017.11:42185432:C:A,NC_000017.11:42185432:C:T
Gene:: HCRT (Varview)
Functional Consequence:: 5_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
HGVS:: NC_000017.11:g.42185433C>A, NC_000017.11:g.42185433C>T, NC_000017.10:g.40337451C>A, NC_000017.10:g.40337451C>T, NG_011448.1:g.5020G>T, NG_011448.1:g.5020G>A, NM_001524.1:c.-68G>T, NM_001524.1:c.-68G>A

Select item 148632271011.

rs1486322710 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->CGGC [Show Flanks]
Chromosome:: 17:42184208 (GRCh38)
17:40336227 (GRCh37)
Canonical SPDI:: NC_000017.11:42184208:CGGC:CGGCCGGC
Gene:: HCRT (Varview)
Functional Consequence:: frameshift_variant,coding_sequence_variant
Validated:: by frequency,by alfa
MAF:: CGGCCGGC=0./0 (ALFA)
CGGC=0.000004/1 (TOPMED)
HGVS:: NC_000017.11:g.42184209_42184212dup, NC_000017.10:g.40336227_40336230dup, NG_011448.1:g.6241_6244dup, NM_001524.1:c.338_341dup, NP_001515.1:p.Cys115fs

Select item 148604194412.

rs1486041944 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 17:42187265 (GRCh38)
17:40339283 (GRCh37)
Canonical SPDI:: NC_000017.11:42187264:A:G
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000015/4 (TOPMED)
HGVS:: NC_000017.11:g.42187265A>G, NC_000017.10:g.40339283A>G, NG_011448.1:g.3188T>C

Select item 148504271313.

rs1485042713 has merged into rs1203126506 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTT>-,T,TT,TTTT,TTTTT,TTTTTT [Show Flanks]
Chromosome:: 17:42186497 (GRCh38)
17:40338515 (GRCh37)
Canonical SPDI:: NC_000017.11:42186485:TTTTTTTTTTTTTT:TTTTTTTTTTT,NC_000017.11:42186485:TTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000017.11:42186485:TTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000017.11:42186485:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000017.11:42186485:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT,NC_000017.11:42186485:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT
Gene:: HCRT (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTT=0./0 (ALFA)
-=0.000008/2 (TOPMED)
T=0.000391/7 (TOMMO)
T=0.018114/116 (1000Genomes)
HGVS:: NC_000017.11:g.42186497_42186499del, NC_000017.11:g.42186498_42186499del, NC_000017.11:g.42186499del, NC_000017.11:g.42186499dup, NC_000017.11:g.42186498_42186499dup, NC_000017.11:g.42186497_42186499dup, NC_000017.10:g.40338515_40338517del, NC_000017.10:g.40338516_40338517del, NC_000017.10:g.40338517del, NC_000017.10:g.40338517dup, NC_000017.10:g.40338516_40338517dup, NC_000017.10:g.40338515_40338517dup, NG_011448.1:g.3965_3967del, NG_011448.1:g.3966_3967del, NG_011448.1:g.3967del, NG_011448.1:g.3967dup, NG_011448.1:g.3966_3967dup, NG_011448.1:g.3965_3967dup

Select item 148474722414.

rs1484747224 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 17:42184469 (GRCh38)
17:40336487 (GRCh37)
Canonical SPDI:: NC_000017.11:42184468:C:T
Gene:: HCRT (Varview)
Functional Consequence:: synonymous_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000005/1 (GnomAD_exomes)
T=0.000007/1 (GnomAD)
HGVS:: NC_000017.11:g.42184469C>T, NC_000017.10:g.40336487C>T, NG_011448.1:g.5984G>A, NM_001524.1:c.81G>A

Select item 148219444615.

rs1482194446 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 17:42184015 (GRCh38)
17:40336033 (GRCh37)
Canonical SPDI:: NC_000017.11:42184014:G:A
Gene:: HCRT (Varview)
Functional Consequence:: downstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000108/2 (ALFA)
A=0.000019/5 (TOPMED)
A=0.000021/3 (GnomAD)
A=0.000212/4 (TOMMO)
A=0.000223/1 (Estonian)
HGVS:: NC_000017.11:g.42184015G>A, NC_000017.10:g.40336033G>A, NG_011448.1:g.6438C>T

Select item 148003054016.

rs1480030540 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 17:42184326 (GRCh38)
17:40336344 (GRCh37)
Canonical SPDI:: NC_000017.11:42184325:C:T
Gene:: HCRT (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
HGVS:: NC_000017.11:g.42184326C>T, NC_000017.10:g.40336344C>T, NG_011448.1:g.6127G>A, NM_001524.1:c.224G>A, NP_001515.1:p.Gly75Asp

Select item 147974076117.

rs1479740761 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 17:42186881 (GRCh38)
17:40338899 (GRCh37)
Canonical SPDI:: NC_000017.11:42186880:G:A,NC_000017.11:42186880:G:C
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
HGVS:: NC_000017.11:g.42186881G>A, NC_000017.11:g.42186881G>C, NC_000017.10:g.40338899G>A, NC_000017.10:g.40338899G>C, NG_011448.1:g.3572C>T, NG_011448.1:g.3572C>G

Select item 147951594818.

rs1479515948 [Homo sapiens]

Variant type:: DELINS
Alleles:: ATC>- [Show Flanks]
Chromosome:: 17:42186133 (GRCh38)
17:40338151 (GRCh37)
Canonical SPDI:: NC_000017.11:42186130:TCATC:TC
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: TC=0./0 (ALFA)
HGVS:: NC_000017.11:g.42186133_42186135del, NC_000017.10:g.40338151_40338153del, NG_011448.1:g.4320_4322del

Select item 147909581619.

rs1479095816 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 17:42185988 (GRCh38)
17:40338006 (GRCh37)
Canonical SPDI:: NC_000017.11:42185987:A:T
Gene:: HCRT (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_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_000017.11:g.42185988A>T, NC_000017.10:g.40338006A>T, NG_011448.1:g.4465T>A

Select item 147859531220.

rs1478595312 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 17:42184392 (GRCh38)
17:40336410 (GRCh37)
Canonical SPDI:: NC_000017.11:42184391:A:C
Gene:: HCRT (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Validated:: by frequency
MAF:: C=0.000005/1 (GnomAD_exomes)
HGVS:: NC_000017.11:g.42184392A>C, NC_000017.10:g.40336410A>C, NG_011448.1:g.6061T>G, NM_001524.1:c.158T>G, NP_001515.1:p.Leu53Arg

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