SNP Links for Gene (Select 550) - SNP

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Select item 14913259671.

rs1491325967 has merged into rs551995892 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAA>-,A,AA,AAA,AAAAA,AAAAAA [Show Flanks]
Chromosome:: 2:74527699 (GRCh38)
2:74754826 (GRCh37)
Canonical SPDI:: NC_000002.12:74527691:AAAAAAAAAAA:AAAAAAA,NC_000002.12:74527691:AAAAAAAAAAA:AAAAAAAA,NC_000002.12:74527691:AAAAAAAAAAA:AAAAAAAAA,NC_000002.12:74527691:AAAAAAAAAAA:AAAAAAAAAA,NC_000002.12:74527691:AAAAAAAAAAA:AAAAAAAAAAAA,NC_000002.12:74527691:AAAAAAAAAAA:AAAAAAAAAAAAA
Gene:: AUP1 (Varview), HTRA2 (Varview), DQX1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAA=0./0 (ALFA)
A=0.02183/40 (Korea1K)
-=0.35988/122 (1000Genomes)
HGVS:: NC_000002.12:g.74527699_74527702del, NC_000002.12:g.74527700_74527702del, NC_000002.12:g.74527701_74527702del, NC_000002.12:g.74527702del, NC_000002.12:g.74527702dup, NC_000002.12:g.74527701_74527702dup, NC_000002.11:g.74754826_74754829del, NC_000002.11:g.74754827_74754829del, NC_000002.11:g.74754828_74754829del, NC_000002.11:g.74754829del, NC_000002.11:g.74754829dup, NC_000002.11:g.74754828_74754829dup, NG_012163.1:g.3295_3298del, NG_012163.1:g.3296_3298del, NG_012163.1:g.3297_3298del, NG_012163.1:g.3298del, NG_012163.1:g.3298dup, NG_012163.1:g.3297_3298dup, NG_033037.1:g.7153_7156del, NG_033037.1:g.7154_7156del, NG_033037.1:g.7155_7156del, NG_033037.1:g.7156del, NG_033037.1:g.7156dup, NG_033037.1:g.7155_7156dup

Select item 14908821162.

rs1490882116 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 2:74530832 (GRCh38)
2:74757959 (GRCh37)
Canonical SPDI:: NC_000002.12:74530831:G:A,NC_000002.12:74530831:G:C
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
HGVS:: NC_000002.12:g.74530832G>A, NC_000002.12:g.74530832G>C, NC_000002.11:g.74757959G>A, NC_000002.11:g.74757959G>C, NG_033047.1:g.28104C>T, NG_033047.1:g.28104C>G, NG_012163.1:g.6428G>A, NG_012163.1:g.6428G>C, NG_033037.1:g.4016C>T, NG_033037.1:g.4016C>G

Select item 14883703183.

rs1488370318 has merged into rs1218602292 [Homo sapiens]

Variant type:: DELINS
Alleles:: ACTGTCCGCCTGCTCGCGTCCT>-,ACTGTCCGCCTGCTCGCGTCCTACTGTCCGCCTGCTCGCGTCCT [Show Flanks]
Chromosome:: 2:74529935 (GRCh38)
2:74757062 (GRCh37)
Canonical SPDI:: NC_000002.12:74529926:CGCGTCCTACTGTCCGCCTGCTCGCGTCCT:CGCGTCCT,NC_000002.12:74529926:CGCGTCCTACTGTCCGCCTGCTCGCGTCCT:CGCGTCCTACTGTCCGCCTGCTCGCGTCCTACTGTCCGCCTGCTCGCGTCCT
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,non_coding_transcript_variant,genic_upstream_transcript_variant,5_prime_UTR_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CGCGTCCTACTGTCCGCCTGCTCGCGTCCTACTGTCCGCCTGCTCGCGTCCT=0./0 (ALFA)
-=0.000011/3 (TOPMED)
HGVS:: NC_000002.12:g.74529935_74529956del, NC_000002.12:g.74529935_74529956dup, NC_000002.11:g.74757062_74757083del, NC_000002.11:g.74757062_74757083dup, NG_012163.1:g.5531_5552del, NG_012163.1:g.5531_5552dup, NM_145074.2:c.-72_-51del, NM_145074.2:c.-72_-51dup, NR_135769.1:n.531_552del, NR_135769.1:n.531_552dup, NM_001321727.1:c.-72_-51del, NM_001321727.1:c.-72_-51dup, NM_001321728.1:c.-72_-51del, NM_001321728.1:c.-72_-51dup, NG_033037.1:g.4900_4921del, NG_033037.1:g.4900_4921dup

Select item 14880849564.

rs1488084956 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:74527063 (GRCh38)
2:74754190 (GRCh37)
Canonical SPDI:: NC_000002.12:74527062:A:G
Gene:: AUP1 (Varview), DQX1 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (GnomAD_exomes)
G=0.000015/4 (TOPMED)
G=0.000021/3 (GnomAD)
HGVS:: NC_000002.12:g.74527063A>G, NC_000002.11:g.74754190A>G, NG_012163.1:g.2659A>G, NG_033037.1:g.7785T>C, NR_126510.2:n.1213T>C, NR_126510.1:n.1404T>C, NM_181576.1:c.*14T>C

Select item 14879051725.

rs1487905172 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 2:74529626 (GRCh38)
2:74756753 (GRCh37)
Canonical SPDI:: NC_000002.12:74529625:C:G
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: coding_sequence_variant,genic_upstream_transcript_variant,5_prime_UTR_variant,upstream_transcript_variant,missense_variant,non_coding_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_000002.12:g.74529626C>G, NC_000002.11:g.74756753C>G, NG_012163.1:g.5222C>G, NM_145074.2:c.-381C>G, NR_135769.1:n.222C>G, NM_001321727.1:c.-381C>G, NM_001321728.1:c.-381C>G, NR_135772.1:n.222C>G, NR_135770.1:n.222C>G, NR_135771.1:n.222C>G, NG_033037.1:g.5222G>C, NM_181575.5:c.4G>C, NM_181575.4:c.4G>C, NM_181575.3:c.4G>C, NM_013247.4:c.-381C>G, NR_126511.2:n.81G>C, NR_126511.1:n.272G>C, NR_126510.2:n.81G>C, NR_126510.1:n.272G>C, NM_012103.2:c.4G>C, NM_181576.1:c.4G>C, NM_012103.1:c.4G>C, NP_853553.1:p.Glu2Gln

Select item 14863124626.

rs1486312462 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:74528182 (GRCh38)
2:74755309 (GRCh37)
Canonical SPDI:: NC_000002.12:74528181:G:A
Gene:: AUP1 (Varview), HTRA2 (Varview), DQX1 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_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_000002.12:g.74528182G>A, NC_000002.11:g.74755309G>A, NG_012163.1:g.3778G>A, NG_033037.1:g.6666C>T

Select item 14858771997.

rs1485877199 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 2:74527764 (GRCh38)
2:74754891 (GRCh37)
Canonical SPDI:: NC_000002.12:74527763:T:C
Gene:: AUP1 (Varview), HTRA2 (Varview), DQX1 (Varview)
Functional Consequence:: synonymous_variant,coding_sequence_variant,upstream_transcript_variant,2KB_upstream_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
HGVS:: NC_000002.12:g.74527764T>C, NC_000002.11:g.74754891T>C, NG_012163.1:g.3360T>C, NG_033037.1:g.7084A>G, NM_181575.5:c.813A>G, NM_181575.4:c.813A>G, NM_181575.3:c.813A>G, NR_126511.2:n.1086A>G, NR_126511.1:n.1277A>G, NR_126510.2:n.890A>G, NR_126510.1:n.1081A>G, NM_012103.2:c.1011A>G, NM_181576.1:c.813A>G, NM_012103.1:c.1011A>G

Select item 14856845048.

rs1485684504 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 2:74531652 (GRCh38)
2:74758779 (GRCh37)
Canonical SPDI:: NC_000002.12:74531651:C:T
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: coding_sequence_variant,upstream_transcript_variant,2KB_upstream_variant,missense_variant,non_coding_transcript_variant
Validated:: by frequency
MAF:: T=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000002.12:g.74531652C>T, NC_000002.11:g.74758779C>T, NG_033047.1:g.27284G>A, NG_012163.1:g.7248C>T, NM_013247.5:c.995C>T, NM_013247.4:c.995C>T, NM_145074.2:c.800C>T, NR_135769.1:n.1637C>T, NM_001321727.1:c.1025C>T, NM_001321728.1:c.995C>T, NR_135772.1:n.1069C>T, NR_135770.1:n.1065C>T, NR_135771.1:n.1049C>T, NG_033037.1:g.3196G>A, NP_037379.1:p.Ala332Val, NP_659540.1:p.Ala267Val, NP_001308656.1:p.Ala342Val, NP_001308657.1:p.Ala332Val

Select item 14846892379.

rs1484689237 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 2:74531331 (GRCh38)
2:74758458 (GRCh37)
Canonical SPDI:: NC_000002.12:74531330:T:C
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000447/2 (ALFA)
C=0.000014/2 (GnomAD)
C=0.000446/2 (Estonian)
HGVS:: NC_000002.12:g.74531331T>C, NC_000002.11:g.74758458T>C, NG_033047.1:g.27605A>G, NG_012163.1:g.6927T>C, NG_033037.1:g.3517A>G

Select item 148458496510.

rs1484584965 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 2:74531219 (GRCh38)
2:74758346 (GRCh37)
Canonical SPDI:: NC_000002.12:74531218:A:G
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000011/3 (TOPMED)
HGVS:: NC_000002.12:g.74531219A>G, NC_000002.11:g.74758346A>G, NG_033047.1:g.27717T>C, NG_012163.1:g.6815A>G, NG_033037.1:g.3629T>C

Select item 148393025711.

rs1483930257 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 2:74526885 (GRCh38)
2:74754012 (GRCh37)
Canonical SPDI:: NC_000002.12:74526884:C:T
Gene:: AUP1 (Varview), DQX1 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000002.12:g.74526885C>T, NC_000002.11:g.74754012C>T, NG_012163.1:g.2481C>T, NG_033037.1:g.7963G>A

Select item 148384203912.

rs1483842039 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 2:74529762 (GRCh38)
2:74756889 (GRCh37)
Canonical SPDI:: NC_000002.12:74529761:G:C
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,genic_upstream_transcript_variant,5_prime_UTR_variant,non_coding_transcript_variant,2KB_upstream_variant
HGVS:: NC_000002.12:g.74529762G>C, NC_000002.11:g.74756889G>C, NG_012163.1:g.5358G>C, NM_145074.2:c.-245G>C, NR_135769.1:n.358G>C, NM_001321727.1:c.-245G>C, NM_001321728.1:c.-245G>C, NR_135772.1:n.358G>C, NR_135770.1:n.358G>C, NR_135771.1:n.358G>C, NG_033037.1:g.5086C>G, NM_013247.4:c.-245G>C, NM_181575.4:c.-133C>G, NM_181575.3:c.-133C>G, NR_126511.1:n.136C>G, NR_126510.1:n.136C>G

Select item 148327094313.

rs1483270943 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:74529957 (GRCh38)
2:74757084 (GRCh37)
Canonical SPDI:: NC_000002.12:74529956:G:A
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,5_prime_UTR_variant,non_coding_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by cluster
MAF:: A=0.000007/1 (GnomAD_exomes)
A=0.000177/3 (TOMMO)
A=0.000343/1 (KOREAN)
HGVS:: NC_000002.12:g.74529957G>A, NC_000002.11:g.74757084G>A, NG_012163.1:g.5553G>A, NM_013247.5:c.-50G>A, NM_013247.4:c.-50G>A, NM_145074.2:c.-50G>A, NR_135769.1:n.553G>A, NM_001321727.1:c.-50G>A, NM_001321728.1:c.-50G>A, NG_033037.1:g.4891C>T

Select item 148295079414.

rs1482950794 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 2:74526379 (GRCh38)
2:74753506 (GRCh37)
Canonical SPDI:: NC_000002.12:74526378:G:T
Gene:: AUP1 (Varview), DQX1 (Varview)
Functional Consequence:: 2KB_upstream_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_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_000002.12:g.74526379G>T, NC_000002.11:g.74753506G>T, NG_012163.1:g.1975G>T, NG_033037.1:g.8469C>A

Select item 148260607915.

rs1482606079 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:74530154 (GRCh38)
2:74757281 (GRCh37)
Canonical SPDI:: NC_000002.12:74530153:G:A
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,coding_sequence_variant,missense_variant,non_coding_transcript_variant,2KB_upstream_variant,intron_variant
Clinical significance:: uncertain-significance
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000028/1 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000002.12:g.74530154G>A, NC_000002.11:g.74757281G>A, NG_012163.1:g.5750G>A, NM_013247.5:c.148G>A, NM_013247.4:c.148G>A, NM_145074.2:c.148G>A, NR_135769.1:n.750G>A, NM_001321727.1:c.148G>A, NM_001321728.1:c.148G>A, NG_033037.1:g.4694C>T, NP_037379.1:p.Val50Met, NP_659540.1:p.Val50Met, NP_001308656.1:p.Val50Met, NP_001308657.1:p.Val50Met

Select item 148236736216.

rs1482367362 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 2:74526245 (GRCh38)
2:74753372 (GRCh37)
Canonical SPDI:: NC_000002.12:74526244:G:T
Gene:: AUP1 (Varview), DQX1 (Varview)
Functional Consequence:: 2KB_upstream_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_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_000002.12:g.74526245G>T, NC_000002.11:g.74753372G>T, NG_012163.1:g.1841G>T, NG_033037.1:g.8603C>A, NM_133637.2:c.-129C>A

Select item 148182503717.

rs1481825037 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 2:74530430 (GRCh38)
2:74757557 (GRCh37)
Canonical SPDI:: NC_000002.12:74530429:T:A
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,coding_sequence_variant,missense_variant,non_coding_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency
MAF:: A=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000002.12:g.74530430T>A, NC_000002.11:g.74757557T>A, NG_012163.1:g.6026T>A, NM_013247.5:c.424T>A, NM_013247.4:c.424T>A, NM_145074.2:c.424T>A, NR_135769.1:n.1026T>A, NM_001321727.1:c.424T>A, NM_001321728.1:c.424T>A, NG_033037.1:g.4418A>T, NP_037379.1:p.Ser142Thr, NP_659540.1:p.Ser142Thr, NP_001308656.1:p.Ser142Thr, NP_001308657.1:p.Ser142Thr

Select item 148145114718.

rs1481451147 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:74530719 (GRCh38)
2:74757846 (GRCh37)
Canonical SPDI:: NC_000002.12:74530718:G:A
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: synonymous_variant,upstream_transcript_variant,coding_sequence_variant,non_coding_transcript_variant,2KB_upstream_variant
Validated:: by frequency
MAF:: A=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000002.12:g.74530719G>A, NC_000002.11:g.74757846G>A, NG_012163.1:g.6315G>A, NM_013247.5:c.609G>A, NM_013247.4:c.609G>A, NM_145074.2:c.609G>A, NR_135769.1:n.1211G>A, NM_001321727.1:c.609G>A, NM_001321728.1:c.609G>A, NR_135772.1:n.683G>A, NR_135770.1:n.679G>A, NR_135771.1:n.663G>A, NG_033037.1:g.4129C>T

Select item 147940946819.

rs1479409468 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 2:74531768 (GRCh38)
2:74758895 (GRCh37)
Canonical SPDI:: NC_000002.12:74531767:G:A
Gene:: HTRA2 (Varview), LOXL3 (Varview)
Functional Consequence:: downstream_transcript_variant,500B_downstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000002.12:g.74531768G>A, NC_000002.11:g.74758895G>A, NG_033047.1:g.27168C>T, NG_012163.1:g.7364G>A, NG_033037.1:g.3080C>T

Select item 147919366920.

rs1479193669 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 2:74529386 (GRCh38)
2:74756513 (GRCh37)
Canonical SPDI:: NC_000002.12:74529385:G:T
Gene:: AUP1 (Varview), HTRA2 (Varview)
Functional Consequence:: upstream_transcript_variant,coding_sequence_variant,missense_variant,non_coding_transcript_variant,2KB_upstream_variant
Validated:: by frequency
MAF:: T=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000002.12:g.74529386G>T, NC_000002.11:g.74756513G>T, NG_012163.1:g.4982G>T, NG_033037.1:g.5462C>A, NM_181575.5:c.164C>A, NM_181575.4:c.164C>A, NM_181575.3:c.164C>A, NR_126511.2:n.241C>A, NR_126511.1:n.432C>A, NR_126510.2:n.241C>A, NR_126510.1:n.432C>A, NM_012103.2:c.164C>A, NM_181576.1:c.164C>A, NM_012103.1:c.164C>A, NP_853553.1:p.Ala55Glu

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